From 31da79af575e8ac954da1c884d031e4eacba3d7c Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 9 Jun 2020 11:29:01 -0700 Subject: [PATCH 01/41] increment version number --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d51093b59..8b7ba27db 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: broom Title: Convert Statistical Objects into Tidy Tibbles -Version: 0.7.0.9000 +Version: 0.7.0 Authors@R: c(person(given = "David", family = "Robinson", From 22286088efc9fe0846c9e49bb0b8bb5110264a49 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 9 Jun 2020 11:39:14 -0700 Subject: [PATCH 02/41] documentation updates re: lint --- man/augment.betamfx.Rd | 3 ++- man/augment.mfx.Rd | 6 ++++-- man/glance.lavaan.Rd | 5 ++++- man/glance.lm.Rd | 5 ++++- man/glance.mfx.Rd | 3 ++- man/tidy.betamfx.Rd | 4 +++- man/tidy.density.Rd | 5 +++-- man/tidy.epi.2by2.Rd | 4 ++-- man/tidy.kmeans.Rd | 3 ++- man/tidy.map.Rd | 3 ++- man/tidy.mediate.Rd | 4 +++- man/tidy.pam.Rd | 6 ++++-- 12 files changed, 35 insertions(+), 16 deletions(-) diff --git a/man/augment.betamfx.Rd b/man/augment.betamfx.Rd index d33e59cce..48a5cb702 100644 --- a/man/augment.betamfx.Rd +++ b/man/augment.betamfx.Rd @@ -88,7 +88,8 @@ We are in the process of defining behaviors for models fit with various missing at this time. } \details{ -This augment method wraps \code{\link[=augment.betareg]{augment.betareg()}} for \code{\link[mfx:betamfx]{mfx::betamfx()}} objects. +This augment method wraps \code{\link[=augment.betareg]{augment.betareg()}} for +\code{\link[mfx:betamfx]{mfx::betamfx()}} objects. } \examples{ \dontrun{ diff --git a/man/augment.mfx.Rd b/man/augment.mfx.Rd index 7935976a6..a5472f5e4 100644 --- a/man/augment.mfx.Rd +++ b/man/augment.mfx.Rd @@ -59,7 +59,8 @@ ) } \arguments{ -\item{x}{A \code{logitmfx}, \code{negbinmfx}, \code{poissonmfx}, or \code{probitmfx} object. (Note that \code{betamfx} objects receive their own set of tidiers.)} +\item{x}{A \code{logitmfx}, \code{negbinmfx}, \code{poissonmfx}, or \code{probitmfx} object. +(Note that \code{betamfx} objects receive their own set of tidiers.)} \item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to @@ -159,7 +160,8 @@ glance(mod_probmfx) } } \seealso{ -\code{\link[=augment.glm]{augment.glm()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} +\code{\link[=augment.glm]{augment.glm()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, +\code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} Other mfx tidiers: \code{\link{augment.betamfx}()}, diff --git a/man/glance.lavaan.Rd b/man/glance.lavaan.Rd index 4422a19ab..2e93a53ab 100644 --- a/man/glance.lavaan.Rd +++ b/man/glance.lavaan.Rd @@ -41,7 +41,10 @@ A one-row \link[tibble:tibble]{tibble::tibble} with columns: \item{estimator}{Estimator used} \item{missing_method}{Method for eliminating missing data} -For further recommendations on reporting SEM and CFA models see Schreiber, J. B. (2017). Update to core reporting practices in structural equation modeling. Research in Social and Administrative Pharmacy, 13(3), 634-643. https://doi.org/10.1016/j.sapharm.2016.06.006 +For further recommendations on reporting SEM and CFA models see +Schreiber, J. B. (2017). Update to core reporting practices in +structural equation modeling. Research in Social and Administrative +Pharmacy, 13(3), 634-643. https://doi.org/10.1016/j.sapharm.2016.06.006 } \description{ Glance accepts a model object and returns a \code{\link[tibble:tibble]{tibble::tibble()}} diff --git a/man/glance.lm.Rd b/man/glance.lm.Rd index 743f87176..22e4844c5 100644 --- a/man/glance.lm.Rd +++ b/man/glance.lm.Rd @@ -118,6 +118,9 @@ A \code{\link[tibble:tibble]{tibble::tibble()}} with exactly one row and columns \item{r.squared}{R squared statistic, or the percent of variation explained by the model. Also known as the coefficient of determination.} \item{sigma}{Estimated standard error of the residuals.} \item{statistic}{Test statistic.} - \item{df}{The degrees for freedom from the numerator of the overall F-statistic. This is new in broom 0.7.0. Previously, this reported the rank of the design matrix, which is one more than the numerator degrees of freedom of the overall F-statistic.} + \item{df}{The degrees for freedom from the numerator of the overall + F-statistic. This is new in broom 0.7.0. Previously, this reported + the rank of the design matrix, which is one more than the numerator + degrees of freedom of the overall F-statistic.} } diff --git a/man/glance.mfx.Rd b/man/glance.mfx.Rd index f1d525e65..dfec4492a 100644 --- a/man/glance.mfx.Rd +++ b/man/glance.mfx.Rd @@ -77,7 +77,8 @@ glance(mod_probmfx) } } \seealso{ -\code{\link[=glance.glm]{glance.glm()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} +\code{\link[=glance.glm]{glance.glm()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, +\code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} Other mfx tidiers: \code{\link{augment.betamfx}()}, diff --git a/man/tidy.betamfx.Rd b/man/tidy.betamfx.Rd index 4e1c66916..ca9c81b21 100644 --- a/man/tidy.betamfx.Rd +++ b/man/tidy.betamfx.Rd @@ -93,6 +93,8 @@ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: \item{statistic}{The value of a T-statistic to use in a hypothesis that the regression term is non-zero.} \item{std.error}{The standard error of the regression term.} \item{term}{The name of the regression term.} - \item{atmean}{TRUE if the marginal effects were originally calculated as the partial effects for the average observation. If FALSE, then these were instead calculated as average partial effects.} + \item{atmean}{TRUE if the marginal effects were originally calculated as the + partial effects for the average observation. If FALSE, then these were + instead calculated as average partial effects.} } diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index e02e11ae3..657cf8793 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -21,8 +21,9 @@ the \code{data} argument.} } \value{ A \link[tibble:tibble]{tibble::tibble} with two columns: points \code{x} where the density -is estimated, and estimated density \code{y}. When the input to the \code{\link[stats:density]{stats::density()}} -function is an \code{nXm} matrix, as opposed to a \verb{1Xm} vector, the input matrix is first flattened into a \verb{1X(m*n)} vector +is estimated, and estimated density \code{y}. When the input to the +\code{\link[stats:density]{stats::density()}} function is an \code{nXm} matrix, as opposed to +a \verb{1Xm} vector, the input matrix is first flattened into a \verb{1X(m*n)} vector and then the density function is applied as usual. } \description{ diff --git a/man/tidy.epi.2by2.Rd b/man/tidy.epi.2by2.Rd index a8d1ec0f7..1b51d057e 100644 --- a/man/tidy.epi.2by2.Rd +++ b/man/tidy.epi.2by2.Rd @@ -32,8 +32,8 @@ If a model has several distinct types of components, you will need to specify which components to return. } \details{ -The tibble has a column for each of the measures of association or tests contained in \code{massoc} when -\code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} is called. +The tibble has a column for each of the measures of association +or tests contained in \code{massoc} when \code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} is called. } \examples{ library(epiR) diff --git a/man/tidy.kmeans.Rd b/man/tidy.kmeans.Rd index 25e878ef7..8abee67f0 100644 --- a/man/tidy.kmeans.Rd +++ b/man/tidy.kmeans.Rd @@ -10,7 +10,8 @@ \arguments{ \item{x}{A \code{kmeans} object created by \code{\link[stats:kmeans]{stats::kmeans()}}.} -\item{col.names}{Dimension names. Defaults to the names of the variables in x. Set to NULL to get names \verb{x1, x2, ...}.} +\item{col.names}{Dimension names. Defaults to the names of the variables +in x. Set to NULL to get names \verb{x1, x2, ...}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be diff --git a/man/tidy.map.Rd b/man/tidy.map.Rd index c4cff2acd..665582a03 100644 --- a/man/tidy.map.Rd +++ b/man/tidy.map.Rd @@ -53,5 +53,6 @@ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: \item{term}{The name of the regression term.} \item{long}{Longitude.} \item{lat}{Latitude.} -Remaining columns give information on geographic attributes and depend on the inputted map object. See ?maps::map for more information. +Remaining columns give information on geographic attributes + and depend on the inputted map object. See ?maps::map for more information. } diff --git a/man/tidy.mediate.Rd b/man/tidy.mediate.Rd index dd50e75ed..2fc49f15c 100644 --- a/man/tidy.mediate.Rd +++ b/man/tidy.mediate.Rd @@ -36,7 +36,9 @@ If a model has several distinct types of components, you will need to specify which components to return. } \details{ -The tibble has four rows. The first two indicate the mediated effect in the control and treatment group, respectively. And the last two the direct effect in each group. +The tibble has four rows. The first two indicate the mediated +effect in the control and treatment group, respectively. And the last +two the direct effect in each group. } \examples{ library(mediation) diff --git a/man/tidy.pam.Rd b/man/tidy.pam.Rd index e2bda7c64..e9a760ba4 100644 --- a/man/tidy.pam.Rd +++ b/man/tidy.pam.Rd @@ -64,8 +64,10 @@ Other pam tidiers: \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: \item{size}{Size of each cluster.} - \item{max.diss}{Maximal dissimilarity between the observations in the cluster and that cluster's medoid.} - \item{avg.diss}{Average dissimilarity between the observations in the cluster and that cluster's medoid.} + \item{max.diss}{Maximal dissimilarity between the observations in the + cluster and that cluster's medoid.} + \item{avg.diss}{Average dissimilarity between the observations in the + cluster and that cluster's medoid.} \item{diameter}{Diameter of the cluster.} \item{separation}{Separation of the cluster.} \item{avg.width}{Average silhouette width of the cluster.} From b2b170c20dd9c7866d72a94311b60d718ae4185f Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 9 Jun 2020 11:58:04 -0700 Subject: [PATCH 03/41] update cran comments --- cran-comments.md | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 692ba3dde..5c88e61a4 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,14 +1,32 @@ -# release summary +# Release summary -broom 0.5.6 is a minor release that fixes failing checks due to changes to the `tibble` package. this is a resubmission that also removes the `xergm` dependency. +broom 0.7.0 is a major release featuring a number of new S3 methods, +bug fixes, and improvements to internal consistency and performance. +This release also carries out a planned deprecation of a number of +methods to the `broom.mixed` package. ## Test environments -- local windows 8 install: release -- travis-ci ubuntu 14.04: devel, release, oldrel -- appveyor windows server 2012: release -- win-builder: devel, release +- local mac OS install: R 4.0.0 +- mac OS (on github actions): R 3.6.3 +- ubuntu 16.04 (on github actions), R 3.6.3 +- Microsoft Windows Server 2019 10.0.17763 (on github actions) devel, release +- win-builder (devel) ## R CMD check results 0 NOTES, 0 WARNINGS, 0 ERRORS + +## revdepcheck results + +We checked 149 reverse dependencies, comparing R CMD check results across +CRAN and dev versions of this package. We saw 37 new problems and failed to +check one package. + +We first notified affected maintainers three weeks ago, and +checked in with maintainers again a week and a half ago. Records +of our initial outreach attempts can be found on this issue: + +https://github.com/tidymodels/broom/issues/862 + + From 65243f6705d1b8ee63061baf5a5f6cc9302e63d5 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 9 Jun 2020 14:30:08 -0700 Subject: [PATCH 04/41] clean up pkgdown yaml --- _pkgdown.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index d9d92eee8..1a2ca61b9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -28,9 +28,6 @@ reference: - title: Miscellaneous contents: - broom - - starts_with("confint") - - finish_glance - - starts_with("process") navbar: type: default @@ -56,4 +53,3 @@ navbar: right: - icon: fa-github fa-lg href: https://github.com/tidymodels/broom - From af38bea8b19ea7ce25d02fba04d59d4b0368d446 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 9 Jun 2020 14:33:14 -0700 Subject: [PATCH 05/41] add myself as author per alex's request --- DESCRIPTION | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 8b7ba27db..ada3f1bfb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,6 +12,10 @@ Authors@R: role = c("aut", "cre"), email = "alexpghayes@gmail.com", comment = c(ORCID = "0000-0002-4985-5160")), + person(given = "Simon", + family = "Couch", + role = "aut", + email = "simonpatrickcouch@gmail.com"), person(given = "Indrajeet", family = "Patil", role = "ctb", From 5ccdba53a5f8b354f7d984e10ac1af5b14b4659f Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 10 Jun 2020 12:00:45 -0700 Subject: [PATCH 06/41] submit to CRAN! --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index a5218b520..0c0a4c29b 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-04-20. -Once it is accepted, delete this file and tag the release (commit f4b3c47b6d). +This package was submitted to CRAN on 2020-06-10. +Once it is accepted, delete this file and tag the release (commit af38bea8b1). From ae3bbb866b9c60ef8ede8c770044f1452dcae19f Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 10 Jun 2020 13:11:43 -0700 Subject: [PATCH 07/41] fixes from CRAN pretest failure - new `fixest` version --- R/fixest-tidiers.R | 3 ++- cran-comments.md | 4 ++++ man/augment.fixest.Rd | 2 +- man/broom.Rd | 1 + 4 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/fixest-tidiers.R b/R/fixest-tidiers.R index 133851223..e6841010c 100644 --- a/R/fixest-tidiers.R +++ b/R/fixest-tidiers.R @@ -143,7 +143,8 @@ tidy_fixest <- function(x, conf.int = conf.int, conf.level = conf.level, ...) { #' @export #' @family fixest tidiers #' @seealso [augment()], [fixest::feglm()], [fixest::femlm()], [fixest::feols()] -augment.fixest <- function(x, data = NULL, newdata = NULL, type.predict="link", ...) { +augment.fixest <- function(x, data = NULL, newdata = NULL, + type.predict = "response", ...) { if (!x$method %in% c("feols", "feglm", "femlm")) { stop("augment is only supported for fixest models estimated with ", "feols, feglm, or femlm\n", diff --git a/cran-comments.md b/cran-comments.md index 5c88e61a4..4d57d1b4c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,9 @@ # Release summary +This is a resubmission following an automated pretest failure. The failure +was due to breaking changes in the `residuals.fixest()` S3 method from +the `fixest` package, a new version of which was released on CRAN earlier today. + broom 0.7.0 is a major release featuring a number of new S3 methods, bug fixes, and improvements to internal consistency and performance. This release also carries out a planned deprecation of a number of diff --git a/man/augment.fixest.Rd b/man/augment.fixest.Rd index a70049ac9..b6038065c 100644 --- a/man/augment.fixest.Rd +++ b/man/augment.fixest.Rd @@ -4,7 +4,7 @@ \alias{augment.fixest} \title{Augment data with information from a(n) fixest object} \usage{ -\method{augment}{fixest}(x, data = NULL, newdata = NULL, type.predict = "link", ...) +\method{augment}{fixest}(x, data = NULL, newdata = NULL, type.predict = "response", ...) } \arguments{ \item{x}{A \code{fixest} object returned from any of the \code{fixest} estimators} diff --git a/man/broom.Rd b/man/broom.Rd index cec40fa4d..34cae83c2 100644 --- a/man/broom.Rd +++ b/man/broom.Rd @@ -38,6 +38,7 @@ Useful links: Authors: \itemize{ \item David Robinson \email{admiral.david@gmail.com} + \item Simon Couch \email{simonpatrickcouch@gmail.com} } Other contributors: From aa7d0978beb7d795d0eb33da1942336c5af15042 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 11 Jun 2020 07:50:25 -0700 Subject: [PATCH 08/41] update timeline --- cran-comments.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 4d57d1b4c..737cf4b2a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,8 @@ # Release summary -This is a resubmission following an automated pretest failure. The failure -was due to breaking changes in the `residuals.fixest()` S3 method from -the `fixest` package, a new version of which was released on CRAN earlier today. +This is a resubmission following an automated pretest failure +yesterday. The failure was due to breaking changes in the `residuals.fixest()` S3 method from the `fixest` package, a +new version of which was released on CRAN yesterday. broom 0.7.0 is a major release featuring a number of new S3 methods, bug fixes, and improvements to internal consistency and performance. From b1e8d271a45dfcad856d52b753b69a1917689d10 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 11 Jun 2020 07:51:52 -0700 Subject: [PATCH 09/41] submit round 2! --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 0c0a4c29b..05fe329e1 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-10. -Once it is accepted, delete this file and tag the release (commit af38bea8b1). +This package was submitted to CRAN on 2020-06-11. +Once it is accepted, delete this file and tag the release (commit aa7d0978be). From c5eedbe88735e2e2e4845e164117205ae05a47ef Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 11 Jun 2020 13:09:32 -0700 Subject: [PATCH 10/41] link to man files rather than topics (r-lib/roxygen2#1109) --- cran-comments.md | 12 +++++++++--- man/augment.betareg.Rd | 2 +- man/augment.clm.Rd | 4 ++-- man/augment.fixest.Rd | 2 +- man/augment.glm.Rd | 4 ++-- man/augment.mfx.Rd | 4 ++-- man/augment.rma.Rd | 2 +- man/augment.rqs.Rd | 2 +- man/augment.sarlm.Rd | 4 ++-- man/glance.ergm.Rd | 2 +- man/glance.lavaan.Rd | 2 +- man/glance.ridgelm.Rd | 2 +- man/glance.rma.Rd | 2 +- man/glance.sarlm.Rd | 8 ++++---- man/metafor_tidiers.Rd | 2 +- man/null_tidiers.Rd | 2 +- man/tidy.acf.Rd | 6 +++--- man/tidy.cld.Rd | 4 ++-- man/tidy.confint.glht.Rd | 4 ++-- man/tidy.emmGrid.Rd | 4 ++-- man/tidy.ergm.Rd | 4 ++-- man/tidy.fixest.Rd | 4 ++-- man/tidy.kappa.Rd | 6 +++--- man/tidy.lsmobj.Rd | 4 ++-- man/tidy.ref.grid.Rd | 4 ++-- man/tidy.rqs.Rd | 2 +- man/tidy.sarlm.Rd | 8 ++++---- man/tidy.summary.glht.Rd | 4 ++-- man/tidy.summary_emm.Rd | 4 ++-- 29 files changed, 60 insertions(+), 54 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 737cf4b2a..2101bf33d 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,14 @@ # Release summary -This is a resubmission following an automated pretest failure -yesterday. The failure was due to breaking changes in the `residuals.fixest()` S3 method from the `fixest` package, a -new version of which was released on CRAN yesterday. +This is a second resubmission following an automated pretest failure due to +"[n]on-file package-anchored link(s) in documentation object[s]." This seems +to be a new test as of yesterday, and has been addressed by linking to +documentation files rather than topics. + +The previous submission was also a resubmission following an automated pretest +failure. The failure was due to breaking changes in the `residuals.fixest()` +S3 method from the `fixest` package, a new version of which was +released on CRAN the same day as the original submission. broom 0.7.0 is a major release featuring a number of new S3 methods, bug fixes, and improvements to internal consistency and performance. diff --git a/man/augment.betareg.Rd b/man/augment.betareg.Rd index 79ecbdf81..67cd183be 100644 --- a/man/augment.betareg.Rd +++ b/man/augment.betareg.Rd @@ -90,7 +90,7 @@ missing at this time. } \details{ For additional details on Cook's distance, see -\code{\link[stats:cooks.distance]{stats::cooks.distance()}}. +\code{\link[stats:influence.measures]{stats::cooks.distance()}}. } \examples{ diff --git a/man/augment.clm.Rd b/man/augment.clm.Rd index 2d3d61b11..d7405069f 100644 --- a/man/augment.clm.Rd +++ b/man/augment.clm.Rd @@ -29,7 +29,7 @@ that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} \item{type.predict}{Which type of prediction to compute, either \code{"prob"} -or \code{"class"}, passed to \code{\link[ordinal:predict.clm]{ordinal::predict.clm()}}. Defaults to \code{"prob"}.} +or \code{"class"}, passed to \code{\link[ordinal:predict]{ordinal::predict.clm()}}. Defaults to \code{"prob"}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -99,7 +99,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict.clm]{ordinal::predict.clm()}} +\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict]{ordinal::predict.clm()}} Other ordinal tidiers: \code{\link{augment.polr}()}, diff --git a/man/augment.fixest.Rd b/man/augment.fixest.Rd index b6038065c..1514b27c1 100644 --- a/man/augment.fixest.Rd +++ b/man/augment.fixest.Rd @@ -75,7 +75,7 @@ data, so you must provide it manually. augment.fixest only works for \code{\link[fixest:feols]{fixest::feols()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, and \code{\link[fixest:femlm]{fixest::femlm()}} models. It does not work with results from -\code{\link[fixest:fenegbin]{fixest::fenegbin()}}, \code{\link[fixest:feNmlm]{fixest::feNmlm()}}, or \code{\link[fixest:fepois]{fixest::fepois()}}. +\code{\link[fixest:femlm]{fixest::fenegbin()}}, \code{\link[fixest:feNmlm]{fixest::feNmlm()}}, or \code{\link[fixest:feglm]{fixest::fepois()}}. } \examples{ \donttest{ diff --git a/man/augment.glm.Rd b/man/augment.glm.Rd index 273cc8315..baa3048b2 100644 --- a/man/augment.glm.Rd +++ b/man/augment.glm.Rd @@ -33,8 +33,8 @@ the \code{data} argument will be ignored.} \item{type.predict}{Passed to \code{\link[stats:predict.glm]{stats::predict.glm()}} \code{type} argument. Defaults to \code{"link"}.} -\item{type.residuals}{Passed to \code{\link[stats:residuals.glm]{stats::residuals.glm()}} and -to \code{\link[stats:rstandard.glm]{stats::rstandard.glm()}} \code{type} arguments. Defaults to \code{"deviance"}.} +\item{type.residuals}{Passed to \code{\link[stats:glm.summaries]{stats::residuals.glm()}} and +to \code{\link[stats:influence.measures]{stats::rstandard.glm()}} \code{type} arguments. Defaults to \code{"deviance"}.} \item{se_fit}{Logical indicating whether or not a \code{.se.fit} column should be added to the augmented output. For some models, this calculation can be diff --git a/man/augment.mfx.Rd b/man/augment.mfx.Rd index a5472f5e4..7c634b9af 100644 --- a/man/augment.mfx.Rd +++ b/man/augment.mfx.Rd @@ -78,8 +78,8 @@ the \code{data} argument will be ignored.} \item{type.predict}{Passed to \code{\link[stats:predict.glm]{stats::predict.glm()}} \code{type} argument. Defaults to \code{"link"}.} -\item{type.residuals}{Passed to \code{\link[stats:residuals.glm]{stats::residuals.glm()}} and -to \code{\link[stats:rstandard.glm]{stats::rstandard.glm()}} \code{type} arguments. Defaults to \code{"deviance"}.} +\item{type.residuals}{Passed to \code{\link[stats:glm.summaries]{stats::residuals.glm()}} and +to \code{\link[stats:influence.measures]{stats::rstandard.glm()}} \code{type} arguments. Defaults to \code{"deviance"}.} \item{se_fit}{Logical indicating whether or not a \code{.se.fit} column should be added to the augmented output. For some models, this calculation can be diff --git a/man/augment.rma.Rd b/man/augment.rma.Rd index 33fa60098..e20df7907 100644 --- a/man/augment.rma.Rd +++ b/man/augment.rma.Rd @@ -7,7 +7,7 @@ \method{augment}{rma}(x, ...) } \arguments{ -\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma]{metafor::rma()}}, +\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma.uni]{metafor::rma()}}, \code{\link[metafor:rma.uni]{metafor::rma.uni()}}, \code{\link[metafor:rma.glmm]{metafor::rma.glmm()}}, \code{\link[metafor:rma.mh]{metafor::rma.mh()}}, \code{\link[metafor:rma.mv]{metafor::rma.mv()}}, or \code{\link[metafor:rma.peto]{metafor::rma.peto()}}.} diff --git a/man/augment.rqs.Rd b/man/augment.rqs.Rd index eba28e7b3..e9f6af526 100644 --- a/man/augment.rqs.Rd +++ b/man/augment.rqs.Rd @@ -94,7 +94,7 @@ columns \code{.conf.low} and \code{.conf.high}. Does not provide confidence intervals when data is specified via the \code{newdata} argument. } \seealso{ -\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rqs]{quantreg::predict.rqs()}} +\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rqs()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/augment.sarlm.Rd b/man/augment.sarlm.Rd index 8603eb58c..579bc59e2 100644 --- a/man/augment.sarlm.Rd +++ b/man/augment.sarlm.Rd @@ -7,8 +7,8 @@ \method{augment}{sarlm}(x, data = x$X, ...) } \arguments{ -\item{x}{An object of object returned from \code{\link[spatialreg:lagsarlm]{spatialreg::lagsarlm()}} -or \code{\link[spatialreg:errorsarlm]{spatialreg::errorsarlm()}}.} +\item{x}{An object of object returned from \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}} +or \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}.} \item{data}{Ignored, but included for internal consistency. See the details below.} diff --git a/man/glance.ergm.Rd b/man/glance.ergm.Rd index 950dd1ce6..389572bd6 100644 --- a/man/glance.ergm.Rd +++ b/man/glance.ergm.Rd @@ -16,7 +16,7 @@ to \code{FALSE}.} \item{mcmc}{Logical indicating whether or not to report MCMC interval, burn-in and sample size used to estimate the model. Defaults to \code{FALSE}.} -\item{...}{Additional arguments to pass to \code{\link[ergm:summary]{ergm::summary()}}. +\item{...}{Additional arguments to pass to \code{\link[ergm:summary.formula]{ergm::summary()}}. \strong{Cautionary note}: Mispecified arguments may be silently ignored.} } \value{ diff --git a/man/glance.lavaan.Rd b/man/glance.lavaan.Rd index 2e93a53ab..0f4167482 100644 --- a/man/glance.lavaan.Rd +++ b/man/glance.lavaan.Rd @@ -81,7 +81,7 @@ glance(cfa.fit) } \seealso{ \code{\link[=glance]{glance()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, -\code{\link[lavaan:fitmeasures]{lavaan::fitmeasures()}} +\code{\link[lavaan:fitMeasures]{lavaan::fitmeasures()}} Other lavaan tidiers: \code{\link{tidy.lavaan}()} diff --git a/man/glance.ridgelm.Rd b/man/glance.ridgelm.Rd index 91ecfe230..3329292a4 100644 --- a/man/glance.ridgelm.Rd +++ b/man/glance.ridgelm.Rd @@ -68,7 +68,7 @@ ggplot(td2, aes(lambda, GCV)) + geom_vline(xintercept = g2$lambdaGCV, col = "red", lty = 2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[MASS:select.ridgelm]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} +\code{\link[=glance]{glance()}}, \code{\link[MASS:lm.ridge]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} Other ridgelm tidiers: \code{\link{tidy.ridgelm}()} diff --git a/man/glance.rma.Rd b/man/glance.rma.Rd index df92e1501..44c87efcb 100644 --- a/man/glance.rma.Rd +++ b/man/glance.rma.Rd @@ -7,7 +7,7 @@ \method{glance}{rma}(x, ...) } \arguments{ -\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma]{metafor::rma()}}, +\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma.uni]{metafor::rma()}}, \code{\link[metafor:rma.uni]{metafor::rma.uni()}}, \code{\link[metafor:rma.glmm]{metafor::rma.glmm()}}, \code{\link[metafor:rma.mh]{metafor::rma.mh()}}, \code{\link[metafor:rma.mv]{metafor::rma.mv()}}, or \code{\link[metafor:rma.peto]{metafor::rma.peto()}}.} diff --git a/man/glance.sarlm.Rd b/man/glance.sarlm.Rd index 4d4e67da1..3890c78fe 100644 --- a/man/glance.sarlm.Rd +++ b/man/glance.sarlm.Rd @@ -7,8 +7,8 @@ \method{glance}{sarlm}(x, ...) } \arguments{ -\item{x}{An object of object returned from \code{\link[spatialreg:lagsarlm]{spatialreg::lagsarlm()}} -or \code{\link[spatialreg:errorsarlm]{spatialreg::errorsarlm()}}.} +\item{x}{An object of object returned from \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}} +or \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -71,8 +71,8 @@ augment(crime_sac) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[spatialreg:lagsarlm]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:errorsarlm]{spatialreg::errorsarlm()}}, -\code{\link[spatialreg:sacsarlm]{spatialreg::sacsarlm()}} +\code{\link[=glance]{glance()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: \code{\link{augment.sarlm}()}, diff --git a/man/metafor_tidiers.Rd b/man/metafor_tidiers.Rd index 785947cfc..3a6db0beb 100644 --- a/man/metafor_tidiers.Rd +++ b/man/metafor_tidiers.Rd @@ -15,7 +15,7 @@ ) } \arguments{ -\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma]{metafor::rma()}}, +\item{x}{An \code{rma} object such as those created by \code{\link[metafor:rma.uni]{metafor::rma()}}, \code{\link[metafor:rma.uni]{metafor::rma.uni()}}, \code{\link[metafor:rma.glmm]{metafor::rma.glmm()}}, \code{\link[metafor:rma.mh]{metafor::rma.mh()}}, \code{\link[metafor:rma.mv]{metafor::rma.mv()}}, or \code{\link[metafor:rma.peto]{metafor::rma.peto()}}.} diff --git a/man/null_tidiers.Rd b/man/null_tidiers.Rd index 70f04aa19..295aa7ff7 100644 --- a/man/null_tidiers.Rd +++ b/man/null_tidiers.Rd @@ -25,7 +25,7 @@ An empty \link[tibble:tibble]{tibble::tibble}. \code{tidy(NULL)}, \code{glance(NULL)} and \code{augment(NULL)} all return an empty \link[tibble:tibble]{tibble::tibble}. This empty tibble can be treated a tibble with zero rows, making it convenient to combine with other tibbles using -functions like \code{\link[purrr:map_df]{purrr::map_df()}} on lists of potentially \code{NULL} objects. +functions like \code{\link[purrr:map]{purrr::map_df()}} on lists of potentially \code{NULL} objects. } \seealso{ \link[tibble:tibble]{tibble::tibble} diff --git a/man/tidy.acf.Rd b/man/tidy.acf.Rd index 0e15250b8..44c90ca2f 100644 --- a/man/tidy.acf.Rd +++ b/man/tidy.acf.Rd @@ -7,8 +7,8 @@ \method{tidy}{acf}(x, ...) } \arguments{ -\item{x}{An \code{acf} object created by \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:pacf]{stats::pacf()}} or -\code{\link[stats:ccf]{stats::ccf()}}.} +\item{x}{An \code{acf} object created by \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}} or +\code{\link[stats:acf]{stats::ccf()}}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -35,7 +35,7 @@ tidy(ccf(mdeaths, fdeaths, plot = FALSE)) tidy(pacf(lh, plot = FALSE)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:pacf]{stats::pacf()}}, \code{\link[stats:ccf]{stats::ccf()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}}, \code{\link[stats:acf]{stats::ccf()}} Other time series tidiers: \code{\link{tidy.spec}()}, diff --git a/man/tidy.cld.Rd b/man/tidy.cld.Rd index 0fda37109..522327817 100644 --- a/man/tidy.cld.Rd +++ b/man/tidy.cld.Rd @@ -55,8 +55,8 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:summary.glht]{multcomp::summary.glht()}}, -\code{\link[multcomp:confint.glht]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, +\code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.confint.glht}()}, diff --git a/man/tidy.confint.glht.Rd b/man/tidy.confint.glht.Rd index 217d82688..cb4b8b2d4 100644 --- a/man/tidy.confint.glht.Rd +++ b/man/tidy.confint.glht.Rd @@ -8,7 +8,7 @@ } \arguments{ \item{x}{A \code{confint.glht} object created by calling -\code{\link[multcomp:confint.glht]{multcomp::confint.glht()}} on a \code{glht} object created with +\code{\link[multcomp:methods]{multcomp::confint.glht()}} on a \code{glht} object created with \code{\link[multcomp:glht]{multcomp::glht()}}.} \item{...}{Additional arguments. Not used. Needed to match generic @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:confint.glht]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.emmGrid.Rd b/man/tidy.emmGrid.Rd index 97190a516..cad8ca626 100644 --- a/man/tidy.emmGrid.Rd +++ b/man/tidy.emmGrid.Rd @@ -17,7 +17,7 @@ if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.} \item{...}{Additional arguments passed to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or -\code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments +\code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments may be silently ignored!} } \description{ @@ -34,7 +34,7 @@ mean, and one column for each combination of factors. When the input is a contrast, each row will contain one estimated contrast. There are a large number of arguments that can be -passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. +passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. } \examples{ diff --git a/man/tidy.ergm.Rd b/man/tidy.ergm.Rd index 117eb6eb5..f3afbd651 100644 --- a/man/tidy.ergm.Rd +++ b/man/tidy.ergm.Rd @@ -22,7 +22,7 @@ the coefficient estimates. This is typical for logistic and multinomial regressions, but a bad idea if there is no log or logit link. Defaults to \code{FALSE}.} -\item{...}{Additional arguments to pass to \code{\link[ergm:summary]{ergm::summary()}}. +\item{...}{Additional arguments to pass to \code{\link[ergm:summary.formula]{ergm::summary()}}. \strong{Cautionary note}: Mispecified arguments may be silently ignored.} } \value{ @@ -77,7 +77,7 @@ Models for Networks. \emph{Journal of Statistical Software}, 24(3). } \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:control.ergm]{ergm::control.ergm()}}, -\code{\link[ergm:summary]{ergm::summary()}} +\code{\link[ergm:summary.formula]{ergm::summary()}} Other ergm tidiers: \code{\link{glance.ergm}()} diff --git a/man/tidy.fixest.Rd b/man/tidy.fixest.Rd index a127aec98..7f84b9a69 100644 --- a/man/tidy.fixest.Rd +++ b/man/tidy.fixest.Rd @@ -72,8 +72,8 @@ augment(gravity_pois, trade) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:fenegbin]{fixest::fenegbin()}}, -\code{\link[fixest:feNmlm]{fixest::feNmlm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}}, \code{\link[fixest:fepois]{fixest::fepois()}} +\code{\link[=tidy]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::fenegbin()}}, +\code{\link[fixest:feNmlm]{fixest::feNmlm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}}, \code{\link[fixest:feglm]{fixest::fepois()}} Other fixest tidiers: \code{\link{augment.fixest}()} diff --git a/man/tidy.kappa.Rd b/man/tidy.kappa.Rd index 38e66e863..2e674f7b4 100644 --- a/man/tidy.kappa.Rd +++ b/man/tidy.kappa.Rd @@ -9,7 +9,7 @@ \method{tidy}{kappa}(x, ...) } \arguments{ -\item{x}{A \code{kappa} object returned from \code{\link[psych:cohen.kappa]{psych::cohen.kappa()}}.} +\item{x}{A \code{kappa} object returned from \code{\link[psych:kappa]{psych::cohen.kappa()}}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -32,7 +32,7 @@ specify which components to return. \details{ Note that confidence level (alpha) for the confidence interval cannot be set in \code{tidy}. Instead you must set the \code{alpha} argument -to \code{\link[psych:cohen.kappa]{psych::cohen.kappa()}} when creating the \code{kappa} object. +to \code{\link[psych:kappa]{psych::cohen.kappa()}} when creating the \code{kappa} object. } \examples{ @@ -51,7 +51,7 @@ ggplot(tidy(ck), aes(estimate, type)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[psych:cohen.kappa]{psych::cohen.kappa()}} +\code{\link[=tidy]{tidy()}}, \code{\link[psych:kappa]{psych::cohen.kappa()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.lsmobj.Rd b/man/tidy.lsmobj.Rd index 0504f3f5c..f6c45c250 100644 --- a/man/tidy.lsmobj.Rd +++ b/man/tidy.lsmobj.Rd @@ -18,7 +18,7 @@ if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.} \item{...}{Additional arguments passed to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or -\code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments +\code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments may be silently ignored!} } \description{ @@ -35,7 +35,7 @@ mean, and one column for each combination of factors. When the input is a contrast, each row will contain one estimated contrast. There are a large number of arguments that can be -passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. +passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. } \examples{ diff --git a/man/tidy.ref.grid.Rd b/man/tidy.ref.grid.Rd index a59313150..906317f09 100644 --- a/man/tidy.ref.grid.Rd +++ b/man/tidy.ref.grid.Rd @@ -17,7 +17,7 @@ if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.} \item{...}{Additional arguments passed to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or -\code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments +\code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments may be silently ignored!} } \description{ @@ -34,7 +34,7 @@ mean, and one column for each combination of factors. When the input is a contrast, each row will contain one estimated contrast. There are a large number of arguments that can be -passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. +passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. } \examples{ diff --git a/man/tidy.rqs.Rd b/man/tidy.rqs.Rd index 2640c4285..395017d3e 100644 --- a/man/tidy.rqs.Rd +++ b/man/tidy.rqs.Rd @@ -21,7 +21,7 @@ interval in the tidied output. Defaults to \code{FALSE}.} if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.} -\item{...}{Additional arguments passed to \code{\link[quantreg:summary.rqs]{quantreg::summary.rqs()}}} +\item{...}{Additional arguments passed to \code{\link[quantreg:summary.rq]{quantreg::summary.rqs()}}} } \description{ Tidy summarizes information about the components of a model. diff --git a/man/tidy.sarlm.Rd b/man/tidy.sarlm.Rd index 63b0e7ec3..ed5ed58eb 100644 --- a/man/tidy.sarlm.Rd +++ b/man/tidy.sarlm.Rd @@ -8,8 +8,8 @@ \method{tidy}{sarlm}(x, conf.int = FALSE, conf.level = 0.95, ...) } \arguments{ -\item{x}{An object of object returned from \code{\link[spatialreg:lagsarlm]{spatialreg::lagsarlm()}} -or \code{\link[spatialreg:errorsarlm]{spatialreg::errorsarlm()}}.} +\item{x}{An object of object returned from \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}} +or \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}.} \item{conf.int}{Logical indicating whether or not to include a confidence interval in the tidied output. Defaults to \code{FALSE}.} @@ -63,8 +63,8 @@ augment(crime_sac) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[spatialreg:lagsarlm]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:errorsarlm]{spatialreg::errorsarlm()}}, -\code{\link[spatialreg:sacsarlm]{spatialreg::sacsarlm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: \code{\link{augment.sarlm}()}, diff --git a/man/tidy.summary.glht.Rd b/man/tidy.summary.glht.Rd index 681565f31..9f750b1f2 100644 --- a/man/tidy.summary.glht.Rd +++ b/man/tidy.summary.glht.Rd @@ -8,7 +8,7 @@ } \arguments{ \item{x}{A \code{summary.glht} object created by calling -\code{\link[multcomp:summary.glht]{multcomp::summary.glht()}} on a \code{glht} object created with +\code{\link[multcomp:methods]{multcomp::summary.glht()}} on a \code{glht} object created with \code{\link[multcomp:glht]{multcomp::glht()}}.} \item{...}{Additional arguments. Not used. Needed to match generic @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:summary.glht]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.summary_emm.Rd b/man/tidy.summary_emm.Rd index 1d4924487..4eaa14606 100644 --- a/man/tidy.summary_emm.Rd +++ b/man/tidy.summary_emm.Rd @@ -12,7 +12,7 @@ \item{null.value}{Value to which estimate is compared.} \item{...}{Additional arguments passed to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or -\code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments +\code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. \strong{Cautionary note}: misspecified arguments may be silently ignored!} } \description{ @@ -29,7 +29,7 @@ mean, and one column for each combination of factors. When the input is a contrast, each row will contain one estimated contrast. There are a large number of arguments that can be -passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:summary.ref.grid]{lsmeans::summary.ref.grid()}}. +passed on to \code{\link[emmeans:summary.emmGrid]{emmeans::summary.emmGrid()}} or \code{\link[lsmeans:ref.grid]{lsmeans::summary.ref.grid()}}. } \examples{ From 99ac7d547753d08fabd08bcc1e45e8d91487eb34 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 11 Jun 2020 13:20:05 -0700 Subject: [PATCH 11/41] cran submission 3 --- CRAN-RELEASE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 05fe329e1..e248c2972 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ This package was submitted to CRAN on 2020-06-11. -Once it is accepted, delete this file and tag the release (commit aa7d0978be). +Once it is accepted, delete this file and tag the release (commit c5eedbe887). From 49c84e53cccd2c5553f6c4ac606c7f2f6d7a30f4 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 11 Jun 2020 18:30:02 -0700 Subject: [PATCH 12/41] adjust docs for reexports --- cran-comments.md | 6 +++--- man/augment.Mclust.Rd | 6 +++--- man/augment.betamfx.Rd | 4 ++-- man/augment.betareg.Rd | 6 +++--- man/augment.clm.Rd | 6 +++--- man/augment.coxph.Rd | 10 +++++----- man/augment.decomposed.ts.Rd | 6 +++--- man/augment.drc.Rd | 6 +++--- man/augment.factanal.Rd | 6 +++--- man/augment.felm.Rd | 6 +++--- man/augment.fixest.Rd | 4 ++-- man/augment.glm.Rd | 4 ++-- man/augment.glmRob.Rd | 2 +- man/augment.htest.Rd | 6 +++--- man/augment.ivreg.Rd | 6 +++--- man/augment.kmeans.Rd | 6 +++--- man/augment.lm.Rd | 10 +++++----- man/augment.lmRob.Rd | 4 ++-- man/augment.loess.Rd | 8 ++++---- man/augment.mfx.Rd | 4 ++-- man/augment.mjoint.Rd | 4 ++-- man/augment.nlrq.Rd | 4 ++-- man/augment.nls.Rd | 6 +++--- man/augment.pam.Rd | 6 +++--- man/augment.plm.Rd | 6 +++--- man/augment.poLCA.Rd | 6 +++--- man/augment.polr.Rd | 6 +++--- man/augment.prcomp.Rd | 6 +++--- man/augment.rlm.Rd | 4 ++-- man/augment.rma.Rd | 4 ++-- man/augment.robustbase.glmrob.Rd | 4 ++-- man/augment.robustbase.lmrob.Rd | 4 ++-- man/augment.rq.Rd | 4 ++-- man/augment.rqs.Rd | 6 +++--- man/augment.sarlm.Rd | 6 +++--- man/augment.smooth.spline.Rd | 4 ++-- man/augment.speedlm.Rd | 4 ++-- man/augment.stl.Rd | 6 +++--- man/augment.survreg.Rd | 6 +++--- man/durbinWatsonTest_tidiers.Rd | 8 ++++---- man/glance.Arima.Rd | 2 +- man/glance.Gam.Rd | 6 +++--- man/glance.Mclust.Rd | 2 +- man/glance.aareg.Rd | 4 ++-- man/glance.aov.Rd | 4 ++-- man/glance.betamfx.Rd | 2 +- man/glance.betareg.Rd | 4 ++-- man/glance.biglm.Rd | 4 ++-- man/glance.binDesign.Rd | 4 ++-- man/glance.cch.Rd | 4 ++-- man/glance.clm.Rd | 4 ++-- man/glance.clmm.Rd | 4 ++-- man/glance.coxph.Rd | 4 ++-- man/glance.cv.glmnet.Rd | 4 ++-- man/glance.drc.Rd | 4 ++-- man/glance.ergm.Rd | 2 +- man/glance.factanal.Rd | 4 ++-- man/glance.felm.Rd | 2 +- man/glance.fitdistr.Rd | 4 ++-- man/glance.garch.Rd | 4 ++-- man/glance.geeglm.Rd | 4 ++-- man/glance.glm.Rd | 2 +- man/glance.glmRob.Rd | 2 +- man/glance.glmnet.Rd | 4 ++-- man/glance.gmm.Rd | 4 ++-- man/glance.ivreg.Rd | 4 ++-- man/glance.kmeans.Rd | 4 ++-- man/glance.lavaan.Rd | 4 ++-- man/glance.lm.Rd | 4 ++-- man/glance.lmRob.Rd | 2 +- man/glance.lmodel2.Rd | 4 ++-- man/glance.mfx.Rd | 2 +- man/glance.mjoint.Rd | 4 ++-- man/glance.muhaz.Rd | 4 ++-- man/glance.multinom.Rd | 4 ++-- man/glance.nlrq.Rd | 4 ++-- man/glance.nls.Rd | 4 ++-- man/glance.orcutt.Rd | 4 ++-- man/glance.pam.Rd | 4 ++-- man/glance.plm.Rd | 4 ++-- man/glance.poLCA.Rd | 4 ++-- man/glance.polr.Rd | 4 ++-- man/glance.pyears.Rd | 4 ++-- man/glance.ridgelm.Rd | 4 ++-- man/glance.rlm.Rd | 4 ++-- man/glance.rma.Rd | 2 +- man/glance.robustbase.lmrob.Rd | 2 +- man/glance.rq.Rd | 4 ++-- man/glance.sarlm.Rd | 4 ++-- man/glance.smooth.spline.Rd | 4 ++-- man/glance.speedglm.Rd | 2 +- man/glance.speedlm.Rd | 2 +- man/glance.survdiff.Rd | 4 ++-- man/glance.survexp.Rd | 4 ++-- man/glance.survfit.Rd | 4 ++-- man/glance.survreg.Rd | 4 ++-- man/glance.svyglm.Rd | 2 +- man/glance.svyolr.Rd | 4 ++-- man/glance_optim.Rd | 4 ++-- man/metafor_tidiers.Rd | 2 +- man/mgcv_glance_gam.Rd | 4 ++-- man/mgcv_tidy_gam.Rd | 4 ++-- man/sparse_tidiers.Rd | 2 +- man/tidy.Arima.Rd | 2 +- man/tidy.Gam.Rd | 6 +++--- man/tidy.Kendall.Rd | 4 ++-- man/tidy.Mclust.Rd | 4 ++-- man/tidy.TukeyHSD.Rd | 4 ++-- man/tidy.aareg.Rd | 4 ++-- man/tidy.acf.Rd | 4 ++-- man/tidy.anova.Rd | 4 ++-- man/tidy.aov.Rd | 4 ++-- man/tidy.aovlist.Rd | 4 ++-- man/tidy.betamfx.Rd | 2 +- man/tidy.betareg.Rd | 4 ++-- man/tidy.biglm.Rd | 4 ++-- man/tidy.binDesign.Rd | 4 ++-- man/tidy.binWidth.Rd | 4 ++-- man/tidy.boot.Rd | 4 ++-- man/tidy.btergm.Rd | 4 ++-- man/tidy.cch.Rd | 4 ++-- man/tidy.cld.Rd | 4 ++-- man/tidy.clm.Rd | 4 ++-- man/tidy.clmm.Rd | 4 ++-- man/tidy.coeftest.Rd | 4 ++-- man/tidy.confint.glht.Rd | 4 ++-- man/tidy.confusionMatrix.Rd | 4 ++-- man/tidy.coxph.Rd | 4 ++-- man/tidy.cv.glmnet.Rd | 4 ++-- man/tidy.density.Rd | 4 ++-- man/tidy.dist.Rd | 4 ++-- man/tidy.drc.Rd | 4 ++-- man/tidy.emmGrid.Rd | 2 +- man/tidy.epi.2by2.Rd | 4 ++-- man/tidy.ergm.Rd | 2 +- man/tidy.factanal.Rd | 4 ++-- man/tidy.felm.Rd | 4 ++-- man/tidy.fitdistr.Rd | 4 ++-- man/tidy.fixest.Rd | 2 +- man/tidy.ftable.Rd | 4 ++-- man/tidy.gamlss.Rd | 2 +- man/tidy.garch.Rd | 4 ++-- man/tidy.geeglm.Rd | 4 ++-- man/tidy.glht.Rd | 4 ++-- man/tidy.glm.Rd | 2 +- man/tidy.glmRob.Rd | 2 +- man/tidy.glmnet.Rd | 4 ++-- man/tidy.gmm.Rd | 4 ++-- man/tidy.htest.Rd | 8 ++++---- man/tidy.ivreg.Rd | 4 ++-- man/tidy.kappa.Rd | 4 ++-- man/tidy.kde.Rd | 4 ++-- man/tidy.kmeans.Rd | 4 ++-- man/tidy.lavaan.Rd | 2 +- man/tidy.lm.Rd | 4 ++-- man/tidy.lm.beta.Rd | 2 +- man/tidy.lmRob.Rd | 2 +- man/tidy.lmodel2.Rd | 4 ++-- man/tidy.lsmobj.Rd | 2 +- man/tidy.manova.Rd | 2 +- man/tidy.map.Rd | 4 ++-- man/tidy.mediate.Rd | 4 ++-- man/tidy.mfx.Rd | 4 ++-- man/tidy.mjoint.Rd | 4 ++-- man/tidy.mle2.Rd | 4 ++-- man/tidy.mlm.Rd | 4 ++-- man/tidy.muhaz.Rd | 4 ++-- man/tidy.multinom.Rd | 4 ++-- man/tidy.nlrq.Rd | 4 ++-- man/tidy.nls.Rd | 4 ++-- man/tidy.orcutt.Rd | 2 +- man/tidy.pairwise.htest.Rd | 4 ++-- man/tidy.pam.Rd | 4 ++-- man/tidy.plm.Rd | 4 ++-- man/tidy.poLCA.Rd | 4 ++-- man/tidy.polr.Rd | 4 ++-- man/tidy.power.htest.Rd | 2 +- man/tidy.prcomp.Rd | 4 ++-- man/tidy.pyears.Rd | 4 ++-- man/tidy.rcorr.Rd | 4 ++-- man/tidy.ref.grid.Rd | 2 +- man/tidy.regsubsets.Rd | 4 ++-- man/tidy.ridgelm.Rd | 4 ++-- man/tidy.rlm.Rd | 2 +- man/tidy.robustbase.glmrob.Rd | 2 +- man/tidy.robustbase.lmrob.Rd | 2 +- man/tidy.roc.Rd | 4 ++-- man/tidy.rq.Rd | 2 +- man/tidy.rqs.Rd | 2 +- man/tidy.sarlm.Rd | 4 ++-- man/tidy.spec.Rd | 4 ++-- man/tidy.speedglm.Rd | 2 +- man/tidy.speedlm.Rd | 2 +- man/tidy.summary.glht.Rd | 4 ++-- man/tidy.summary_emm.Rd | 2 +- man/tidy.survdiff.Rd | 4 ++-- man/tidy.survexp.Rd | 4 ++-- man/tidy.survfit.Rd | 4 ++-- man/tidy.survreg.Rd | 4 ++-- man/tidy.svyglm.Rd | 2 +- man/tidy.svyolr.Rd | 4 ++-- man/tidy.systemfit.Rd | 4 ++-- man/tidy.table.Rd | 6 +++--- man/tidy.ts.Rd | 4 ++-- man/tidy.zoo.Rd | 4 ++-- man/tidy_irlba.Rd | 4 ++-- man/tidy_optim.Rd | 4 ++-- man/tidy_svd.Rd | 2 +- man/tidy_xyz.Rd | 4 ++-- 209 files changed, 411 insertions(+), 411 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 2101bf33d..799b2a892 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,9 @@ # Release summary -This is a second resubmission following an automated pretest failure due to +This is a resubmission following an automated pretest failure due to "[n]on-file package-anchored link(s) in documentation object[s]." This seems -to be a new test as of yesterday, and has been addressed by linking to -documentation files rather than topics. +to be a new test as of our previous submission, and has been addressed by +linking to documentation files rather than topics. The previous submission was also a resubmission following an automated pretest failure. The failure was due to breaking changes in the `residuals.fixest()` diff --git a/man/augment.Mclust.Rd b/man/augment.Mclust.Rd index d4978fcef..2c8585d32 100644 --- a/man/augment.Mclust.Rd +++ b/man/augment.Mclust.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -94,7 +94,7 @@ augment(m, points) glance(m) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} +\code{\link[=reexports]{augment()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} Other mclust tidiers: \code{\link{tidy.Mclust}()} diff --git a/man/augment.betamfx.Rd b/man/augment.betamfx.Rd index 48a5cb702..fe54916dc 100644 --- a/man/augment.betamfx.Rd +++ b/man/augment.betamfx.Rd @@ -44,7 +44,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -84,7 +84,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.betareg.Rd b/man/augment.betareg.Rd index 67cd183be..1c26e8264 100644 --- a/man/augment.betareg.Rd +++ b/man/augment.betareg.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -109,7 +109,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=reexports]{augment()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/augment.clm.Rd b/man/augment.clm.Rd index d7405069f..0f0b73a73 100644 --- a/man/augment.clm.Rd +++ b/man/augment.clm.Rd @@ -37,7 +37,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -99,7 +99,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict]{ordinal::predict.clm()}} +\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict]{ordinal::predict.clm()}} Other ordinal tidiers: \code{\link{augment.polr}()}, diff --git a/man/augment.coxph.Rd b/man/augment.coxph.Rd index 5d45c2a98..c640340eb 100644 --- a/man/augment.coxph.Rd +++ b/man/augment.coxph.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -95,7 +95,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. } \examples{ @@ -141,9 +141,9 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\link{na.action} +\link[=na.action]{na.action} -\code{\link[=augment]{augment()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=reexports]{augment()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{glance.coxph}()}, diff --git a/man/augment.decomposed.ts.Rd b/man/augment.decomposed.ts.Rd index ac8d6f23a..faa361611 100644 --- a/man/augment.decomposed.ts.Rd +++ b/man/augment.decomposed.ts.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -123,7 +123,7 @@ ggplot(decomps) + )) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:decompose]{stats::decompose()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:decompose]{stats::decompose()}} Other decompose tidiers: \code{\link{augment.stl}()} diff --git a/man/augment.drc.Rd b/man/augment.drc.Rd index f69ba1263..5ff975bb8 100644 --- a/man/augment.drc.Rd +++ b/man/augment.drc.Rd @@ -47,7 +47,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -87,7 +87,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -106,7 +106,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=reexports]{augment()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{glance.drc}()}, diff --git a/man/augment.factanal.Rd b/man/augment.factanal.Rd index 109ff055b..766aec2c5 100644 --- a/man/augment.factanal.Rd +++ b/man/augment.factanal.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -73,11 +73,11 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{glance.factanal}()}, diff --git a/man/augment.felm.Rd b/man/augment.felm.Rd index 56d279969..58ddf782a 100644 --- a/man/augment.felm.Rd +++ b/man/augment.felm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -99,7 +99,7 @@ augment(result_felm) glance(result_felm) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[lfe:felm]{lfe::felm()}} +\code{\link[=reexports]{augment()}}, \code{\link[lfe:felm]{lfe::felm()}} Other felm tidiers: \code{\link{tidy.felm}()} diff --git a/man/augment.fixest.Rd b/man/augment.fixest.Rd index 1514b27c1..da76c1fbd 100644 --- a/man/augment.fixest.Rd +++ b/man/augment.fixest.Rd @@ -66,7 +66,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \note{ @@ -103,7 +103,7 @@ augment(gravity_pois, trade) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}} +\code{\link[=reexports]{augment()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}} Other fixest tidiers: \code{\link{tidy.fixest}()} diff --git a/man/augment.glm.Rd b/man/augment.glm.Rd index baa3048b2..84b1fd06a 100644 --- a/man/augment.glm.Rd +++ b/man/augment.glm.Rd @@ -46,7 +46,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -86,7 +86,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.glmRob.Rd b/man/augment.glmRob.Rd index ab89398dd..0a8dd4472 100644 --- a/man/augment.glmRob.Rd +++ b/man/augment.glmRob.Rd @@ -47,7 +47,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. \code{augment.glmRob()} has been removed from broom. We regret diff --git a/man/augment.htest.Rd b/man/augment.htest.Rd index b7c999373..cd8fd5e9a 100644 --- a/man/augment.htest.Rd +++ b/man/augment.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -83,7 +83,7 @@ tidy(chit) augment(chit) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} Other htest tidiers: \code{\link{tidy.htest}()}, diff --git a/man/augment.ivreg.Rd b/man/augment.ivreg.Rd index 8f134bc03..1245db648 100644 --- a/man/augment.ivreg.Rd +++ b/man/augment.ivreg.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -96,7 +96,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=reexports]{augment()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{glance.ivreg}()}, diff --git a/man/augment.kmeans.Rd b/man/augment.kmeans.Rd index f2c14944a..ed511d406 100644 --- a/man/augment.kmeans.Rd +++ b/man/augment.kmeans.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -81,7 +81,7 @@ glance(fit) augment(fit, x) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{glance.kmeans}()}, diff --git a/man/augment.lm.Rd b/man/augment.lm.Rd index ec9b17a25..54459802d 100644 --- a/man/augment.lm.Rd +++ b/man/augment.lm.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -82,7 +82,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. Some unusual \code{lm} objects, such as \code{rlm} from MASS, may omit @@ -144,9 +144,9 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\link{na.action} +\link[=na.action]{na.action} -\code{\link[=augment]{augment()}}, \code{\link[stats:predict.lm]{stats::predict.lm()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:predict.lm]{stats::predict.lm()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/augment.lmRob.Rd b/man/augment.lmRob.Rd index a67c61590..1e53fd758 100644 --- a/man/augment.lmRob.Rd +++ b/man/augment.lmRob.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.loess.Rd b/man/augment.loess.Rd index c2d2814c8..c183e4821 100644 --- a/man/augment.loess.Rd +++ b/man/augment.loess.Rd @@ -33,7 +33,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. Note that \code{loess} objects by default will not predict on data @@ -78,9 +78,9 @@ augment(lo, mtcars) augment(lo, newdata = head(mtcars)) } \seealso{ -\link{na.action} +\link[=na.action]{na.action} -\code{\link[=augment]{augment()}}, \code{\link[stats:loess]{stats::loess()}}, \code{\link[stats:predict.loess]{stats::predict.loess()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:loess]{stats::loess()}}, \code{\link[stats:predict.loess]{stats::predict.loess()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/augment.mfx.Rd b/man/augment.mfx.Rd index 7c634b9af..ee2c20b4f 100644 --- a/man/augment.mfx.Rd +++ b/man/augment.mfx.Rd @@ -91,7 +91,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -131,7 +131,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.mjoint.Rd b/man/augment.mjoint.Rd index 3d3bb41f9..9ae813be4 100644 --- a/man/augment.mjoint.Rd +++ b/man/augment.mjoint.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -75,7 +75,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.nlrq.Rd b/man/augment.nlrq.Rd index 018250a19..036ecf16d 100644 --- a/man/augment.nlrq.Rd +++ b/man/augment.nlrq.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=reexports]{augment()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.rqs}()}, diff --git a/man/augment.nls.Rd b/man/augment.nls.Rd index 10e34d09d..4ad6f6682 100644 --- a/man/augment.nls.Rd +++ b/man/augment.nls.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -93,7 +93,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:predict.nls]{stats::predict.nls()}} +\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:predict.nls]{stats::predict.nls()}} Other nls tidiers: \code{\link{glance.nls}()}, diff --git a/man/augment.pam.Rd b/man/augment.pam.Rd index 6f270d034..628a72b27 100644 --- a/man/augment.pam.Rd +++ b/man/augment.pam.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -86,7 +86,7 @@ augment(p, x) \%>\% geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=reexports]{augment()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{glance.pam}()}, diff --git a/man/augment.plm.Rd b/man/augment.plm.Rd index 64105ced4..365a493f8 100644 --- a/man/augment.plm.Rd +++ b/man/augment.plm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -85,7 +85,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[plm:plm]{plm::plm()}} +\code{\link[=reexports]{augment()}}, \code{\link[plm:plm]{plm::plm()}} Other plm tidiers: \code{\link{glance.plm}()}, diff --git a/man/augment.poLCA.Rd b/man/augment.poLCA.Rd index 2afb1bd19..37793f48e 100644 --- a/man/augment.poLCA.Rd +++ b/man/augment.poLCA.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -126,7 +126,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=reexports]{augment()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{glance.poLCA}()}, diff --git a/man/augment.polr.Rd b/man/augment.polr.Rd index 298da3804..7cc400cd0 100644 --- a/man/augment.polr.Rd +++ b/man/augment.polr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -78,7 +78,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -97,7 +97,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[MASS:polr]{MASS::polr()}} +\code{\link[=reexports]{tidy()}}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/augment.prcomp.Rd b/man/augment.prcomp.Rd index d32760678..b2a3f7aef 100644 --- a/man/augment.prcomp.Rd +++ b/man/augment.prcomp.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -73,11 +73,11 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ -\code{\link[stats:prcomp]{stats::prcomp()}}, \link{svd_tidiers} +\code{\link[stats:prcomp]{stats::prcomp()}}, \link[=tidy_svd]{svd_tidiers} Other svd tidiers: \code{\link{tidy.prcomp}()}, diff --git a/man/augment.rlm.Rd b/man/augment.rlm.Rd index 1a4bc58d3..16c64545c 100644 --- a/man/augment.rlm.Rd +++ b/man/augment.rlm.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.rma.Rd b/man/augment.rma.Rd index e20df7907..038e139cc 100644 --- a/man/augment.rma.Rd +++ b/man/augment.rma.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -57,7 +57,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.robustbase.glmrob.Rd b/man/augment.robustbase.glmrob.Rd index a397a1ee7..d6afdccf4 100644 --- a/man/augment.robustbase.glmrob.Rd +++ b/man/augment.robustbase.glmrob.Rd @@ -50,7 +50,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -90,7 +90,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.robustbase.lmrob.Rd b/man/augment.robustbase.lmrob.Rd index 61bba6a81..5700ac4e4 100644 --- a/man/augment.robustbase.lmrob.Rd +++ b/man/augment.robustbase.lmrob.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.rq.Rd b/man/augment.rq.Rd index 56d284fe7..ca59cddf8 100644 --- a/man/augment.rq.Rd +++ b/man/augment.rq.Rd @@ -83,7 +83,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -93,7 +93,7 @@ columns \code{.conf.low} and \code{.conf.high}. Does not provide confidence intervals when data is specified via the \code{newdata} argument. } \seealso{ -\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rq()}} +\link[=reexports]{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/augment.rqs.Rd b/man/augment.rqs.Rd index e9f6af526..b35af7d99 100644 --- a/man/augment.rqs.Rd +++ b/man/augment.rqs.Rd @@ -23,7 +23,7 @@ that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} \item{...}{ - Arguments passed on to \code{\link[quantreg:predict.rqs]{quantreg::predict.rqs}} + Arguments passed on to quantreg's predict method \describe{ \item{\code{object}}{ object of class rq or rqs or rq.process produced by \code{rq} } \item{\code{type}}{For \code{predict.rq}, the method for 'confidence' intervals, if desired. @@ -84,7 +84,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -94,7 +94,7 @@ columns \code{.conf.low} and \code{.conf.high}. Does not provide confidence intervals when data is specified via the \code{newdata} argument. } \seealso{ -\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rqs()}} +\link[=reexports]{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rqs()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/augment.sarlm.Rd b/man/augment.sarlm.Rd index 579bc59e2..12c547e79 100644 --- a/man/augment.sarlm.Rd +++ b/man/augment.sarlm.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -59,7 +59,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -99,7 +99,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=augment]{augment()}} +\code{\link[=reexports]{augment()}} Other spatialreg tidiers: \code{\link{glance.sarlm}()}, diff --git a/man/augment.smooth.spline.Rd b/man/augment.smooth.spline.Rd index 79a4b0966..076f09ed7 100644 --- a/man/augment.smooth.spline.Rd +++ b/man/augment.smooth.spline.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -48,7 +48,7 @@ ggplot(augment(spl, mtcars), aes(wt, mpg)) + geom_line(aes(y = .fitted)) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}}, +\code{\link[=reexports]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}}, \code{\link[stats:predict.smooth.spline]{stats::predict.smooth.spline()}} Other smoothing spline tidiers: diff --git a/man/augment.speedlm.Rd b/man/augment.speedlm.Rd index cd7cfd8c2..d74e31e12 100644 --- a/man/augment.speedlm.Rd +++ b/man/augment.speedlm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.stl.Rd b/man/augment.stl.Rd index 7abef5c98..e4635b0f9 100644 --- a/man/augment.stl.Rd +++ b/man/augment.stl.Rd @@ -20,7 +20,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -72,11 +72,11 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:stl]{stats::stl()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:stl]{stats::stl()}} Other decompose tidiers: \code{\link{augment.decomposed.ts}()} diff --git a/man/augment.survreg.Rd b/man/augment.survreg.Rd index 6fa5171fe..71a3b5881 100644 --- a/man/augment.survreg.Rd +++ b/man/augment.survreg.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link{na.action} arguments, but make no guarantees about behavior when data is +\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ @@ -111,7 +111,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=reexports]{augment()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{glance.survreg}()}, diff --git a/man/durbinWatsonTest_tidiers.Rd b/man/durbinWatsonTest_tidiers.Rd index f56bfdfa3..45901cc3a 100644 --- a/man/durbinWatsonTest_tidiers.Rd +++ b/man/durbinWatsonTest_tidiers.Rd @@ -20,13 +20,13 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \description{ -For models that have only a single component, the \code{\link[=tidy]{tidy()}} and -\code{\link[=glance]{glance()}} methods are identical. Please see the documentation for both +For models that have only a single component, the \code{\link[=reexports]{tidy()}} and +\code{\link[=reexports]{glance()}} methods are identical. Please see the documentation for both of those methods. } \examples{ @@ -36,7 +36,7 @@ tidy(dw) glance(dw) # same output for all durbinWatsonTests } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[=glance]{glance()}}, \code{\link[car:durbinWatsonTest]{car::durbinWatsonTest()}} +\code{\link[=reexports]{tidy()}}, \code{\link[=reexports]{glance()}}, \code{\link[car:durbinWatsonTest]{car::durbinWatsonTest()}} } \concept{car tidiers} \value{ diff --git a/man/glance.Arima.Rd b/man/glance.Arima.Rd index ef852c3c4..f996192b8 100644 --- a/man/glance.Arima.Rd +++ b/man/glance.Arima.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.Gam.Rd b/man/glance.Gam.Rd index 34f831881..ea987f96b 100644 --- a/man/glance.Gam.Rd +++ b/man/glance.Gam.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,10 +41,10 @@ of the appropriate type. } \details{ Glance at \code{gam} objects created by calls to \code{\link[mgcv:gam]{mgcv::gam()}} with -\code{\link[=glance.gam]{glance.gam()}}. +\code{\link[=mgcv_glance_gam]{glance.gam()}}. } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[gam:gam]{gam::gam()}} +\code{\link[=reexports]{glance()}}, \code{\link[gam:gam]{gam::gam()}} Other gam tidiers: \code{\link{tidy.Gam}()} diff --git a/man/glance.Mclust.Rd b/man/glance.Mclust.Rd index 02b56a761..7bb3665ea 100644 --- a/man/glance.Mclust.Rd +++ b/man/glance.Mclust.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.aareg.Rd b/man/glance.aareg.Rd index 7d42bbbba..cbb39712c 100644 --- a/man/glance.aareg.Rd +++ b/man/glance.aareg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ afit <- aareg( tidy(afit) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:aareg]{survival::aareg()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:aareg]{survival::aareg()}} Other aareg tidiers: \code{\link{tidy.aareg}()} diff --git a/man/glance.aov.Rd b/man/glance.aov.Rd index 375758482..4971d15bc 100644 --- a/man/glance.aov.Rd +++ b/man/glance.aov.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -50,7 +50,7 @@ a <- aov(mpg ~ wt + qsec + disp, mtcars) tidy(a) } \seealso{ -\code{\link[=glance]{glance()}} +\code{\link[=reexports]{glance()}} Other anova tidiers: \code{\link{tidy.TukeyHSD}()}, diff --git a/man/glance.betamfx.Rd b/man/glance.betamfx.Rd index 073da0918..18c0fb6be 100644 --- a/man/glance.betamfx.Rd +++ b/man/glance.betamfx.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.betareg.Rd b/man/glance.betareg.Rd index afd42dadc..77d31cc86 100644 --- a/man/glance.betareg.Rd +++ b/man/glance.betareg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=reexports]{glance()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with exactly one row and columns: diff --git a/man/glance.biglm.Rd b/man/glance.biglm.Rd index 33f9e51b7..4f3830b19 100644 --- a/man/glance.biglm.Rd +++ b/man/glance.biglm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ glance(bgfit) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} +\code{\link[=reexports]{glance()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} Other biglm tidiers: \code{\link{tidy.biglm}()} diff --git a/man/glance.binDesign.Rd b/man/glance.binDesign.Rd index 0cff02655..2910b446c 100644 --- a/man/glance.binDesign.Rd +++ b/man/glance.binDesign.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ ggplot(tidy(des), aes(n, power)) + geom_line() } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} +\code{\link[=reexports]{glance()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} Other bingroup tidiers: \code{\link{tidy.binDesign}()}, diff --git a/man/glance.cch.Rd b/man/glance.cch.Rd index 70422201c..9e884a3a8 100644 --- a/man/glance.cch.Rd +++ b/man/glance.cch.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -69,7 +69,7 @@ ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:cch]{survival::cch()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:cch]{survival::cch()}} Other cch tidiers: \code{\link{glance.survfit}()}, diff --git a/man/glance.clm.Rd b/man/glance.clm.Rd index 46605e0cb..a051b91b6 100644 --- a/man/glance.clm.Rd +++ b/man/glance.clm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}} +\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.clmm.Rd b/man/glance.clmm.Rd index 0f322873f..0c450403b 100644 --- a/man/glance.clmm.Rd +++ b/man/glance.clmm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}} +\link[=reexports]{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.coxph.Rd b/man/glance.coxph.Rd index 21f0b8840..ec1b94159 100644 --- a/man/glance.coxph.Rd +++ b/man/glance.coxph.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -82,7 +82,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{augment.coxph}()}, diff --git a/man/glance.cv.glmnet.Rd b/man/glance.cv.glmnet.Rd index 20abf0772..5a8fd595b 100644 --- a/man/glance.cv.glmnet.Rd +++ b/man/glance.cv.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -93,7 +93,7 @@ ggplot(tidied, aes(lambda, estimate, group = term)) + geom_vline(xintercept = glance_cv$lambda.1se, lty = 2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} +\code{\link[=reexports]{glance()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} Other glmnet tidiers: \code{\link{glance.glmnet}()}, diff --git a/man/glance.drc.Rd b/man/glance.drc.Rd index 90d8df8ef..2c69ae09f 100644 --- a/man/glance.drc.Rd +++ b/man/glance.drc.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=reexports]{glance()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{augment.drc}()}, diff --git a/man/glance.ergm.Rd b/man/glance.ergm.Rd index 389572bd6..b31099f53 100644 --- a/man/glance.ergm.Rd +++ b/man/glance.ergm.Rd @@ -55,7 +55,7 @@ that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:summary.ergm]{ergm::summary.ergm()}} +\code{\link[=reexports]{glance()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:summary.ergm]{ergm::summary.ergm()}} Other ergm tidiers: \code{\link{tidy.ergm}()} diff --git a/man/glance.factanal.Rd b/man/glance.factanal.Rd index 30107b5fa..fb18398f5 100644 --- a/man/glance.factanal.Rd +++ b/man/glance.factanal.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -73,7 +73,7 @@ augment(fit1, data = m2) augment(fit2, data = m2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=reexports]{glance()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{augment.factanal}()}, diff --git a/man/glance.felm.Rd b/man/glance.felm.Rd index 1b2a5d032..6937baf88 100644 --- a/man/glance.felm.Rd +++ b/man/glance.felm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.fitdistr.Rd b/man/glance.fitdistr.Rd index 5d7ecb263..a0acf9c45 100644 --- a/man/glance.fitdistr.Rd +++ b/man/glance.fitdistr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ tidy(fit) glance(fit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} +\code{\link[=reexports]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} Other fitdistr tidiers: \code{\link{tidy.fitdistr}()} diff --git a/man/glance.garch.Rd b/man/glance.garch.Rd index bed5d0482..c686a1b70 100644 --- a/man/glance.garch.Rd +++ b/man/glance.garch.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -32,7 +32,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[tseries:garch]{tseries::garch()}}, [] +\code{\link[=reexports]{glance()}}, \code{\link[tseries:garch]{tseries::garch()}}, [] Other garch tidiers: \code{\link{tidy.garch}()} diff --git a/man/glance.geeglm.Rd b/man/glance.geeglm.Rd index 7a51e5a5b..12adac491 100644 --- a/man/glance.geeglm.Rd +++ b/man/glance.geeglm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(geefit) tidy(geefit, conf.int = TRUE) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} +\code{\link[=reexports]{glance()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} } \concept{geepack tidiers} \value{ diff --git a/man/glance.glm.Rd b/man/glance.glm.Rd index 0b5134bbf..bd3dd403c 100644 --- a/man/glance.glm.Rd +++ b/man/glance.glm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.glmRob.Rd b/man/glance.glmRob.Rd index 15f386bce..52bbb4375 100644 --- a/man/glance.glmRob.Rd +++ b/man/glance.glmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.glmnet.Rd b/man/glance.glmnet.Rd index 1c3b226ba..3e1d0b10b 100644 --- a/man/glance.glmnet.Rd +++ b/man/glance.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,7 +71,7 @@ fit2 <- glmnet(x, g2, family = "binomial") tidy(fit2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} +\code{\link[=reexports]{glance()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/glance.gmm.Rd b/man/glance.gmm.Rd index 338888b41..f7e4ed155 100644 --- a/man/glance.gmm.Rd +++ b/man/glance.gmm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -105,7 +105,7 @@ td2 \%>\% geom_vline(xintercept = 0, color = "red", lty = 2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[gmm:gmm]{gmm::gmm()}} +\code{\link[=reexports]{glance()}}, \code{\link[gmm:gmm]{gmm::gmm()}} Other gmm tidiers: \code{\link{tidy.gmm}()} diff --git a/man/glance.ivreg.Rd b/man/glance.ivreg.Rd index 2e98f2e52..3074fca46 100644 --- a/man/glance.ivreg.Rd +++ b/man/glance.ivreg.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=reexports]{glance()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{augment.ivreg}()}, diff --git a/man/glance.kmeans.Rd b/man/glance.kmeans.Rd index 07cfb5977..f0b1ccfd4 100644 --- a/man/glance.kmeans.Rd +++ b/man/glance.kmeans.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ glance(fit) augment(fit, x) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=reexports]{glance()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{augment.kmeans}()}, diff --git a/man/glance.lavaan.Rd b/man/glance.lavaan.Rd index 0f4167482..e1e9656e7 100644 --- a/man/glance.lavaan.Rd +++ b/man/glance.lavaan.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -80,7 +80,7 @@ glance(cfa.fit) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, +\code{\link[=reexports]{glance()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, \code{\link[lavaan:fitMeasures]{lavaan::fitmeasures()}} Other lavaan tidiers: diff --git a/man/glance.lm.Rd b/man/glance.lm.Rd index 22e4844c5..f15f1fe4a 100644 --- a/man/glance.lm.Rd +++ b/man/glance.lm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -92,7 +92,7 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\code{\link[=glance]{glance()}} +\code{\link[=reexports]{glance()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/glance.lmRob.Rd b/man/glance.lmRob.Rd index 2ffb77fb3..256c5df5d 100644 --- a/man/glance.lmRob.Rd +++ b/man/glance.lmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.lmodel2.Rd b/man/glance.lmodel2.Rd index eba5790ec..3f812d043 100644 --- a/man/glance.lmodel2.Rd +++ b/man/glance.lmodel2.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(tidy(Ex2.res), aes(estimate, term, color = method)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} +\code{\link[=reexports]{glance()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} Other lmodel2 tidiers: \code{\link{tidy.lmodel2}()} diff --git a/man/glance.mfx.Rd b/man/glance.mfx.Rd index dfec4492a..44eef64da 100644 --- a/man/glance.mfx.Rd +++ b/man/glance.mfx.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.mjoint.Rd b/man/glance.mjoint.Rd index b202c92bb..4c1a1b705 100644 --- a/man/glance.mjoint.Rd +++ b/man/glance.mjoint.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ glance(fit) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}} +\code{\link[=reexports]{glance()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}} Other mjoint tidiers: \code{\link{tidy.mjoint}()} diff --git a/man/glance.muhaz.Rd b/man/glance.muhaz.Rd index 40e92be23..266a082c7 100644 --- a/man/glance.muhaz.Rd +++ b/man/glance.muhaz.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ tidy(x) glance(x) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} +\code{\link[=reexports]{glance()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} Other muhaz tidiers: \code{\link{tidy.muhaz}()} diff --git a/man/glance.multinom.Rd b/man/glance.multinom.Rd index 0c4ce9532..34ace308d 100644 --- a/man/glance.multinom.Rd +++ b/man/glance.multinom.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit.gear) glance(fit.gear) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[nnet:multinom]{nnet::multinom()}} +\code{\link[=reexports]{glance()}}, \code{\link[nnet:multinom]{nnet::multinom()}} Other multinom tidiers: \code{\link{tidy.multinom}()} diff --git a/man/glance.nlrq.Rd b/man/glance.nlrq.Rd index 7e2560be8..d2776af55 100644 --- a/man/glance.nlrq.Rd +++ b/man/glance.nlrq.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -40,7 +40,7 @@ that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=reexports]{glance()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/glance.nls.Rd b/man/glance.nls.Rd index 136553a1c..f205f214a 100644 --- a/man/glance.nls.Rd +++ b/man/glance.nls.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -57,7 +57,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link{tidy}, \code{\link[stats:nls]{stats::nls()}} +\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}} Other nls tidiers: \code{\link{augment.nls}()}, diff --git a/man/glance.orcutt.Rd b/man/glance.orcutt.Rd index 358a5e40f..2fcffa07f 100644 --- a/man/glance.orcutt.Rd +++ b/man/glance.orcutt.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(co) glance(co) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[orcutt:cochrane.orcutt]{orcutt::cochrane.orcutt()}} +\code{\link[=reexports]{glance()}}, \code{\link[orcutt:cochrane.orcutt]{orcutt::cochrane.orcutt()}} Other orcutt tidiers: \code{\link{tidy.orcutt}()} diff --git a/man/glance.pam.Rd b/man/glance.pam.Rd index a38935932..529250167 100644 --- a/man/glance.pam.Rd +++ b/man/glance.pam.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -59,7 +59,7 @@ augment(p, x) \%>\% geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=reexports]{glance()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{augment.pam}()}, diff --git a/man/glance.plm.Rd b/man/glance.plm.Rd index efe06312e..422fc8528 100644 --- a/man/glance.plm.Rd +++ b/man/glance.plm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[plm:plm]{plm::plm()}} +\code{\link[=reexports]{glance()}}, \code{\link[plm:plm]{plm::plm()}} Other plm tidiers: \code{\link{augment.plm}()}, diff --git a/man/glance.poLCA.Rd b/man/glance.poLCA.Rd index a53a6cf13..8ab80b2cd 100644 --- a/man/glance.poLCA.Rd +++ b/man/glance.poLCA.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -88,7 +88,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=reexports]{glance()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{augment.poLCA}()}, diff --git a/man/glance.polr.Rd b/man/glance.polr.Rd index 18fb43798..2e51e696d 100644 --- a/man/glance.polr.Rd +++ b/man/glance.polr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\link{tidy}, \code{\link[MASS:polr]{MASS::polr()}} +\link[=reexports]{tidy}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.pyears.Rd b/man/glance.pyears.Rd index c004c8c28..a4bdc82be 100644 --- a/man/glance.pyears.Rd +++ b/man/glance.pyears.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -60,7 +60,7 @@ tidy(pfit2) glance(pfit2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:pyears]{survival::pyears()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:pyears]{survival::pyears()}} Other pyears tidiers: \code{\link{tidy.pyears}()} diff --git a/man/glance.ridgelm.Rd b/man/glance.ridgelm.Rd index 3329292a4..09c4d2666 100644 --- a/man/glance.ridgelm.Rd +++ b/man/glance.ridgelm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ ggplot(td2, aes(lambda, GCV)) + geom_vline(xintercept = g2$lambdaGCV, col = "red", lty = 2) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[MASS:lm.ridge]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} +\code{\link[=reexports]{glance()}}, \code{\link[MASS:lm.ridge]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} Other ridgelm tidiers: \code{\link{tidy.ridgelm}()} diff --git a/man/glance.rlm.Rd b/man/glance.rlm.Rd index 36f180fff..e7518d052 100644 --- a/man/glance.rlm.Rd +++ b/man/glance.rlm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ augment(r) glance(r) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[MASS:rlm]{MASS::rlm()}} +\code{\link[=reexports]{glance()}}, \code{\link[MASS:rlm]{MASS::rlm()}} Other rlm tidiers: \code{\link{augment.rlm}()}, diff --git a/man/glance.rma.Rd b/man/glance.rma.Rd index 44c87efcb..ce658cbdf 100644 --- a/man/glance.rma.Rd +++ b/man/glance.rma.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.robustbase.lmrob.Rd b/man/glance.robustbase.lmrob.Rd index 47064f932..d00f4de97 100644 --- a/man/glance.robustbase.lmrob.Rd +++ b/man/glance.robustbase.lmrob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.rq.Rd b/man/glance.rq.Rd index 91ac8342e..832984377 100644 --- a/man/glance.rq.Rd +++ b/man/glance.rq.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ For multiple values, please use a \code{\link[purrr:map]{purrr::map()}} workflow } } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=reexports]{glance()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/glance.sarlm.Rd b/man/glance.sarlm.Rd index 3890c78fe..ca6afc805 100644 --- a/man/glance.sarlm.Rd +++ b/man/glance.sarlm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,7 +71,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[=reexports]{glance()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: diff --git a/man/glance.smooth.spline.Rd b/man/glance.smooth.spline.Rd index c8dc10747..f56e3b713 100644 --- a/man/glance.smooth.spline.Rd +++ b/man/glance.smooth.spline.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ ggplot(augment(spl, mtcars), aes(wt, mpg)) + geom_line(aes(y = .fitted)) } \seealso{ -\code{\link[=augment]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}} +\code{\link[=reexports]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}} Other smoothing spline tidiers: \code{\link{augment.smooth.spline}()} diff --git a/man/glance.speedglm.Rd b/man/glance.speedglm.Rd index 8fa322a8f..b8c156340 100644 --- a/man/glance.speedglm.Rd +++ b/man/glance.speedglm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.speedlm.Rd b/man/glance.speedlm.Rd index db32cd18c..dc30f8e8a 100644 --- a/man/glance.speedlm.Rd +++ b/man/glance.speedlm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.survdiff.Rd b/man/glance.survdiff.Rd index 301a1abcd..43eb42d56 100644 --- a/man/glance.survdiff.Rd +++ b/man/glance.survdiff.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ tidy(s) glance(s) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:survdiff]{survival::survdiff()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:survdiff]{survival::survdiff()}} Other survdiff tidiers: \code{\link{tidy.survdiff}()} diff --git a/man/glance.survexp.Rd b/man/glance.survexp.Rd index e50ba0268..4f52f6ea3 100644 --- a/man/glance.survexp.Rd +++ b/man/glance.survexp.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -57,7 +57,7 @@ tidy(sexpfit) glance(sexpfit) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:survexp]{survival::survexp()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:survexp]{survival::survexp()}} Other survexp tidiers: \code{\link{tidy.survexp}()} diff --git a/man/glance.survfit.Rd b/man/glance.survfit.Rd index 0116002e0..e50e62fc5 100644 --- a/man/glance.survfit.Rd +++ b/man/glance.survfit.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ ggplot(td_multi, aes(time, estimate, group = state)) + geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:survfit]{survival::survfit()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:survfit]{survival::survfit()}} Other cch tidiers: \code{\link{glance.cch}()}, diff --git a/man/glance.survreg.Rd b/man/glance.survreg.Rd index a0e3476a3..3e9486aa7 100644 --- a/man/glance.survreg.Rd +++ b/man/glance.survreg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=reexports]{glance()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{augment.survreg}()}, diff --git a/man/glance.svyglm.Rd b/man/glance.svyglm.Rd index 84795f20b..de8d23b23 100644 --- a/man/glance.svyglm.Rd +++ b/man/glance.svyglm.Rd @@ -20,7 +20,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.svyolr.Rd b/man/glance.svyolr.Rd index 500e1e48e..0849db1da 100644 --- a/man/glance.svyolr.Rd +++ b/man/glance.svyolr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ tidy(fit, exponentiate = TRUE, conf.int = TRUE) glance(fit) } \seealso{ -\link{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} +\link[=reexports]{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance_optim.Rd b/man/glance_optim.Rd index 0cb434209..04b0c661c 100644 --- a/man/glance_optim.Rd +++ b/man/glance_optim.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -40,7 +40,7 @@ o <- optim(c(1, 1, 1), f) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[=optim]{optim()}} +\code{\link[=reexports]{glance()}}, \code{\link[=optim]{optim()}} Other list tidiers: \code{\link{list_tidiers}}, diff --git a/man/metafor_tidiers.Rd b/man/metafor_tidiers.Rd index 3a6db0beb..36d824e69 100644 --- a/man/metafor_tidiers.Rd +++ b/man/metafor_tidiers.Rd @@ -42,7 +42,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/mgcv_glance_gam.Rd b/man/mgcv_glance_gam.Rd index e174da770..890a06c45 100644 --- a/man/mgcv_glance_gam.Rd +++ b/man/mgcv_glance_gam.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=glance]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=glance.Gam]{glance.Gam()}} +\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=glance.Gam]{glance.Gam()}} Other mgcv tidiers: \code{\link{tidy.gam}()} diff --git a/man/mgcv_tidy_gam.Rd b/man/mgcv_tidy_gam.Rd index 3b0eb0493..0ce34bee7 100644 --- a/man/mgcv_tidy_gam.Rd +++ b/man/mgcv_tidy_gam.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=tidy.Gam]{tidy.Gam()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=tidy.Gam]{tidy.Gam()}} Other mgcv tidiers: \code{\link{glance.gam}()} diff --git a/man/sparse_tidiers.Rd b/man/sparse_tidiers.Rd index 9dc43fd8b..3c54690ae 100644 --- a/man/sparse_tidiers.Rd +++ b/man/sparse_tidiers.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.Arima.Rd b/man/tidy.Arima.Rd index ba8f68638..21d232686 100644 --- a/man/tidy.Arima.Rd +++ b/man/tidy.Arima.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.Gam.Rd b/man/tidy.Gam.Rd index 99c266353..a5627f6a3 100644 --- a/man/tidy.Gam.Rd +++ b/man/tidy.Gam.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -30,7 +30,7 @@ specify which components to return. } \details{ Tidy \code{gam} objects created by calls to \code{\link[mgcv:gam]{mgcv::gam()}} with -\code{\link[=tidy.gam]{tidy.gam()}}. +\code{\link[=mgcv_tidy_gam]{tidy.gam()}}. } \examples{ @@ -41,7 +41,7 @@ tidy(g) glance(g) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[gam:gam]{gam::gam()}}, \code{\link[=tidy.anova]{tidy.anova()}}, \code{\link[=tidy.gam]{tidy.gam()}} +\code{\link[=reexports]{tidy()}}, \code{\link[gam:gam]{gam::gam()}}, \code{\link[=tidy.anova]{tidy.anova()}}, \code{\link[=mgcv_tidy_gam]{tidy.gam()}} Other gam tidiers: \code{\link{glance.Gam}()} diff --git a/man/tidy.Kendall.Rd b/man/tidy.Kendall.Rd index 54253c822..1a7aab9b2 100644 --- a/man/tidy.Kendall.Rd +++ b/man/tidy.Kendall.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -46,7 +46,7 @@ t_res <- SeasonalMannKendall(ts(A)) tidy(t_res) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[Kendall:Kendall]{Kendall::Kendall()}}, \code{\link[Kendall:MannKendall]{Kendall::MannKendall()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[Kendall:Kendall]{Kendall::Kendall()}}, \code{\link[Kendall:MannKendall]{Kendall::MannKendall()}}, \code{\link[Kendall:SeasonalMannKendall]{Kendall::SeasonalMannKendall()}} } \value{ diff --git a/man/tidy.Mclust.Rd b/man/tidy.Mclust.Rd index a0ba5b202..1b51c637a 100644 --- a/man/tidy.Mclust.Rd +++ b/man/tidy.Mclust.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ augment(m, points) glance(m) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} Other mclust tidiers: \code{\link{augment.Mclust}()} diff --git a/man/tidy.TukeyHSD.Rd b/man/tidy.TukeyHSD.Rd index e46421b3a..fbb97129e 100644 --- a/man/tidy.TukeyHSD.Rd +++ b/man/tidy.TukeyHSD.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -38,7 +38,7 @@ fm2 <- aov(mpg ~ as.factor(gear) * as.factor(cyl), data = mtcars) tidy(TukeyHSD(fm2)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:TukeyHSD]{stats::TukeyHSD()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:TukeyHSD]{stats::TukeyHSD()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aareg.Rd b/man/tidy.aareg.Rd index 0c73a21bd..56267c17d 100644 --- a/man/tidy.aareg.Rd +++ b/man/tidy.aareg.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -45,7 +45,7 @@ afit <- aareg( tidy(afit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:aareg]{survival::aareg()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:aareg]{survival::aareg()}} Other aareg tidiers: \code{\link{glance.aareg}()} diff --git a/man/tidy.acf.Rd b/man/tidy.acf.Rd index 44c90ca2f..fee101212 100644 --- a/man/tidy.acf.Rd +++ b/man/tidy.acf.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ tidy(ccf(mdeaths, fdeaths, plot = FALSE)) tidy(pacf(lh, plot = FALSE)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}}, \code{\link[stats:acf]{stats::ccf()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}}, \code{\link[stats:acf]{stats::ccf()}} Other time series tidiers: \code{\link{tidy.spec}()}, diff --git a/man/tidy.anova.Rd b/man/tidy.anova.Rd index 890a4f5d7..2d4bf7fe9 100644 --- a/man/tidy.anova.Rd +++ b/man/tidy.anova.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ b <- lm(mpg ~ wt + qsec, mtcars) tidy(anova(a, b)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:anova]{stats::anova()}}, \code{\link[car:Anova]{car::Anova()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:anova]{stats::anova()}}, \code{\link[car:Anova]{car::Anova()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aov.Rd b/man/tidy.aov.Rd index 2fa4d61f6..187f44a90 100644 --- a/man/tidy.aov.Rd +++ b/man/tidy.aov.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ a <- aov(mpg ~ wt + qsec + disp, mtcars) tidy(a) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aovlist.Rd b/man/tidy.aovlist.Rd index c6eda4f0e..fcd1cc709 100644 --- a/man/tidy.aovlist.Rd +++ b/man/tidy.aovlist.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ a <- aov(mpg ~ wt + qsec + Error(disp / am), mtcars) tidy(a) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.betamfx.Rd b/man/tidy.betamfx.Rd index ca9c81b21..390c55db6 100644 --- a/man/tidy.betamfx.Rd +++ b/man/tidy.betamfx.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.betareg.Rd b/man/tidy.betareg.Rd index 35f1e96f7..0678cffe1 100644 --- a/man/tidy.betareg.Rd +++ b/man/tidy.betareg.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -59,7 +59,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=reexports]{tidy()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \concept{betareg tidiers} \value{ diff --git a/man/tidy.biglm.Rd b/man/tidy.biglm.Rd index dd7e2ced9..c86da4eba 100644 --- a/man/tidy.biglm.Rd +++ b/man/tidy.biglm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ glance(bgfit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} Other biglm tidiers: \code{\link{glance.biglm}()} diff --git a/man/tidy.binDesign.Rd b/man/tidy.binDesign.Rd index 65ae3e60c..b9c5fc46a 100644 --- a/man/tidy.binDesign.Rd +++ b/man/tidy.binDesign.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -45,7 +45,7 @@ ggplot(tidy(des), aes(n, power)) + geom_line() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} +\code{\link[=reexports]{tidy()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} Other bingroup tidiers: \code{\link{glance.binDesign}()}, diff --git a/man/tidy.binWidth.Rd b/man/tidy.binWidth.Rd index 311c9298f..557c659dc 100644 --- a/man/tidy.binWidth.Rd +++ b/man/tidy.binWidth.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ bw tidy(bw) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[binGroup:binWidth]{binGroup::binWidth()}} +\code{\link[=reexports]{tidy()}}, \code{\link[binGroup:binWidth]{binGroup::binWidth()}} Other bingroup tidiers: \code{\link{glance.binDesign}()}, diff --git a/man/tidy.boot.Rd b/man/tidy.boot.Rd index f69a11851..4dc78a73c 100644 --- a/man/tidy.boot.Rd +++ b/man/tidy.boot.Rd @@ -33,7 +33,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -76,7 +76,7 @@ tidy(g1, conf.int = TRUE) tidy(bootres, conf.int = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[boot:boot]{boot::boot()}}, \code{\link[boot:tsboot]{boot::tsboot()}}, \code{\link[boot:boot.ci]{boot::boot.ci()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[boot:boot]{boot::boot()}}, \code{\link[boot:tsboot]{boot::tsboot()}}, \code{\link[boot:boot.ci]{boot::boot.ci()}}, \code{\link[rsample:bootstraps]{rsample::bootstraps()}} } \value{ diff --git a/man/tidy.btergm.Rd b/man/tidy.btergm.Rd index e17691a22..d3e82c91b 100644 --- a/man/tidy.btergm.Rd +++ b/man/tidy.btergm.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ tidy(btfit) tidy(btfit, exponentiate = TRUE, conf.level = 0.99) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[btergm:btergm]{btergm::btergm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[btergm:btergm]{btergm::btergm()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.cch.Rd b/man/tidy.cch.Rd index 2b7cdaf45..750f51ea7 100644 --- a/man/tidy.cch.Rd +++ b/man/tidy.cch.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -60,7 +60,7 @@ ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:cch]{survival::cch()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:cch]{survival::cch()}} Other cch tidiers: \code{\link{glance.cch}()}, diff --git a/man/tidy.cld.Rd b/man/tidy.cld.Rd index 522327817..d8e0b115f 100644 --- a/man/tidy.cld.Rd +++ b/man/tidy.cld.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: diff --git a/man/tidy.clm.Rd b/man/tidy.clm.Rd index 64a7ef68a..8bc03affa 100644 --- a/man/tidy.clm.Rd +++ b/man/tidy.clm.Rd @@ -39,7 +39,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -79,7 +79,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} +\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.clmm.Rd b/man/tidy.clmm.Rd index c14935f0f..fc4f143b9 100644 --- a/man/tidy.clmm.Rd +++ b/man/tidy.clmm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} +\link[=reexports]{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.coeftest.Rd b/man/tidy.coeftest.Rd index 1c019383b..8930c2a0d 100644 --- a/man/tidy.coeftest.Rd +++ b/man/tidy.coeftest.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ lmtest::coeftest(fm) tidy(coeftest(fm)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[lmtest:coeftest]{lmtest::coeftest()}} +\code{\link[=reexports]{tidy()}}, \code{\link[lmtest:coeftest]{lmtest::coeftest()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.confint.glht.Rd b/man/tidy.confint.glht.Rd index cb4b8b2d4..804ececc9 100644 --- a/man/tidy.confint.glht.Rd +++ b/man/tidy.confint.glht.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.confusionMatrix.Rd b/man/tidy.confusionMatrix.Rd index 62e2e4f5c..c00eb9298 100644 --- a/man/tidy.confusionMatrix.Rd +++ b/man/tidy.confusionMatrix.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ tidy(six_class_cm) tidy(six_class_cm, by_class = FALSE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[caret:confusionMatrix]{caret::confusionMatrix()}} +\code{\link[=reexports]{tidy()}}, \code{\link[caret:confusionMatrix]{caret::confusionMatrix()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.coxph.Rd b/man/tidy.coxph.Rd index 67cd44932..4bcea4cb3 100644 --- a/man/tidy.coxph.Rd +++ b/man/tidy.coxph.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -83,7 +83,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{augment.coxph}()}, diff --git a/man/tidy.cv.glmnet.Rd b/man/tidy.cv.glmnet.Rd index 4530ceca5..f0be87ab5 100644 --- a/man/tidy.cv.glmnet.Rd +++ b/man/tidy.cv.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -81,7 +81,7 @@ ggplot(tidied, aes(lambda, estimate, group = term)) + geom_vline(xintercept = glance_cv$lambda.1se, lty = 2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} +\code{\link[=reexports]{tidy()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index 657cf8793..89d4d7dc5 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:density]{stats::density()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:density]{stats::density()}} Other stats tidiers: \code{\link{tidy.dist}()}, diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index 2b21bbf3c..ed85e295c 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -45,7 +45,7 @@ tidy(iris_dist, upper = TRUE) tidy(iris_dist, diagonal = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} Other stats tidiers: \code{\link{tidy.density}()}, diff --git a/man/tidy.drc.Rd b/man/tidy.drc.Rd index 0780e2eed..ba9141665 100644 --- a/man/tidy.drc.Rd +++ b/man/tidy.drc.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{augment.drc}()}, diff --git a/man/tidy.emmGrid.Rd b/man/tidy.emmGrid.Rd index cad8ca626..d1e5151f2 100644 --- a/man/tidy.emmGrid.Rd +++ b/man/tidy.emmGrid.Rd @@ -80,7 +80,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.epi.2by2.Rd b/man/tidy.epi.2by2.Rd index 1b51d057e..21c961f1e 100644 --- a/man/tidy.epi.2by2.Rd +++ b/man/tidy.epi.2by2.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -48,7 +48,7 @@ fit <- epi.2by2( tidy(fit, parameters = "moa") } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} +\code{\link[=reexports]{tidy()}}, \code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} } \concept{epiR tidiers} \value{ diff --git a/man/tidy.ergm.Rd b/man/tidy.ergm.Rd index f3afbd651..269fb5936 100644 --- a/man/tidy.ergm.Rd +++ b/man/tidy.ergm.Rd @@ -76,7 +76,7 @@ Models for Networks. \emph{Journal of Statistical Software}, 24(3). \url{http://www.jstatsoft.org/v24/i03/}. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:control.ergm]{ergm::control.ergm()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:control.ergm]{ergm::control.ergm()}}, \code{\link[ergm:summary.formula]{ergm::summary()}} Other ergm tidiers: diff --git a/man/tidy.factanal.Rd b/man/tidy.factanal.Rd index da0a31fa2..ae43a9002 100644 --- a/man/tidy.factanal.Rd +++ b/man/tidy.factanal.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ augment(fit1, data = m2) augment(fit2, data = m2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{augment.factanal}()}, diff --git a/man/tidy.felm.Rd b/man/tidy.felm.Rd index eb206a274..0458af5c9 100644 --- a/man/tidy.felm.Rd +++ b/man/tidy.felm.Rd @@ -30,7 +30,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -75,7 +75,7 @@ augment(result_felm) glance(result_felm) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[lfe:felm]{lfe::felm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[lfe:felm]{lfe::felm()}} Other felm tidiers: \code{\link{augment.felm}()} diff --git a/man/tidy.fitdistr.Rd b/man/tidy.fitdistr.Rd index 8f7c4a7a2..20650d51d 100644 --- a/man/tidy.fitdistr.Rd +++ b/man/tidy.fitdistr.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -40,7 +40,7 @@ tidy(fit) glance(fit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} +\code{\link[=reexports]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} Other fitdistr tidiers: \code{\link{glance.fitdistr}()} diff --git a/man/tidy.fixest.Rd b/man/tidy.fixest.Rd index 7f84b9a69..9f3b30529 100644 --- a/man/tidy.fixest.Rd +++ b/man/tidy.fixest.Rd @@ -72,7 +72,7 @@ augment(gravity_pois, trade) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::fenegbin()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::fenegbin()}}, \code{\link[fixest:feNmlm]{fixest::feNmlm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}}, \code{\link[fixest:feglm]{fixest::fepois()}} Other fixest tidiers: diff --git a/man/tidy.ftable.Rd b/man/tidy.ftable.Rd index 05d724164..465deef36 100644 --- a/man/tidy.ftable.Rd +++ b/man/tidy.ftable.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ specify which components to return. This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} Other stats tidiers: \code{\link{tidy.density}()}, diff --git a/man/tidy.gamlss.Rd b/man/tidy.gamlss.Rd index d3a574e66..ef5ab1e5f 100644 --- a/man/tidy.gamlss.Rd +++ b/man/tidy.gamlss.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.garch.Rd b/man/tidy.garch.Rd index f72361dcb..4e0907fd3 100644 --- a/man/tidy.garch.Rd +++ b/man/tidy.garch.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ tidy(dax.garch) glance(dax.garch) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[tseries:garch]{tseries::garch()}} +\code{\link[=reexports]{tidy()}}, \code{\link[tseries:garch]{tseries::garch()}} Other garch tidiers: \code{\link{glance.garch}()} diff --git a/man/tidy.geeglm.Rd b/man/tidy.geeglm.Rd index 10452a68b..1e96459ef 100644 --- a/man/tidy.geeglm.Rd +++ b/man/tidy.geeglm.Rd @@ -29,7 +29,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ tidy(geefit) tidy(geefit, conf.int = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.glht.Rd b/man/tidy.glht.Rd index 0552fa899..237558e76 100644 --- a/man/tidy.glht.Rd +++ b/man/tidy.glht.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.glm.Rd b/man/tidy.glm.Rd index c35c4ea6e..097831b84 100644 --- a/man/tidy.glm.Rd +++ b/man/tidy.glm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.glmRob.Rd b/man/tidy.glmRob.Rd index 504496571..532517307 100644 --- a/man/tidy.glmRob.Rd +++ b/man/tidy.glmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.glmnet.Rd b/man/tidy.glmnet.Rd index 03ea8040a..22b780ef3 100644 --- a/man/tidy.glmnet.Rd +++ b/man/tidy.glmnet.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ fit2 <- glmnet(x, g2, family = "binomial") tidy(fit2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} +\code{\link[=reexports]{tidy()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/tidy.gmm.Rd b/man/tidy.gmm.Rd index d6a56b0bb..9f56f521f 100644 --- a/man/tidy.gmm.Rd +++ b/man/tidy.gmm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -106,7 +106,7 @@ td2 \%>\% geom_vline(xintercept = 0, color = "red", lty = 2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[gmm:gmm]{gmm::gmm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[gmm:gmm]{gmm::gmm()}} Other gmm tidiers: \code{\link{glance.gmm}()} diff --git a/man/tidy.htest.Rd b/man/tidy.htest.Rd index 023a166f3..a388923e4 100644 --- a/man/tidy.htest.Rd +++ b/man/tidy.htest.Rd @@ -20,13 +20,13 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \description{ -For models that have only a single component, the \code{\link[=tidy]{tidy()}} and -\code{\link[=glance]{glance()}} methods are identical. Please see the documentation for both +For models that have only a single component, the \code{\link[=reexports]{tidy()}} and +\code{\link[=reexports]{glance()}} methods are identical. Please see the documentation for both of those methods. } \examples{ @@ -49,7 +49,7 @@ tidy(chit) augment(chit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:cor.test]{stats::cor.test()}}, \code{\link[stats:t.test]{stats::t.test()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[stats:cor.test]{stats::cor.test()}}, \code{\link[stats:t.test]{stats::t.test()}}, \code{\link[stats:wilcox.test]{stats::wilcox.test()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} Other htest tidiers: diff --git a/man/tidy.ivreg.Rd b/man/tidy.ivreg.Rd index 1285fae96..a6eb9857c 100644 --- a/man/tidy.ivreg.Rd +++ b/man/tidy.ivreg.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=reexports]{tidy()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{augment.ivreg}()}, diff --git a/man/tidy.kappa.Rd b/man/tidy.kappa.Rd index 2e674f7b4..5d774354c 100644 --- a/man/tidy.kappa.Rd +++ b/man/tidy.kappa.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ ggplot(tidy(ck), aes(estimate, type)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[psych:kappa]{psych::cohen.kappa()}} +\code{\link[=reexports]{tidy()}}, \code{\link[psych:kappa]{psych::cohen.kappa()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.kde.Rd b/man/tidy.kde.Rd index c0dd2cf76..1114e34fa 100644 --- a/man/tidy.kde.Rd +++ b/man/tidy.kde.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ td3 <- tidy(k3) td3 } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[ks:kde]{ks::kde()}} +\code{\link[=reexports]{tidy()}}, \code{\link[ks:kde]{ks::kde()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.kmeans.Rd b/man/tidy.kmeans.Rd index 8abee67f0..fbf490cf1 100644 --- a/man/tidy.kmeans.Rd +++ b/man/tidy.kmeans.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ glance(fit) augment(fit, x) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{augment.kmeans}()}, diff --git a/man/tidy.lavaan.Rd b/man/tidy.lavaan.Rd index 3ff5a55c4..20019fdb8 100644 --- a/man/tidy.lavaan.Rd +++ b/man/tidy.lavaan.Rd @@ -66,7 +66,7 @@ tidy(cfa.fit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, \code{\link[lavaan:parameterEstimates]{lavaan::parameterEstimates()}} Other lavaan tidiers: diff --git a/man/tidy.lm.Rd b/man/tidy.lm.Rd index 0365b4b81..d1573754f 100644 --- a/man/tidy.lm.Rd +++ b/man/tidy.lm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -92,7 +92,7 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:summary.lm]{stats::summary.lm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:summary.lm]{stats::summary.lm()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/tidy.lm.beta.Rd b/man/tidy.lm.beta.Rd index 60d41ae06..1cf14be97 100644 --- a/man/tidy.lm.beta.Rd +++ b/man/tidy.lm.beta.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.lmRob.Rd b/man/tidy.lmRob.Rd index 1a0252be0..b79f3272f 100644 --- a/man/tidy.lmRob.Rd +++ b/man/tidy.lmRob.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.lmodel2.Rd b/man/tidy.lmodel2.Rd index d19760f97..01f58e878 100644 --- a/man/tidy.lmodel2.Rd +++ b/man/tidy.lmodel2.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(tidy(Ex2.res), aes(estimate, term, color = method)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} +\code{\link[=reexports]{tidy()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} Other lmodel2 tidiers: \code{\link{glance.lmodel2}()} diff --git a/man/tidy.lsmobj.Rd b/man/tidy.lsmobj.Rd index f6c45c250..535f82921 100644 --- a/man/tidy.lsmobj.Rd +++ b/man/tidy.lsmobj.Rd @@ -81,7 +81,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.manova.Rd b/man/tidy.manova.Rd index 9a7ef57b4..efd0b9a05 100644 --- a/man/tidy.manova.Rd +++ b/man/tidy.manova.Rd @@ -43,7 +43,7 @@ m <- manova(cbind(yield, foo) ~ block + N * P * K, npk2) tidy(m) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:summary.manova]{stats::summary.manova()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:summary.manova]{stats::summary.manova()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.map.Rd b/man/tidy.map.Rd index 665582a03..465f939be 100644 --- a/man/tidy.map.Rd +++ b/man/tidy.map.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -46,7 +46,7 @@ qplot(long, lat, ) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[maps:map]{maps::map()}} +\code{\link[=reexports]{tidy()}}, \code{\link[maps:map]{maps::map()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.mediate.Rd b/man/tidy.mediate.Rd index 2fc49f15c..2a4426176 100644 --- a/man/tidy.mediate.Rd +++ b/man/tidy.mediate.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(mod, conf.int = TRUE) tidy(mod, conf.int = TRUE, conf.level = .99) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[mediation:mediate]{mediation::mediate()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mediation:mediate]{mediation::mediate()}} } \concept{mediate tidiers} \value{ diff --git a/man/tidy.mfx.Rd b/man/tidy.mfx.Rd index f2115a67d..92b34378e 100644 --- a/man/tidy.mfx.Rd +++ b/man/tidy.mfx.Rd @@ -35,7 +35,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -88,7 +88,7 @@ glance(mod_probmfx) } } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} Other mfx tidiers: \code{\link{augment.betamfx}()}, diff --git a/man/tidy.mjoint.Rd b/man/tidy.mjoint.Rd index ae4ff1005..09d666b7f 100644 --- a/man/tidy.mjoint.Rd +++ b/man/tidy.mjoint.Rd @@ -40,7 +40,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -98,7 +98,7 @@ glance(fit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}}, \code{\link[joineRML:bootSE]{joineRML::bootSE()}} +\code{\link[=reexports]{tidy()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}}, \code{\link[joineRML:bootSE]{joineRML::bootSE()}} Other mjoint tidiers: \code{\link{glance.mjoint}()} diff --git a/man/tidy.mle2.Rd b/man/tidy.mle2.Rd index 6cd821af9..9c4afacfd 100644 --- a/man/tidy.mle2.Rd +++ b/man/tidy.mle2.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ fit <- mle2(y ~ dpois(lambda = ymean), tidy(fit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[bbmle:mle2]{bbmle::mle2()}}, \code{\link[=tidy_optim]{tidy_optim()}} +\code{\link[=reexports]{tidy()}}, \code{\link[bbmle:mle2]{bbmle::mle2()}}, \code{\link[=tidy_optim]{tidy_optim()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.mlm.Rd b/man/tidy.mlm.Rd index fdaa08f44..4298935eb 100644 --- a/man/tidy.mlm.Rd +++ b/man/tidy.mlm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ mod <- lm(cbind(mpg, disp) ~ wt, mtcars) tidy(mod, conf.int = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}} +\code{\link[=reexports]{tidy()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/tidy.muhaz.Rd b/man/tidy.muhaz.Rd index 9146d8338..353e9633c 100644 --- a/man/tidy.muhaz.Rd +++ b/man/tidy.muhaz.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -38,7 +38,7 @@ tidy(x) glance(x) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} +\code{\link[=reexports]{tidy()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} Other muhaz tidiers: \code{\link{glance.muhaz}()} diff --git a/man/tidy.multinom.Rd b/man/tidy.multinom.Rd index 6bc68d203..e000af9b5 100644 --- a/man/tidy.multinom.Rd +++ b/man/tidy.multinom.Rd @@ -29,7 +29,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(fit.gear) glance(fit.gear) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[nnet:multinom]{nnet::multinom()}} +\code{\link[=reexports]{tidy()}}, \code{\link[nnet:multinom]{nnet::multinom()}} Other multinom tidiers: \code{\link{glance.multinom}()} diff --git a/man/tidy.nlrq.Rd b/man/tidy.nlrq.Rd index f1a3f597f..68c40539a 100644 --- a/man/tidy.nlrq.Rd +++ b/man/tidy.nlrq.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -36,7 +36,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.nls.Rd b/man/tidy.nls.Rd index 188841edd..0a01d9864 100644 --- a/man/tidy.nls.Rd +++ b/man/tidy.nls.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:summary.nls]{stats::summary.nls()}} +\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:summary.nls]{stats::summary.nls()}} Other nls tidiers: \code{\link{augment.nls}()}, diff --git a/man/tidy.orcutt.Rd b/man/tidy.orcutt.Rd index 4545b07e3..9cf261248 100644 --- a/man/tidy.orcutt.Rd +++ b/man/tidy.orcutt.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.pairwise.htest.Rd b/man/tidy.pairwise.htest.Rd index 829a4eaa6..62e5f2aa5 100644 --- a/man/tidy.pairwise.htest.Rd +++ b/man/tidy.pairwise.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(pairwise.wilcox.test(Petal.Length, Species)) } \seealso{ \code{\link[stats:pairwise.t.test]{stats::pairwise.t.test()}}, \code{\link[stats:pairwise.wilcox.test]{stats::pairwise.wilcox.test()}}, -\code{\link[=tidy]{tidy()}} +\code{\link[=reexports]{tidy()}} Other htest tidiers: \code{\link{augment.htest}()}, diff --git a/man/tidy.pam.Rd b/man/tidy.pam.Rd index e9a760ba4..fe0a2ce1a 100644 --- a/man/tidy.pam.Rd +++ b/man/tidy.pam.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ augment(p, x) \%>\% geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=reexports]{tidy()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{augment.pam}()}, diff --git a/man/tidy.plm.Rd b/man/tidy.plm.Rd index 96403adb0..a7378531e 100644 --- a/man/tidy.plm.Rd +++ b/man/tidy.plm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[plm:plm]{plm::plm()}}, \code{\link[=tidy.lm]{tidy.lm()}} +\code{\link[=reexports]{tidy()}}, \code{\link[plm:plm]{plm::plm()}}, \code{\link[=tidy.lm]{tidy.lm()}} Other plm tidiers: \code{\link{augment.plm}()}, diff --git a/man/tidy.poLCA.Rd b/man/tidy.poLCA.Rd index c0179c5cd..c1ec349f3 100644 --- a/man/tidy.poLCA.Rd +++ b/man/tidy.poLCA.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=reexports]{tidy()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{augment.poLCA}()}, diff --git a/man/tidy.polr.Rd b/man/tidy.polr.Rd index 3bb6d7389..6f0e18b22 100644 --- a/man/tidy.polr.Rd +++ b/man/tidy.polr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -80,7 +80,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\link{tidy}, \code{\link[MASS:polr]{MASS::polr()}} +\link[=reexports]{tidy}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.power.htest.Rd b/man/tidy.power.htest.Rd index b03e73041..ee4451f23 100644 --- a/man/tidy.power.htest.Rd +++ b/man/tidy.power.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.prcomp.Rd b/man/tidy.prcomp.Rd index 08953cd1b..0aee38f44 100644 --- a/man/tidy.prcomp.Rd +++ b/man/tidy.prcomp.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -112,7 +112,7 @@ ggplot(au, aes(.fittedPC1, .fittedPC2)) + geom_text(aes(label = .rownames), vjust = 1, hjust = 1) } \seealso{ -\code{\link[stats:prcomp]{stats::prcomp()}}, \link{svd_tidiers} +\code{\link[stats:prcomp]{stats::prcomp()}}, \link[=tidy_svd]{svd_tidiers} Other svd tidiers: \code{\link{augment.prcomp}()}, diff --git a/man/tidy.pyears.Rd b/man/tidy.pyears.Rd index c826583e8..3c0443e3b 100644 --- a/man/tidy.pyears.Rd +++ b/man/tidy.pyears.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(pfit2) glance(pfit2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:pyears]{survival::pyears()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:pyears]{survival::pyears()}} Other pyears tidiers: \code{\link{glance.pyears}()} diff --git a/man/tidy.rcorr.Rd b/man/tidy.rcorr.Rd index cea186db6..2a979e9b1 100644 --- a/man/tidy.rcorr.Rd +++ b/man/tidy.rcorr.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -64,7 +64,7 @@ ggplot(td, aes(estimate, p.value)) + scale_y_log10() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[Hmisc:rcorr]{Hmisc::rcorr()}} +\code{\link[=reexports]{tidy()}}, \code{\link[Hmisc:rcorr]{Hmisc::rcorr()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.ref.grid.Rd b/man/tidy.ref.grid.Rd index 906317f09..a3bb4e701 100644 --- a/man/tidy.ref.grid.Rd +++ b/man/tidy.ref.grid.Rd @@ -80,7 +80,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.regsubsets.Rd b/man/tidy.regsubsets.Rd index 38e33d435..5d0758af2 100644 --- a/man/tidy.regsubsets.Rd +++ b/man/tidy.regsubsets.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -34,7 +34,7 @@ all_fits <- leaps::regsubsets(hp ~ ., mtcars) tidy(all_fits) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[leaps:regsubsets]{leaps::regsubsets()}} +\code{\link[=reexports]{tidy()}}, \code{\link[leaps:regsubsets]{leaps::regsubsets()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.ridgelm.Rd b/man/tidy.ridgelm.Rd index e618de943..29b4e70ff 100644 --- a/man/tidy.ridgelm.Rd +++ b/man/tidy.ridgelm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ ggplot(td2, aes(lambda, GCV)) + geom_vline(xintercept = g2$lambdaGCV, col = "red", lty = 2) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} +\code{\link[=reexports]{tidy()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} Other ridgelm tidiers: \code{\link{glance.ridgelm}()} diff --git a/man/tidy.rlm.Rd b/man/tidy.rlm.Rd index 559a25ee4..29ba5b016 100644 --- a/man/tidy.rlm.Rd +++ b/man/tidy.rlm.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.robustbase.glmrob.Rd b/man/tidy.robustbase.glmrob.Rd index d4930e424..bfe3a8105 100644 --- a/man/tidy.robustbase.glmrob.Rd +++ b/man/tidy.robustbase.glmrob.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.robustbase.lmrob.Rd b/man/tidy.robustbase.lmrob.Rd index fb8dab65e..1cb63ba57 100644 --- a/man/tidy.robustbase.lmrob.Rd +++ b/man/tidy.robustbase.lmrob.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.roc.Rd b/man/tidy.roc.Rd index 60816a177..06658e636 100644 --- a/man/tidy.roc.Rd +++ b/man/tidy.roc.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -61,7 +61,7 @@ ggplot(rocs, aes(fpr, tpr, color = algorithm)) + geom_line() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[AUC:roc]{AUC::roc()}} +\code{\link[=reexports]{tidy()}}, \code{\link[AUC:roc]{AUC::roc()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.rq.Rd b/man/tidy.rq.Rd index 14bd0af25..d6fe008c0 100644 --- a/man/tidy.rq.Rd +++ b/man/tidy.rq.Rd @@ -41,7 +41,7 @@ no confidence intervals are calculated and the confidence limits are set to NA. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.rqs.Rd b/man/tidy.rqs.Rd index 395017d3e..614633b1b 100644 --- a/man/tidy.rqs.Rd +++ b/man/tidy.rqs.Rd @@ -38,7 +38,7 @@ no confidence intervals are calculated and the confidence limits are set to NA. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.sarlm.Rd b/man/tidy.sarlm.Rd index ed5ed58eb..6bdcf04bf 100644 --- a/man/tidy.sarlm.Rd +++ b/man/tidy.sarlm.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: diff --git a/man/tidy.spec.Rd b/man/tidy.spec.Rd index e1f2c0c58..e372f62c7 100644 --- a/man/tidy.spec.Rd +++ b/man/tidy.spec.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ ggplot(tidy(spc), aes(freq, spec)) + geom_line() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:spectrum]{stats::spectrum()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:spectrum]{stats::spectrum()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy.speedglm.Rd b/man/tidy.speedglm.Rd index 11ed7f04d..3b27bb0e3 100644 --- a/man/tidy.speedglm.Rd +++ b/man/tidy.speedglm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.speedlm.Rd b/man/tidy.speedlm.Rd index 6d5014d62..3dff4534c 100644 --- a/man/tidy.speedlm.Rd +++ b/man/tidy.speedlm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.summary.glht.Rd b/man/tidy.summary.glht.Rd index 9f750b1f2..1e31f46a2 100644 --- a/man/tidy.summary.glht.Rd +++ b/man/tidy.summary.glht.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.summary_emm.Rd b/man/tidy.summary_emm.Rd index 4eaa14606..d46b80b60 100644 --- a/man/tidy.summary_emm.Rd +++ b/man/tidy.summary_emm.Rd @@ -75,7 +75,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.survdiff.Rd b/man/tidy.survdiff.Rd index c8fc264d1..06b5b1570 100644 --- a/man/tidy.survdiff.Rd +++ b/man/tidy.survdiff.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ tidy(s) glance(s) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:survdiff]{survival::survdiff()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:survdiff]{survival::survdiff()}} Other survdiff tidiers: \code{\link{glance.survdiff}()} diff --git a/man/tidy.survexp.Rd b/man/tidy.survexp.Rd index 9cc4a7c49..484d1cac3 100644 --- a/man/tidy.survexp.Rd +++ b/man/tidy.survexp.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ tidy(sexpfit) glance(sexpfit) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:survexp]{survival::survexp()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:survexp]{survival::survexp()}} Other survexp tidiers: \code{\link{glance.survexp}()} diff --git a/man/tidy.survfit.Rd b/man/tidy.survfit.Rd index d95a4688b..35f781486 100644 --- a/man/tidy.survfit.Rd +++ b/man/tidy.survfit.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ ggplot(td_multi, aes(time, estimate, group = state)) + geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:survfit]{survival::survfit()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:survfit]{survival::survfit()}} Other survival tidiers: \code{\link{augment.coxph}()}, diff --git a/man/tidy.survreg.Rd b/man/tidy.survreg.Rd index caebef934..3c97b9c40 100644 --- a/man/tidy.survreg.Rd +++ b/man/tidy.survreg.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=reexports]{tidy()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{augment.survreg}()}, diff --git a/man/tidy.svyglm.Rd b/man/tidy.svyglm.Rd index bf4318561..0ee8f0932 100644 --- a/man/tidy.svyglm.Rd +++ b/man/tidy.svyglm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.svyolr.Rd b/man/tidy.svyolr.Rd index 480cea543..035b103c2 100644 --- a/man/tidy.svyolr.Rd +++ b/man/tidy.svyolr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ tidy(fit, exponentiate = TRUE, conf.int = TRUE) glance(fit) } \seealso{ -\link{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} +\link[=reexports]{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.systemfit.Rd b/man/tidy.systemfit.Rd index a66197b34..5255263cd 100644 --- a/man/tidy.systemfit.Rd +++ b/man/tidy.systemfit.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit) tidy(fit, conf.int = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[systemfit:systemfit]{systemfit::systemfit()}} +\code{\link[=reexports]{tidy()}}, \code{\link[systemfit:systemfit]{systemfit::systemfit()}} } \concept{systemfit tidiers} \value{ diff --git a/man/tidy.table.Rd b/man/tidy.table.Rd index 8fbc6901b..e96b29411 100644 --- a/man/tidy.table.Rd +++ b/man/tidy.table.Rd @@ -7,7 +7,7 @@ \method{tidy}{table}(x, ...) } \arguments{ -\item{x}{A \link{table} object.} +\item{x}{A \link[=table]{table} object.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ specify which components to return. Deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. } \details{ -Directly calls \code{\link[tibble:as_tibble]{tibble::as_tibble()}} on a \link{table} object, which +Directly calls \code{\link[tibble:as_tibble]{tibble::as_tibble()}} on a \link[=table]{table} object, which does the same things as \code{\link[=as.data.frame.table]{as.data.frame.table()}} but also gives the returned object \link[tibble:tibble]{tibble::tibble} class. } diff --git a/man/tidy.ts.Rd b/man/tidy.ts.Rd index 9f7fbe529..ef2981743 100644 --- a/man/tidy.ts.Rd +++ b/man/tidy.ts.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ colnames(z) <- c("Aa", "Bb", "Cc") tidy(z) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:ts]{stats::ts()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:ts]{stats::ts()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy.zoo.Rd b/man/tidy.zoo.Rd index 51823c821..703ff082c 100644 --- a/man/tidy.zoo.Rd +++ b/man/tidy.zoo.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ ggplot(tidy(Zrolled), aes(index, value, color = series)) + geom_line() } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[zoo:zoo]{zoo::zoo()}} +\code{\link[=reexports]{tidy()}}, \code{\link[zoo:zoo]{zoo::zoo()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy_irlba.Rd b/man/tidy_irlba.Rd index 0d424bb5c..990c22371 100644 --- a/man/tidy_irlba.Rd +++ b/man/tidy_irlba.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -97,7 +97,7 @@ tidy_u \%>\% facet_wrap(~PC, scale = "free_y") } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[irlba:irlba]{irlba::irlba()}} +\code{\link[=reexports]{tidy()}}, \code{\link[irlba:irlba]{irlba::irlba()}} Other list tidiers: \code{\link{glance_optim}()}, diff --git a/man/tidy_optim.Rd b/man/tidy_optim.Rd index d9d55ca80..7b60eb055 100644 --- a/man/tidy_optim.Rd +++ b/man/tidy_optim.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ o <- optim(c(1, 1, 1), f) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:optim]{stats::optim()}} +\code{\link[=reexports]{tidy()}}, \code{\link[stats:optim]{stats::optim()}} Other list tidiers: \code{\link{glance_optim}()}, diff --git a/man/tidy_svd.Rd b/man/tidy_svd.Rd index dbf9c4b3d..3969ab359 100644 --- a/man/tidy_svd.Rd +++ b/man/tidy_svd.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy_xyz.Rd b/man/tidy_xyz.Rd index b31730834..c8a9f3f6d 100644 --- a/man/tidy_xyz.Rd +++ b/man/tidy_xyz.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -50,7 +50,7 @@ image(A) tidy(A) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[graphics:persp]{graphics::persp()}}, \code{\link[graphics:image]{graphics::image()}}, +\code{\link[=reexports]{tidy()}}, \code{\link[graphics:persp]{graphics::persp()}}, \code{\link[graphics:image]{graphics::image()}}, \code{\link[akima:interp]{akima::interp()}} Other list tidiers: From fd04047fd8a86db321a26f4545002625944613f2 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 09:33:20 -0700 Subject: [PATCH 13/41] specify base and stats namespaces --- R/base-tidiers.R | 8 ++-- R/list-optim-tidiers.R | 2 +- R/list-svd-tidiers.R | 4 +- R/list-tidiers.R | 2 +- R/mgcv-tidiers.R | 2 - R/stats-factanal-tidiers.R | 4 +- R/utilities.R | 2 +- man-roxygen/augment_NAs.R | 2 +- man-roxygen/param_data.R | 2 +- man-roxygen/param_newdata.R | 2 +- man-roxygen/title_desc_augment.R | 2 +- man-roxygen/title_desc_tidy_list.R | 5 +- man/augment.Mclust.Rd | 4 +- man/augment.betamfx.Rd | 6 +-- man/augment.betareg.Rd | 6 +-- man/augment.clm.Rd | 6 +-- man/augment.coxph.Rd | 8 ++-- man/augment.decomposed.ts.Rd | 2 +- man/augment.drc.Rd | 6 +-- man/augment.factanal.Rd | 8 ++-- man/augment.felm.Rd | 4 +- man/augment.fixest.Rd | 6 +-- man/augment.glm.Rd | 6 +-- man/augment.glmRob.Rd | 2 +- man/augment.htest.Rd | 2 +- man/augment.ivreg.Rd | 6 +-- man/augment.kmeans.Rd | 4 +- man/augment.lm.Rd | 8 ++-- man/augment.lmRob.Rd | 6 +-- man/augment.loess.Rd | 6 +-- man/augment.mfx.Rd | 6 +-- man/augment.mjoint.Rd | 4 +- man/augment.nlrq.Rd | 4 +- man/augment.nls.Rd | 6 +-- man/augment.pam.Rd | 4 +- man/augment.plm.Rd | 4 +- man/augment.poLCA.Rd | 4 +- man/augment.polr.Rd | 6 +-- man/augment.prcomp.Rd | 6 +-- man/augment.rlm.Rd | 6 +-- man/augment.rma.Rd | 2 +- man/augment.robustbase.glmrob.Rd | 6 +-- man/augment.robustbase.lmrob.Rd | 6 +-- man/augment.rq.Rd | 6 +-- man/augment.rqs.Rd | 8 ++-- man/augment.sarlm.Rd | 2 +- man/augment.smooth.spline.Rd | 2 +- man/augment.speedlm.Rd | 6 +-- man/augment.stl.Rd | 2 +- man/augment.survreg.Rd | 6 +-- man/glance.Gam.Rd | 32 ++++++++----- man/glance_optim.Rd | 7 +-- man/list_tidiers.Rd | 2 +- man/mgcv_glance_gam.Rd | 71 --------------------------- man/mgcv_tidy_gam.Rd | 77 ------------------------------ man/tidy.Gam.Rd | 54 ++++++++++++++------- man/tidy.table.Rd | 8 ++-- man/tidy_irlba.Rd | 5 +- man/tidy_optim.Rd | 5 +- man/tidy_svd.Rd | 9 ++-- man/tidy_xyz.Rd | 5 +- 61 files changed, 193 insertions(+), 311 deletions(-) delete mode 100644 man/mgcv_glance_gam.Rd delete mode 100644 man/mgcv_tidy_gam.Rd diff --git a/R/base-tidiers.R b/R/base-tidiers.R index 99ae1e333..44b9b01b3 100644 --- a/R/base-tidiers.R +++ b/R/base-tidiers.R @@ -3,18 +3,18 @@ #' #' @description Deprecated. Please use [tibble::as_tibble()] instead. #' -#' @param x A [table] object. +#' @param x A [base::table] object. #' @template param_unused_dots #' #' @return A [tibble::tibble] in long-form containing frequency information #' for the table in a `Freq` column. The result is much like what you get #' from [tidyr::pivot_longer()]. #' -#' @details Directly calls [tibble::as_tibble()] on a [table] object, which -#' does the same things as [as.data.frame.table()] but also gives the +#' @details Directly calls [tibble::as_tibble()] on a [base::table] object, which +#' does the same things as [base::as.data.frame.table()] but also gives the #' returned object [tibble::tibble] class. #' -#' @seealso [as_tibble.table()] +#' @seealso [tibble::as_tibble.table()] #' @export tidy.table <- function(x, ...) { .Deprecated() diff --git a/R/list-optim-tidiers.R b/R/list-optim-tidiers.R index 675db8b1d..c8651affe 100644 --- a/R/list-optim-tidiers.R +++ b/R/list-optim-tidiers.R @@ -51,7 +51,7 @@ tidy_optim <- function(x, ...) { #' #' @aliases glance.optim #' @family list tidiers -#' @seealso [glance()], [optim()] +#' @seealso [glance()], [stats::optim()] glance_optim <- function(x, ...) { as_glance_tibble( value = x$value, diff --git a/R/list-svd-tidiers.R b/R/list-svd-tidiers.R index c5ea129d8..1feada086 100644 --- a/R/list-svd-tidiers.R +++ b/R/list-svd-tidiers.R @@ -2,7 +2,7 @@ #' @template title_desc_tidy_list #' #' @inherit tidy.prcomp return details params -#' @param x A list with components `u`, `d`, `v` returned by [svd()]. +#' @param x A list with components `u`, `d`, `v` returned by [base::svd()]. #' #' @examples #' @@ -30,7 +30,7 @@ #' ggplot(aes(Species, value)) + #' geom_boxplot() + #' facet_wrap(~PC, scale = "free_y") -#' @seealso [svd()] +#' @seealso [base::svd()] #' @aliases svd_tidiers #' @family svd tidiers #' @family list tidiers diff --git a/R/list-tidiers.R b/R/list-tidiers.R index 041ba0f9f..56c7a2615 100644 --- a/R/list-tidiers.R +++ b/R/list-tidiers.R @@ -1,7 +1,7 @@ #' Tidying methods for lists / returned values that are not S3 objects #' #' Broom tidies a number of lists that are effectively S3 objects without -#' a class attribute. For example, [stats::optim()], [svd()] and +#' a class attribute. For example, [stats::optim()], [base::svd()] and #' [akima::interp()] produce consistent output, but because they do not #' have a class attribute, they cannot be handled by S3 dispatch. #' diff --git a/R/mgcv-tidiers.R b/R/mgcv-tidiers.R index 6837fe5be..3e01f2198 100644 --- a/R/mgcv-tidiers.R +++ b/R/mgcv-tidiers.R @@ -33,7 +33,6 @@ #' tidy(g) #' tidy(g, parametric = TRUE) #' glance(g) -#' @rdname mgcv_tidy_gam #' @export #' @aliases mgcv_tidiers gam_tidiers tidy.gam #' @family mgcv tidiers @@ -87,7 +86,6 @@ tidy.gam <- function(x, parametric = FALSE, conf.int = FALSE, #' @details To glance `Gam` objects created by calls to [gam::gam()], see #' [glance.Gam()]. #' -#' @rdname mgcv_glance_gam #' @export #' @family mgcv tidiers #' @seealso [glance()], [mgcv::gam()], [glance.Gam()] diff --git a/R/stats-factanal-tidiers.R b/R/stats-factanal-tidiers.R index 127959bbd..f0b0ff02f 100644 --- a/R/stats-factanal-tidiers.R +++ b/R/stats-factanal-tidiers.R @@ -76,8 +76,8 @@ tidy.factanal <- function(x, ...) { #' #' @return When `data` is not supplied `augment.factanal` returns one #' row for each observation, with a factor score column added for each factor -#' X, (`.fsX`). This is because [factanal()], unlike other -#' stats methods like [lm()], does not retain the original data. +#' X, (`.fsX`). This is because [stats::factanal()], unlike other +#' stats methods like [stats::lm()], does not retain the original data. #' #' When `data` is supplied, `augment.factanal` returns one row for #' each observation, with a factor score column added for each factor X, diff --git a/R/utilities.R b/R/utilities.R index f3133d1f8..7aa23a9d3 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -29,7 +29,7 @@ exponentiate <- function(data) { #' interesting (i.e. more than `1, 2, 3, ...`). This function is #' meant for use inside of `augment.*` methods. #' -#' @param data A [data.frame()] or [tibble::tibble()]. +#' @param data A [base::data.frame()] or [tibble::tibble()]. #' #' @return A `tibble` potentially with a `.rownames` column #' @noRd diff --git a/man-roxygen/augment_NAs.R b/man-roxygen/augment_NAs.R index 45d87dc34..4e7535fba 100644 --- a/man-roxygen/augment_NAs.R +++ b/man-roxygen/augment_NAs.R @@ -7,5 +7,5 @@ #' is not provided to [augment()] and `na.action = "na.exclude"`, a #' warning is raised and the incomplete rows are dropped. #' -#' @seealso [na.action] +#' @seealso [stats::na.action] #' @md diff --git a/man-roxygen/param_data.R b/man-roxygen/param_data.R index 02f16916e..a71da23cb 100644 --- a/man-roxygen/param_data.R +++ b/man-roxygen/param_data.R @@ -1,4 +1,4 @@ -#' @param data A [data.frame()] or [tibble::tibble()] containing the original +#' @param data A [base::data.frame] or [tibble::tibble()] containing the original #' data that was used to produce the object `x`. Defaults to #' `stats::model.frame(x)` so that `augment(my_fit)` returns the augmented #' original data. **Do not** pass new data to the `data` argument. diff --git a/man-roxygen/param_newdata.R b/man-roxygen/param_newdata.R index 867c2493a..f339b03e4 100644 --- a/man-roxygen/param_newdata.R +++ b/man-roxygen/param_newdata.R @@ -1,4 +1,4 @@ -#' @param newdata A [data.frame()] or [tibble::tibble()] containing all +#' @param newdata A [base::data.frame()] or [tibble::tibble()] containing all #' the original predictors used to create `x`. Defaults to `NULL`, indicating #' that nothing has been passed to `newdata`. If `newdata` is specified, #' the `data` argument will be ignored. diff --git a/man-roxygen/title_desc_augment.R b/man-roxygen/title_desc_augment.R index 6ce4d0f36..4e7be08c3 100644 --- a/man-roxygen/title_desc_augment.R +++ b/man-roxygen/title_desc_augment.R @@ -35,7 +35,7 @@ #' model on data in a tibble. #' #' We are in the process of defining behaviors for models fit with various -#' [na.action] arguments, but make no guarantees about behavior when data is +#' `na.action` arguments, but make no guarantees about behavior when data is #' missing at this time. #' #' @md diff --git a/man-roxygen/title_desc_tidy_list.R b/man-roxygen/title_desc_tidy_list.R index 94c4949ee..732719e3a 100644 --- a/man-roxygen/title_desc_tidy_list.R +++ b/man-roxygen/title_desc_tidy_list.R @@ -2,8 +2,9 @@ #' #' @description Broom tidies a number of lists that are effectively S3 #' objects without a class attribute. For example, [stats::optim()], -#' [svd()] and [akima::interp()] produce consistent output, but because -#' they do not have a class attribute, they cannot be handled by S3 dispatch. +#' [svd()][base::svd()] and [akima::interp()] produce consistent output, but +#' because they do not have a class attribute, they cannot be handled by S3 +#' dispatch. #' #' These functions look at the elements of a list and determine if there is #' an appropriate tidying method to apply to the list. Those tidiers are diff --git a/man/augment.Mclust.Rd b/man/augment.Mclust.Rd index 2c8585d32..037e36aac 100644 --- a/man/augment.Mclust.Rd +++ b/man/augment.Mclust.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{Mclust} object return from \code{\link[mclust:Mclust]{mclust::Mclust()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.betamfx.Rd b/man/augment.betamfx.Rd index fe54916dc..1865f0e06 100644 --- a/man/augment.betamfx.Rd +++ b/man/augment.betamfx.Rd @@ -17,7 +17,7 @@ \arguments{ \item{x}{A \code{betamfx} object.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -25,7 +25,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -84,7 +84,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.betareg.Rd b/man/augment.betareg.Rd index 1c26e8264..0b9093c5d 100644 --- a/man/augment.betareg.Rd +++ b/man/augment.betareg.Rd @@ -16,7 +16,7 @@ \arguments{ \item{x}{A \code{betareg} object produced by a call to \code{\link[betareg:betareg]{betareg::betareg()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -24,7 +24,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.clm.Rd b/man/augment.clm.Rd index 0f0b73a73..20f50af78 100644 --- a/man/augment.clm.Rd +++ b/man/augment.clm.Rd @@ -15,7 +15,7 @@ \arguments{ \item{x}{A \code{clm} object returned from \code{\link[ordinal:clm]{ordinal::clm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -23,7 +23,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -77,7 +77,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.coxph.Rd b/man/augment.coxph.Rd index c640340eb..4ab67cf9c 100644 --- a/man/augment.coxph.Rd +++ b/man/augment.coxph.Rd @@ -16,7 +16,7 @@ \arguments{ \item{x}{A \code{coxph} object returned from \code{\link[survival:coxph]{survival::coxph()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -24,7 +24,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -141,7 +141,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\link[=na.action]{na.action} +\link[stats:na.action]{stats::na.action} \code{\link[=reexports]{augment()}}, \code{\link[survival:coxph]{survival::coxph()}} diff --git a/man/augment.decomposed.ts.Rd b/man/augment.decomposed.ts.Rd index faa361611..2694ccce2 100644 --- a/man/augment.decomposed.ts.Rd +++ b/man/augment.decomposed.ts.Rd @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.drc.Rd b/man/augment.drc.Rd index 5ff975bb8..a35c87696 100644 --- a/man/augment.drc.Rd +++ b/man/augment.drc.Rd @@ -17,7 +17,7 @@ \arguments{ \item{x}{A \code{drc} object produced by a call to \code{\link[drc:drm]{drc::drm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -25,7 +25,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -87,7 +87,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.factanal.Rd b/man/augment.factanal.Rd index 766aec2c5..f6e1b853d 100644 --- a/man/augment.factanal.Rd +++ b/man/augment.factanal.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{factanal} object created by \code{\link[stats:factanal]{stats::factanal()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -30,8 +30,8 @@ the \code{data} argument.} \value{ When \code{data} is not supplied \code{augment.factanal} returns one row for each observation, with a factor score column added for each factor -X, (\code{.fsX}). This is because \code{\link[=factanal]{factanal()}}, unlike other -stats methods like \code{\link[=lm]{lm()}}, does not retain the original data. +X, (\code{.fsX}). This is because \code{\link[stats:factanal]{stats::factanal()}}, unlike other +stats methods like \code{\link[stats:lm]{stats::lm()}}, does not retain the original data. When \code{data} is supplied, \code{augment.factanal} returns one row for each observation, with a factor score column added for each factor X, @@ -73,7 +73,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ diff --git a/man/augment.felm.Rd b/man/augment.felm.Rd index 58ddf782a..1736c51ce 100644 --- a/man/augment.felm.Rd +++ b/man/augment.felm.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{felm} object returned from \code{\link[lfe:felm]{lfe::felm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.fixest.Rd b/man/augment.fixest.Rd index da76c1fbd..f7b8875fc 100644 --- a/man/augment.fixest.Rd +++ b/man/augment.fixest.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{fixest} object returned from any of the \code{fixest} estimators} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -66,7 +66,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \note{ diff --git a/man/augment.glm.Rd b/man/augment.glm.Rd index 84b1fd06a..3044b9a44 100644 --- a/man/augment.glm.Rd +++ b/man/augment.glm.Rd @@ -17,7 +17,7 @@ \arguments{ \item{x}{A \code{glm} object returned from \code{\link[stats:glm]{stats::glm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -25,7 +25,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -86,7 +86,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.glmRob.Rd b/man/augment.glmRob.Rd index 0a8dd4472..7e7410408 100644 --- a/man/augment.glmRob.Rd +++ b/man/augment.glmRob.Rd @@ -47,7 +47,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. \code{augment.glmRob()} has been removed from broom. We regret diff --git a/man/augment.htest.Rd b/man/augment.htest.Rd index cd8fd5e9a..dd7ac3ef0 100644 --- a/man/augment.htest.Rd +++ b/man/augment.htest.Rd @@ -56,7 +56,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.ivreg.Rd b/man/augment.ivreg.Rd index 1245db648..16e4a326b 100644 --- a/man/augment.ivreg.Rd +++ b/man/augment.ivreg.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{ivreg} object created by a call to \code{\link[AER:ivreg]{AER::ivreg()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.kmeans.Rd b/man/augment.kmeans.Rd index ed511d406..7143c6b41 100644 --- a/man/augment.kmeans.Rd +++ b/man/augment.kmeans.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{kmeans} object created by \code{\link[stats:kmeans]{stats::kmeans()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.lm.Rd b/man/augment.lm.Rd index 54459802d..05bd804bb 100644 --- a/man/augment.lm.Rd +++ b/man/augment.lm.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{lm} object created by \code{\link[stats:lm]{stats::lm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ @@ -144,7 +144,7 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\link[=na.action]{na.action} +\link[stats:na.action]{stats::na.action} \code{\link[=reexports]{augment()}}, \code{\link[stats:predict.lm]{stats::predict.lm()}} diff --git a/man/augment.lmRob.Rd b/man/augment.lmRob.Rd index 1e53fd758..d55af84c4 100644 --- a/man/augment.lmRob.Rd +++ b/man/augment.lmRob.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{lmRob} object returned from \code{\link[robust:lmRob]{robust::lmRob()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.loess.Rd b/man/augment.loess.Rd index c183e4821..a2dbe72a9 100644 --- a/man/augment.loess.Rd +++ b/man/augment.loess.Rd @@ -10,7 +10,7 @@ \arguments{ \item{x}{A \code{loess} objects returned by \code{\link[stats:loess]{stats::loess()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -18,7 +18,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -78,7 +78,7 @@ augment(lo, mtcars) augment(lo, newdata = head(mtcars)) } \seealso{ -\link[=na.action]{na.action} +\link[stats:na.action]{stats::na.action} \code{\link[=reexports]{augment()}}, \code{\link[stats:loess]{stats::loess()}}, \code{\link[stats:predict.loess]{stats::predict.loess()}} } diff --git a/man/augment.mfx.Rd b/man/augment.mfx.Rd index ee2c20b4f..d83fcecc8 100644 --- a/man/augment.mfx.Rd +++ b/man/augment.mfx.Rd @@ -62,7 +62,7 @@ \item{x}{A \code{logitmfx}, \code{negbinmfx}, \code{poissonmfx}, or \code{probitmfx} object. (Note that \code{betamfx} objects receive their own set of tidiers.)} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -70,7 +70,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -131,7 +131,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.mjoint.Rd b/man/augment.mjoint.Rd index 9ae813be4..a85460e69 100644 --- a/man/augment.mjoint.Rd +++ b/man/augment.mjoint.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{mjoint} object returned from \code{\link[joineRML:mjoint]{joineRML::mjoint()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -75,7 +75,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.nlrq.Rd b/man/augment.nlrq.Rd index 036ecf16d..d8638df5f 100644 --- a/man/augment.nlrq.Rd +++ b/man/augment.nlrq.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{nlrq} object returned from \code{\link[quantreg:nlrq]{quantreg::nlrq()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} diff --git a/man/augment.nls.Rd b/man/augment.nls.Rd index 4ad6f6682..9b12439ca 100644 --- a/man/augment.nls.Rd +++ b/man/augment.nls.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{nls} object returned from \code{\link[stats:nls]{stats::nls()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.pam.Rd b/man/augment.pam.Rd index 628a72b27..662c125dc 100644 --- a/man/augment.pam.Rd +++ b/man/augment.pam.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{pam} object returned from \code{\link[cluster:pam]{cluster::pam()}}} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.plm.Rd b/man/augment.plm.Rd index 365a493f8..55e0ea5bf 100644 --- a/man/augment.plm.Rd +++ b/man/augment.plm.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{plm} objected returned by \code{\link[plm:plm]{plm::plm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.poLCA.Rd b/man/augment.poLCA.Rd index 37793f48e..4364eb59d 100644 --- a/man/augment.poLCA.Rd +++ b/man/augment.poLCA.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{poLCA} object returned from \code{\link[poLCA:poLCA]{poLCA::poLCA()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -63,7 +63,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.polr.Rd b/man/augment.polr.Rd index 7cc400cd0..c5e43010b 100644 --- a/man/augment.polr.Rd +++ b/man/augment.polr.Rd @@ -15,7 +15,7 @@ \arguments{ \item{x}{A \code{polr} object returned from \code{\link[MASS:polr]{MASS::polr()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -23,7 +23,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -78,7 +78,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.prcomp.Rd b/man/augment.prcomp.Rd index b2a3f7aef..8cd2f61e8 100644 --- a/man/augment.prcomp.Rd +++ b/man/augment.prcomp.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{prcomp} object returned by \code{\link[stats:prcomp]{stats::prcomp()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -73,7 +73,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ diff --git a/man/augment.rlm.Rd b/man/augment.rlm.Rd index 16c64545c..398cebfa0 100644 --- a/man/augment.rlm.Rd +++ b/man/augment.rlm.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{rlm} object returned by \code{\link[MASS:rlm]{MASS::rlm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.rma.Rd b/man/augment.rma.Rd index 038e139cc..dda656717 100644 --- a/man/augment.rma.Rd +++ b/man/augment.rma.Rd @@ -57,7 +57,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.robustbase.glmrob.Rd b/man/augment.robustbase.glmrob.Rd index d6afdccf4..b5344ffd2 100644 --- a/man/augment.robustbase.glmrob.Rd +++ b/man/augment.robustbase.glmrob.Rd @@ -17,7 +17,7 @@ \arguments{ \item{x}{A \code{glmrob} object returned from \code{\link[robustbase:glmrob]{robustbase::glmrob()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -25,7 +25,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -90,7 +90,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.robustbase.lmrob.Rd b/man/augment.robustbase.lmrob.Rd index 5700ac4e4..be98ab7dc 100644 --- a/man/augment.robustbase.lmrob.Rd +++ b/man/augment.robustbase.lmrob.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{lmrob} object returned from \code{\link[robustbase:lmrob]{robustbase::lmrob()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.rq.Rd b/man/augment.rq.Rd index ca59cddf8..a868086dc 100644 --- a/man/augment.rq.Rd +++ b/man/augment.rq.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{rq} object returned from \code{\link[quantreg:rq]{quantreg::rq()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -83,7 +83,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.rqs.Rd b/man/augment.rqs.Rd index b35af7d99..71d6ce174 100644 --- a/man/augment.rqs.Rd +++ b/man/augment.rqs.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{An \code{rqs} object returned from \code{\link[quantreg:rq]{quantreg::rq()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,13 +17,13 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} \item{...}{ - Arguments passed on to quantreg's predict method + Arguments passed on to \code{\link[quantreg:predict.rqs]{quantreg::predict.rqs}} \describe{ \item{\code{object}}{ object of class rq or rqs or rq.process produced by \code{rq} } \item{\code{type}}{For \code{predict.rq}, the method for 'confidence' intervals, if desired. @@ -84,7 +84,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.sarlm.Rd b/man/augment.sarlm.Rd index 12c547e79..bd43fa3d4 100644 --- a/man/augment.sarlm.Rd +++ b/man/augment.sarlm.Rd @@ -59,7 +59,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \details{ diff --git a/man/augment.smooth.spline.Rd b/man/augment.smooth.spline.Rd index 076f09ed7..77b28a635 100644 --- a/man/augment.smooth.spline.Rd +++ b/man/augment.smooth.spline.Rd @@ -10,7 +10,7 @@ \arguments{ \item{x}{A \code{smooth.spline} object returned from \code{\link[stats:smooth.spline]{stats::smooth.spline()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. diff --git a/man/augment.speedlm.Rd b/man/augment.speedlm.Rd index d74e31e12..1bc56a0d9 100644 --- a/man/augment.speedlm.Rd +++ b/man/augment.speedlm.Rd @@ -9,7 +9,7 @@ \arguments{ \item{x}{A \code{speedlm} object returned from \code{\link[speedglm:speedlm]{speedglm::speedlm()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -17,7 +17,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -68,7 +68,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/augment.stl.Rd b/man/augment.stl.Rd index e4635b0f9..750ec65be 100644 --- a/man/augment.stl.Rd +++ b/man/augment.stl.Rd @@ -72,7 +72,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \seealso{ diff --git a/man/augment.survreg.Rd b/man/augment.survreg.Rd index 71a3b5881..bcdca028a 100644 --- a/man/augment.survreg.Rd +++ b/man/augment.survreg.Rd @@ -16,7 +16,7 @@ \arguments{ \item{x}{An \code{survreg} object returned from \code{\link[survival:survreg]{survival::survreg()}}.} -\item{data}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original +\item{data}{A \link[base:data.frame]{base::data.frame} or \code{\link[tibble:tibble]{tibble::tibble()}} containing the original data that was used to produce the object \code{x}. Defaults to \code{stats::model.frame(x)} so that \code{augment(my_fit)} returns the augmented original data. \strong{Do not} pass new data to the \code{data} argument. @@ -24,7 +24,7 @@ Augment will report information such as influence and cooks distance for data passed to the \code{data} argument. These measures are only defined for the original training data.} -\item{newdata}{A \code{\link[=data.frame]{data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all +\item{newdata}{A \code{\link[base:data.frame]{base::data.frame()}} or \code{\link[tibble:tibble]{tibble::tibble()}} containing all the original predictors used to create \code{x}. Defaults to \code{NULL}, indicating that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} @@ -85,7 +85,7 @@ encounter errors, try explicitly passing a tibble, or fitting the original model on data in a tibble. We are in the process of defining behaviors for models fit with various -\link[=na.action]{na.action} arguments, but make no guarantees about behavior when data is +\code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. } \examples{ diff --git a/man/glance.Gam.Rd b/man/glance.Gam.Rd index ea987f96b..890a06c45 100644 --- a/man/glance.Gam.Rd +++ b/man/glance.Gam.Rd @@ -1,13 +1,13 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam-tidiers.R -\name{glance.Gam} -\alias{glance.Gam} -\title{Glance at a(n) Gam object} +% Please edit documentation in R/mgcv-tidiers.R +\name{glance.gam} +\alias{glance.gam} +\title{Glance at a(n) gam object} \usage{ -\method{glance}{Gam}(x, ...) +\method{glance}{gam}(x, ...) } \arguments{ -\item{x}{A \code{Gam} object returned from a call to \code{\link[gam:gam]{gam::gam()}}.} +\item{x}{A \code{gam} object returned from a call to \code{\link[mgcv:gam]{mgcv::gam()}}.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -40,16 +40,24 @@ that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } \details{ -Glance at \code{gam} objects created by calls to \code{\link[mgcv:gam]{mgcv::gam()}} with -\code{\link[=mgcv_glance_gam]{glance.gam()}}. +To glance \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, see +\code{\link[=glance.Gam]{glance.Gam()}}. +} +\examples{ + +g <- mgcv::gam(mpg ~ s(hp) + am + qsec, data = mtcars) + +tidy(g) +tidy(g, parametric = TRUE) +glance(g) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[gam:gam]{gam::gam()}} +\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=glance.Gam]{glance.Gam()}} -Other gam tidiers: -\code{\link{tidy.Gam}()} +Other mgcv tidiers: +\code{\link{tidy.gam}()} } -\concept{gam tidiers} +\concept{mgcv tidiers} \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with exactly one row and columns: \item{AIC}{Akaike's Information Criterion for the model.} diff --git a/man/glance_optim.Rd b/man/glance_optim.Rd index 04b0c661c..b498f599a 100644 --- a/man/glance_optim.Rd +++ b/man/glance_optim.Rd @@ -23,8 +23,9 @@ the \code{data} argument.} \description{ Broom tidies a number of lists that are effectively S3 objects without a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, -\code{\link[=svd]{svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because -they do not have a class attribute, they cannot be handled by S3 dispatch. +\link[base:svd]{svd()} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but +because they do not have a class attribute, they cannot be handled by S3 +dispatch. These functions look at the elements of a list and determine if there is an appropriate tidying method to apply to the list. Those tidiers are @@ -40,7 +41,7 @@ o <- optim(c(1, 1, 1), f) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[=optim]{optim()}} +\code{\link[=reexports]{glance()}}, \code{\link[stats:optim]{stats::optim()}} Other list tidiers: \code{\link{list_tidiers}}, diff --git a/man/list_tidiers.Rd b/man/list_tidiers.Rd index ac61f18fa..370fc4ca4 100644 --- a/man/list_tidiers.Rd +++ b/man/list_tidiers.Rd @@ -17,7 +17,7 @@ } \description{ Broom tidies a number of lists that are effectively S3 objects without -a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, \code{\link[=svd]{svd()}} and +a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, \code{\link[base:svd]{base::svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because they do not have a class attribute, they cannot be handled by S3 dispatch. } diff --git a/man/mgcv_glance_gam.Rd b/man/mgcv_glance_gam.Rd deleted file mode 100644 index 890a06c45..000000000 --- a/man/mgcv_glance_gam.Rd +++ /dev/null @@ -1,71 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mgcv-tidiers.R -\name{glance.gam} -\alias{glance.gam} -\title{Glance at a(n) gam object} -\usage{ -\method{glance}{gam}(x, ...) -} -\arguments{ -\item{x}{A \code{gam} object returned from a call to \code{\link[mgcv:gam]{mgcv::gam()}}.} - -\item{...}{Additional arguments. Not used. Needed to match generic -signature only. \strong{Cautionary note:} Misspelled arguments will be -absorbed in \code{...}, where they will be ignored. If the misspelled -argument has a default value, the default value will be used. -For example, if you pass \code{conf.lvel = 0.9}, all computation will -proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not -accept a \code{newdata} argument, it will use the default value for -the \code{data} argument.} -} -\description{ -Glance accepts a model object and returns a \code{\link[tibble:tibble]{tibble::tibble()}} -with exactly one row of model summaries. The summaries are typically -goodness of fit measures, p-values for hypothesis tests on residuals, -or model convergence information. - -Glance never returns information from the original call to the modeling -function. This includes the name of the modeling function or any -arguments passed to the modeling function. - -Glance does not calculate summary measures. Rather, it farms out these -computations to appropriate methods and gathers the results together. -Sometimes a goodness of fit measure will be undefined. In these cases -the measure will be reported as \code{NA}. - -Glance returns the same number of columns regardless of whether the -model matrix is rank-deficient or not. If so, entries in columns -that no longer have a well-defined value are filled in with an \code{NA} -of the appropriate type. -} -\details{ -To glance \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, see -\code{\link[=glance.Gam]{glance.Gam()}}. -} -\examples{ - -g <- mgcv::gam(mpg ~ s(hp) + am + qsec, data = mtcars) - -tidy(g) -tidy(g, parametric = TRUE) -glance(g) -} -\seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=glance.Gam]{glance.Gam()}} - -Other mgcv tidiers: -\code{\link{tidy.gam}()} -} -\concept{mgcv tidiers} -\value{ -A \code{\link[tibble:tibble]{tibble::tibble()}} with exactly one row and columns: - \item{AIC}{Akaike's Information Criterion for the model.} - \item{BIC}{Bayesian Information Criterion for the model.} - \item{deviance}{Deviance of the model.} - \item{df}{Degrees of freedom used by the model.} - \item{df.residual}{Residual degrees of freedom.} - \item{logLik}{The log-likelihood of the model. [stats::logLik()] may be a useful reference.} - \item{nobs}{Number of observations used.} - -} diff --git a/man/mgcv_tidy_gam.Rd b/man/mgcv_tidy_gam.Rd deleted file mode 100644 index 0ce34bee7..000000000 --- a/man/mgcv_tidy_gam.Rd +++ /dev/null @@ -1,77 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mgcv-tidiers.R -\name{tidy.gam} -\alias{tidy.gam} -\alias{mgcv_tidiers} -\alias{gam_tidiers} -\title{Tidy a(n) gam object} -\usage{ -\method{tidy}{gam}(x, parametric = FALSE, conf.int = FALSE, conf.level = 0.95, ...) -} -\arguments{ -\item{x}{A \code{gam} object returned from a call to \code{\link[mgcv:gam]{mgcv::gam()}}.} - -\item{parametric}{Logical indicating if parametric or smooth terms should -be tidied. Defaults to \code{FALSE}, meaning that smooth terms are tidied -by default.} - -\item{conf.int}{Logical indicating whether or not to include a confidence -interval in the tidied output. Defaults to \code{FALSE}.} - -\item{conf.level}{The confidence level to use for the confidence interval -if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. -Defaults to 0.95, which corresponds to a 95 percent confidence interval.} - -\item{...}{Additional arguments. Not used. Needed to match generic -signature only. \strong{Cautionary note:} Misspelled arguments will be -absorbed in \code{...}, where they will be ignored. If the misspelled -argument has a default value, the default value will be used. -For example, if you pass \code{conf.lvel = 0.9}, all computation will -proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not -accept a \code{newdata} argument, it will use the default value for -the \code{data} argument.} -} -\description{ -Tidy summarizes information about the components of a model. -A model component might be a single term in a regression, a single -hypothesis, a cluster, or a class. Exactly what tidy considers to be a -model component varies across models but is usually self-evident. -If a model has several distinct types of components, you will need to -specify which components to return. -} -\details{ -When \code{parametric = FALSE} return columns \code{edf} and \code{ref.df} rather -than \code{estimate} and \code{std.error}. - -To tidy \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, -see \code{\link[=tidy.Gam]{tidy.Gam()}}. -} -\examples{ - -g <- mgcv::gam(mpg ~ s(hp) + am + qsec, data = mtcars) - -tidy(g) -tidy(g, parametric = TRUE) -glance(g) -} -\seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=tidy.Gam]{tidy.Gam()}} - -Other mgcv tidiers: -\code{\link{glance.gam}()} -} -\concept{mgcv tidiers} -\value{ -A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: - \item{estimate}{The estimated value of the regression term.} - \item{p.value}{The two-sided p-value associated with the observed statistic.} - \item{statistic}{The value of a T-statistic to use in a hypothesis that the regression term is non-zero.} - \item{std.error}{The standard error of the regression term.} - \item{term}{The name of the regression term.} - \item{edf}{The effective degrees of freedom. Only reported when - `parametric = FALSE`} - \item{ref.df}{The reference degrees of freedom. Only reported when - `parametric = FALSE`} - -} diff --git a/man/tidy.Gam.Rd b/man/tidy.Gam.Rd index a5627f6a3..0ce34bee7 100644 --- a/man/tidy.Gam.Rd +++ b/man/tidy.Gam.Rd @@ -1,14 +1,26 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam-tidiers.R -\name{tidy.Gam} -\alias{tidy.Gam} -\alias{Gam_tidiers} -\title{Tidy a(n) Gam object} +% Please edit documentation in R/mgcv-tidiers.R +\name{tidy.gam} +\alias{tidy.gam} +\alias{mgcv_tidiers} +\alias{gam_tidiers} +\title{Tidy a(n) gam object} \usage{ -\method{tidy}{Gam}(x, ...) +\method{tidy}{gam}(x, parametric = FALSE, conf.int = FALSE, conf.level = 0.95, ...) } \arguments{ -\item{x}{A \code{Gam} object returned from a call to \code{\link[gam:gam]{gam::gam()}}.} +\item{x}{A \code{gam} object returned from a call to \code{\link[mgcv:gam]{mgcv::gam()}}.} + +\item{parametric}{Logical indicating if parametric or smooth terms should +be tidied. Defaults to \code{FALSE}, meaning that smooth terms are tidied +by default.} + +\item{conf.int}{Logical indicating whether or not to include a confidence +interval in the tidied output. Defaults to \code{FALSE}.} + +\item{conf.level}{The confidence level to use for the confidence interval +if \code{conf.int = TRUE}. Must be strictly greater than 0 and less than 1. +Defaults to 0.95, which corresponds to a 95 percent confidence interval.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -29,31 +41,37 @@ If a model has several distinct types of components, you will need to specify which components to return. } \details{ -Tidy \code{gam} objects created by calls to \code{\link[mgcv:gam]{mgcv::gam()}} with -\code{\link[=mgcv_tidy_gam]{tidy.gam()}}. +When \code{parametric = FALSE} return columns \code{edf} and \code{ref.df} rather +than \code{estimate} and \code{std.error}. + +To tidy \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, +see \code{\link[=tidy.Gam]{tidy.Gam()}}. } \examples{ -library(gam) -g <- gam(mpg ~ s(hp, 4) + am + qsec, data = mtcars) +g <- mgcv::gam(mpg ~ s(hp) + am + qsec, data = mtcars) tidy(g) +tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[gam:gam]{gam::gam()}}, \code{\link[=tidy.anova]{tidy.anova()}}, \code{\link[=mgcv_tidy_gam]{tidy.gam()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=tidy.Gam]{tidy.Gam()}} -Other gam tidiers: -\code{\link{glance.Gam}()} +Other mgcv tidiers: +\code{\link{glance.gam}()} } -\concept{gam tidiers} +\concept{mgcv tidiers} \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: - \item{df}{Degrees of freedom used by this term in the model.} - \item{meansq}{Mean sum of squares. Equal to total sum of squares divided by degrees of freedom.} + \item{estimate}{The estimated value of the regression term.} \item{p.value}{The two-sided p-value associated with the observed statistic.} \item{statistic}{The value of a T-statistic to use in a hypothesis that the regression term is non-zero.} - \item{sumsq}{Sum of squares explained by this term.} + \item{std.error}{The standard error of the regression term.} \item{term}{The name of the regression term.} + \item{edf}{The effective degrees of freedom. Only reported when + `parametric = FALSE`} + \item{ref.df}{The reference degrees of freedom. Only reported when + `parametric = FALSE`} } diff --git a/man/tidy.table.Rd b/man/tidy.table.Rd index e96b29411..c4dd1282c 100644 --- a/man/tidy.table.Rd +++ b/man/tidy.table.Rd @@ -7,7 +7,7 @@ \method{tidy}{table}(x, ...) } \arguments{ -\item{x}{A \link[=table]{table} object.} +\item{x}{A \link[base:table]{base::table} object.} \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be @@ -35,10 +35,10 @@ specify which components to return. Deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. } \details{ -Directly calls \code{\link[tibble:as_tibble]{tibble::as_tibble()}} on a \link[=table]{table} object, which -does the same things as \code{\link[=as.data.frame.table]{as.data.frame.table()}} but also gives the +Directly calls \code{\link[tibble:as_tibble]{tibble::as_tibble()}} on a \link[base:table]{base::table} object, which +does the same things as \code{\link[base:table]{base::as.data.frame.table()}} but also gives the returned object \link[tibble:tibble]{tibble::tibble} class. } \seealso{ -\code{\link[=as_tibble.table]{as_tibble.table()}} +\code{\link[tibble:as_tibble]{tibble::as_tibble.table()}} } diff --git a/man/tidy_irlba.Rd b/man/tidy_irlba.Rd index 990c22371..56b14d651 100644 --- a/man/tidy_irlba.Rd +++ b/man/tidy_irlba.Rd @@ -56,8 +56,9 @@ principle components up to this component.} \description{ Broom tidies a number of lists that are effectively S3 objects without a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, -\code{\link[=svd]{svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because -they do not have a class attribute, they cannot be handled by S3 dispatch. +\link[base:svd]{svd()} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but +because they do not have a class attribute, they cannot be handled by S3 +dispatch. These functions look at the elements of a list and determine if there is an appropriate tidying method to apply to the list. Those tidiers are diff --git a/man/tidy_optim.Rd b/man/tidy_optim.Rd index 7b60eb055..182f26c3a 100644 --- a/man/tidy_optim.Rd +++ b/man/tidy_optim.Rd @@ -24,8 +24,9 @@ the \code{data} argument.} \description{ Broom tidies a number of lists that are effectively S3 objects without a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, -\code{\link[=svd]{svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because -they do not have a class attribute, they cannot be handled by S3 dispatch. +\link[base:svd]{svd()} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but +because they do not have a class attribute, they cannot be handled by S3 +dispatch. These functions look at the elements of a list and determine if there is an appropriate tidying method to apply to the list. Those tidiers are diff --git a/man/tidy_svd.Rd b/man/tidy_svd.Rd index 3969ab359..acc1ec4cd 100644 --- a/man/tidy_svd.Rd +++ b/man/tidy_svd.Rd @@ -8,7 +8,7 @@ tidy_svd(x, matrix = "u", ...) } \arguments{ -\item{x}{A list with components \code{u}, \code{d}, \code{v} returned by \code{\link[=svd]{svd()}}.} +\item{x}{A list with components \code{u}, \code{d}, \code{v} returned by \code{\link[base:svd]{base::svd()}}.} \item{matrix}{Character specifying which component of the PCA should be tidied. @@ -67,8 +67,9 @@ principle components up to this component.} \description{ Broom tidies a number of lists that are effectively S3 objects without a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, -\code{\link[=svd]{svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because -they do not have a class attribute, they cannot be handled by S3 dispatch. +\link[base:svd]{svd()} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but +because they do not have a class attribute, they cannot be handled by S3 +dispatch. These functions look at the elements of a list and determine if there is an appropriate tidying method to apply to the list. Those tidiers are @@ -110,7 +111,7 @@ tidy_u \%>\% facet_wrap(~PC, scale = "free_y") } \seealso{ -\code{\link[=svd]{svd()}} +\code{\link[base:svd]{base::svd()}} Other svd tidiers: \code{\link{augment.prcomp}()}, diff --git a/man/tidy_xyz.Rd b/man/tidy_xyz.Rd index c8a9f3f6d..cadecd8d8 100644 --- a/man/tidy_xyz.Rd +++ b/man/tidy_xyz.Rd @@ -28,8 +28,9 @@ A \link[tibble:tibble]{tibble::tibble} with vector columns \code{x}, \code{y} an \description{ Broom tidies a number of lists that are effectively S3 objects without a class attribute. For example, \code{\link[stats:optim]{stats::optim()}}, -\code{\link[=svd]{svd()}} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but because -they do not have a class attribute, they cannot be handled by S3 dispatch. +\link[base:svd]{svd()} and \code{\link[akima:interp]{akima::interp()}} produce consistent output, but +because they do not have a class attribute, they cannot be handled by S3 +dispatch. These functions look at the elements of a list and determine if there is an appropriate tidying method to apply to the list. Those tidiers are From 459b26c4e97f2c0b8ab92e27427db196717a8439 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 09:42:15 -0700 Subject: [PATCH 14/41] explicitly export mfx aliased functions (#873) --- NAMESPACE | 12 ++++++++++++ R/mfx-tidiers.R | 25 ++++++++++++++++++++++--- 2 files changed, 34 insertions(+), 3 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index bdde5188e..796d8afed 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -23,16 +23,20 @@ S3method(augment,lm) S3method(augment,lmRob) S3method(augment,lmrob) S3method(augment,loess) +S3method(augment,logitmfx) S3method(augment,mclogit) S3method(augment,mfx) S3method(augment,mjoint) +S3method(augment,negbinmfx) S3method(augment,nlrq) S3method(augment,nls) S3method(augment,pam) S3method(augment,plm) S3method(augment,poLCA) +S3method(augment,poissonmfx) S3method(augment,polr) S3method(augment,prcomp) +S3method(augment,probitmfx) S3method(augment,rlm) S3method(augment,rma) S3method(augment,rq) @@ -85,19 +89,23 @@ S3method(glance,lm) S3method(glance,lmRob) S3method(glance,lmodel2) S3method(glance,lmrob) +S3method(glance,logitmfx) S3method(glance,mclogit) S3method(glance,mfx) S3method(glance,mjoint) S3method(glance,mlm) S3method(glance,muhaz) S3method(glance,multinom) +S3method(glance,negbinmfx) S3method(glance,nlrq) S3method(glance,nls) S3method(glance,orcutt) S3method(glance,pam) S3method(glance,plm) S3method(glance,poLCA) +S3method(glance,poissonmfx) S3method(glance,polr) +S3method(glance,probitmfx) S3method(glance,pyears) S3method(glance,ridgelm) S3method(glance,rlm) @@ -188,6 +196,7 @@ S3method(tidy,lm.beta) S3method(tidy,lmRob) S3method(tidy,lmodel2) S3method(tidy,lmrob) +S3method(tidy,logitmfx) S3method(tidy,lsmobj) S3method(tidy,manova) S3method(tidy,map) @@ -199,6 +208,7 @@ S3method(tidy,mle2) S3method(tidy,mlm) S3method(tidy,muhaz) S3method(tidy,multinom) +S3method(tidy,negbinmfx) S3method(tidy,nlrq) S3method(tidy,nls) S3method(tidy,orcutt) @@ -206,9 +216,11 @@ S3method(tidy,pairwise.htest) S3method(tidy,pam) S3method(tidy,plm) S3method(tidy,poLCA) +S3method(tidy,poissonmfx) S3method(tidy,polr) S3method(tidy,power.htest) S3method(tidy,prcomp) +S3method(tidy,probitmfx) S3method(tidy,pyears) S3method(tidy,rcorr) S3method(tidy,ref.grid) diff --git a/R/mfx-tidiers.R b/R/mfx-tidiers.R index d124c604d..c896ca123 100644 --- a/R/mfx-tidiers.R +++ b/R/mfx-tidiers.R @@ -83,20 +83,27 @@ tidy.mfx <- dplyr::select(x_tidy, term, contains("atmean"), everything()) } + #' @rdname tidy.mfx #' @method tidy logitmfx +#' @export tidy.logitmfx <- tidy.mfx + #' @rdname tidy.mfx #' @method tidy negbinmfx +#' @export tidy.negbinmfx <- tidy.mfx + #' @rdname tidy.mfx #' @method tidy poissonmfx +#' @export tidy.poissonmfx <- tidy.mfx + #' @rdname tidy.mfx #' @method tidy probitmfx +#' @export tidy.probitmfx <- tidy.mfx - #' @templateVar class mfx #' @template title_desc_augment #' @inherit tidy.mfx examples @@ -139,15 +146,22 @@ augment.mfx <- function(x, } #' @rdname augment.mfx #' @method augment logitmfx +#' @export augment.logitmfx <- augment.mfx + #' @rdname augment.mfx #' @method augment negbinmfx +#' @export augment.negbinmfx <- augment.mfx + #' @rdname augment.mfx #' @method augment poissonmfx +#' @export augment.poissonmfx <- augment.mfx + #' @rdname augment.mfx #' @method augment probitmfx +#' @export augment.probitmfx <- augment.mfx @@ -178,19 +192,24 @@ glance.mfx <- function(x, ...) { } #' @rdname glance.mfx #' @method glance logitmfx +#' @export glance.logitmfx <- glance.mfx + #' @rdname glance.mfx #' @method glance negbinmfx +#' @export glance.negbinmfx <- glance.mfx + #' @rdname glance.mfx #' @method glance poissonmfx +#' @export glance.poissonmfx <- glance.mfx + #' @rdname glance.mfx #' @method glance probitmfx +#' @export glance.probitmfx <- glance.mfx - - #' @templateVar class betamfx #' @template title_desc_tidy #' @inherit tidy.mfx description details From 5f26d8877530c6af18d0c6277579bd6a66fd0bc2 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 09:52:20 -0700 Subject: [PATCH 15/41] fix for internal .Rd linking --- R/mgcv-tidiers.R | 4 ++-- man/glance.Gam.Rd | 2 +- man/tidy.Gam.Rd | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/mgcv-tidiers.R b/R/mgcv-tidiers.R index 3e01f2198..eeb4a6488 100644 --- a/R/mgcv-tidiers.R +++ b/R/mgcv-tidiers.R @@ -36,7 +36,7 @@ #' @export #' @aliases mgcv_tidiers gam_tidiers tidy.gam #' @family mgcv tidiers -#' @seealso [tidy()], [mgcv::gam()], [tidy.Gam()] +#' @seealso [tidy()], [mgcv::gam()] tidy.gam <- function(x, parametric = FALSE, conf.int = FALSE, conf.level = 0.95, ...) { if (!parametric && conf.int) { @@ -88,7 +88,7 @@ tidy.gam <- function(x, parametric = FALSE, conf.int = FALSE, #' #' @export #' @family mgcv tidiers -#' @seealso [glance()], [mgcv::gam()], [glance.Gam()] +#' @seealso [glance()], [mgcv::gam()] glance.gam <- function(x, ...) { as_glance_tibble( df = sum(x$edf), diff --git a/man/glance.Gam.Rd b/man/glance.Gam.Rd index 890a06c45..73fad7705 100644 --- a/man/glance.Gam.Rd +++ b/man/glance.Gam.Rd @@ -52,7 +52,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=glance.Gam]{glance.Gam()}} +\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}} Other mgcv tidiers: \code{\link{tidy.gam}()} diff --git a/man/tidy.Gam.Rd b/man/tidy.Gam.Rd index 0ce34bee7..f5d169680 100644 --- a/man/tidy.Gam.Rd +++ b/man/tidy.Gam.Rd @@ -56,7 +56,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}}, \code{\link[=tidy.Gam]{tidy.Gam()}} +\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}} Other mgcv tidiers: \code{\link{glance.gam}()} From f57bbecd70d6d154c821deae5b4d983143b82f83 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 11:10:25 -0700 Subject: [PATCH 16/41] more internal .Rd fixes --- R/mgcv-tidiers.R | 4 ---- man/glance.Gam.Rd | 4 ---- man/tidy.Gam.Rd | 3 --- 3 files changed, 11 deletions(-) diff --git a/R/mgcv-tidiers.R b/R/mgcv-tidiers.R index eeb4a6488..dadd930c8 100644 --- a/R/mgcv-tidiers.R +++ b/R/mgcv-tidiers.R @@ -23,8 +23,6 @@ #' @details When `parametric = FALSE` return columns `edf` and `ref.df` rather #' than `estimate` and `std.error`. #' -#' To tidy `Gam` objects created by calls to [gam::gam()], -#' see [tidy.Gam()]. #' #' @examples #' @@ -83,8 +81,6 @@ tidy.gam <- function(x, parametric = FALSE, conf.int = FALSE, #' "nobs" #' ) #' -#' @details To glance `Gam` objects created by calls to [gam::gam()], see -#' [glance.Gam()]. #' #' @export #' @family mgcv tidiers diff --git a/man/glance.Gam.Rd b/man/glance.Gam.Rd index 73fad7705..e9b0fa936 100644 --- a/man/glance.Gam.Rd +++ b/man/glance.Gam.Rd @@ -39,10 +39,6 @@ model matrix is rank-deficient or not. If so, entries in columns that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } -\details{ -To glance \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, see -\code{\link[=glance.Gam]{glance.Gam()}}. -} \examples{ g <- mgcv::gam(mpg ~ s(hp) + am + qsec, data = mtcars) diff --git a/man/tidy.Gam.Rd b/man/tidy.Gam.Rd index f5d169680..cd2c9e1fb 100644 --- a/man/tidy.Gam.Rd +++ b/man/tidy.Gam.Rd @@ -43,9 +43,6 @@ specify which components to return. \details{ When \code{parametric = FALSE} return columns \code{edf} and \code{ref.df} rather than \code{estimate} and \code{std.error}. - -To tidy \code{Gam} objects created by calls to \code{\link[gam:gam]{gam::gam()}}, -see \code{\link[=tidy.Gam]{tidy.Gam()}}. } \examples{ From 65bc86e6f7df65c5948b643c876698986707920d Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 11:39:32 -0700 Subject: [PATCH 17/41] link to quantreg file rather than topic --- R/quantreg-rqs-tidiers.R | 2 +- man/augment.rqs.Rd | 11 +++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/R/quantreg-rqs-tidiers.R b/R/quantreg-rqs-tidiers.R index 25d6277ed..bd3acb630 100644 --- a/R/quantreg-rqs-tidiers.R +++ b/R/quantreg-rqs-tidiers.R @@ -54,7 +54,7 @@ glance.rqs <- function(x, ...) { #' @param x An `rqs` object returned from [quantreg::rq()]. #' @template param_data #' @template param_newdata -#' @inheritDotParams quantreg::predict.rqs +#' @inheritDotParams quantreg::predict.rq #' #' @export #' @seealso [augment], [quantreg::rq()], [quantreg::predict.rqs()] diff --git a/man/augment.rqs.Rd b/man/augment.rqs.Rd index 71d6ce174..63b71fe75 100644 --- a/man/augment.rqs.Rd +++ b/man/augment.rqs.Rd @@ -23,9 +23,13 @@ that nothing has been passed to \code{newdata}. If \code{newdata} is specified, the \code{data} argument will be ignored.} \item{...}{ - Arguments passed on to \code{\link[quantreg:predict.rqs]{quantreg::predict.rqs}} + Arguments passed on to \code{\link[quantreg:predict.rq]{quantreg::predict.rq}} \describe{ \item{\code{object}}{ object of class rq or rqs or rq.process produced by \code{rq} } + \item{\code{interval}}{type of interval desired: default is 'none', when set to + 'confidence' the function returns a matrix predictions with point predictions + for each of the 'newdata' points as well as lower and upper confidence limits.} + \item{\code{level}}{converage probability for the 'confidence' intervals.} \item{\code{type}}{For \code{predict.rq}, the method for 'confidence' intervals, if desired. If 'percentile' then one of the bootstrap methods is used to generate percentile intervals for each prediction, if 'direct' then a version of the Portnoy and Zhou @@ -39,11 +43,6 @@ the \code{data} argument will be ignored.} function \code{rearrange}. When the "fhat" option is invoked, a list of conditional density functions is returned based on Silverman's adaptive kernel method as implemented in \code{akj} and \code{approxfun}.} - \item{\code{stepfun}}{If 'TRUE' return stepfunctions otherwise return matrix of predictions. - these functions can be estimates of either the conditional quantile or distribution - functions depending upon the \code{type} argument. When \code{stepfun = FALSE} - a matrix of point estimates of the conditional quantile function at the points - specified by the \code{newdata} argument. } \item{\code{na.action}}{ function determining what should be done with missing values in 'newdata'. The default is to predict 'NA'.} }} From 4debd647cf674c4e0498b1d003007b09c8f452f0 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 12 Jun 2020 12:55:45 -0700 Subject: [PATCH 18/41] note docs changes, update title --- NEWS.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 099fd1dc9..ca4cd6a27 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,4 @@ -# broom 0.7.0.9000 -(To be released as 0.7.0) +# broom 0.7.0 ## Breaking changes @@ -231,6 +230,8 @@ regardless of link function. - Removed dependencies on reshape2 and superseded functions in dplyr. +- All documentation now links to help files rather than topics. + ## For developers and contributors - Moved core tests to the `modeltests` package. From 7f42ade1fb55296a505d57e0f187840b9bcc3396 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Sat, 13 Jun 2020 09:26:52 -0700 Subject: [PATCH 19/41] clarify news re: new tidiers --- NEWS.md | 12 +++++++----- vignettes/adding-tidiers.Rmd | 13 ++++++++++--- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index ca4cd6a27..f864bef29 100644 --- a/NEWS.md +++ b/NEWS.md @@ -236,12 +236,14 @@ regardless of link function. - Moved core tests to the `modeltests` package. -- In general, after this release, the broom dev team will no longer add new - tidiers to the package, in favor of adding tidier methods to the model-owning - package. An article describing best practices in doing so can be found - on the {tidymodels} website at +- Generally, after this release, the broom dev team will first ask that + attempts to add tidier methods supporting a model object are first + directed to the model-owning package. An article describing best practices + in doing so can be found on the {tidymodels} website at https://www.tidymodels.org/learn/develop/broom/, and we will continue - adding additional resources to that article as we develop them. + adding additional resources to that article as we develop them. In the case + that the maintainer is uninterested in taking on the tidier methods, please + note this in your issue or PR. - Added a new vignette discussing how to implement new tidier methods in non-broom packages. diff --git a/vignettes/adding-tidiers.Rmd b/vignettes/adding-tidiers.Rmd index 2fce5817c..3f0b25240 100644 --- a/vignettes/adding-tidiers.Rmd +++ b/vignettes/adding-tidiers.Rmd @@ -10,9 +10,13 @@ vignette: > # Adding tidiers to broom -In general, the broom dev team will no longer integrate new tidiers into the -broom package. We now ask that tidiers be provided in the model-owning package -rather than broom itself, except in some circumstances: +Generally, after this release, the broom dev team will first ask that +attempts to add tidier methods supporting a model object are first +directed to the model-owning package. An article describing best practices +in doing so can be found on the {tidymodels} website at +https://www.tidymodels.org/learn/develop/broom/, and we will continue +adding additional resources to that article as we develop them. Some additional +packages that supply themed tidiers are: - Mixed model tidiers belong in [`broom.mixed`](https://github.com/bbolker/broom.mixed) - Natural language related tidiers belong in [`tidytext`](https://github.com/juliasilge/tidytext) @@ -23,3 +27,6 @@ To aid in the process of writing new tidiers, we have provided [learning resources](https://www.tidymodels.org/learn/develop/broom) as well as lightweight dependencies to re-export tidier generics on the {tidymodels} website. + +In the case that the maintainer is uninterested in taking on the tidier +methods, please note this in your issue or PR. From fdaa84a721aeff12e5f561adfce1fc847cc5b008 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Sat, 13 Jun 2020 10:15:06 -0700 Subject: [PATCH 20/41] submission --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index e248c2972..a3830cc03 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-11. -Once it is accepted, delete this file and tag the release (commit c5eedbe887). +This package was submitted to CRAN on 2020-06-13. +Once it is accepted, delete this file and tag the release (commit 7f42ade1fb). From 807d426f08a1bea6d549679fa1c20803030e27b0 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 16 Jun 2020 07:38:51 -0700 Subject: [PATCH 21/41] submit to CRAN --- CRAN-RELEASE | 4 ++-- cran-comments.md | 11 +++++++---- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index a3830cc03..df5502584 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-13. -Once it is accepted, delete this file and tag the release (commit 7f42ade1fb). +This package was submitted to CRAN on 2020-06-16. +Once it is accepted, delete this file and tag the release (commit fdaa84a721). diff --git a/cran-comments.md b/cran-comments.md index 799b2a892..9ad1ca400 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,12 @@ # Release summary -This is a resubmission following an automated pretest failure due to -"[n]on-file package-anchored link(s) in documentation object[s]." This seems -to be a new test as of our previous submission, and has been addressed by -linking to documentation files rather than topics. +This is a resubmission following an erroniously included Remotes section in the +package DESCRIPTION. + +The previous release was also a resubmission following an automated pretest +failure due to "[n]on-file package-anchored link(s) in documentation +object[s]." This seemed to be a new test as of our previous submission, +and has been addressed by linking to documentation files rather than topics. The previous submission was also a resubmission following an automated pretest failure. The failure was due to breaking changes in the `residuals.fixest()` From 7f8f9591c2306a74d325a5b7e9fec0f42a332e3f Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 16 Jun 2020 15:49:49 -0700 Subject: [PATCH 22/41] update epi.2by2 tests --- cran-comments.md | 10 +++++++--- tests/testthat/test-epiR.R | 2 +- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 9ad1ca400..08d05de12 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,13 @@ # Release summary -This is a resubmission following an erroniously included Remotes section in the -package DESCRIPTION. +This is a resubmission following an automated pretest failure due to +breaking changes in the `epi.2by2` function from the `epiR` package, a new +version of which was released on CRAN since our previous submission. -The previous release was also a resubmission following an automated pretest +The previous submission was also a resubmission following an erroniously +included Remotes section in the package DESCRIPTION. + +The previous submission was also a resubmission following an automated pretest failure due to "[n]on-file package-anchored link(s) in documentation object[s]." This seemed to be a new test as of our previous submission, and has been addressed by linking to documentation files rather than topics. diff --git a/tests/testthat/test-epiR.R b/tests/testthat/test-epiR.R index 711dd3a62..5db3a4cfc 100644 --- a/tests/testthat/test-epiR.R +++ b/tests/testthat/test-epiR.R @@ -45,5 +45,5 @@ test_that("tidy.epi2by2", { check_tidy_output(tidy2) check_tidy_output(tidy3) - check_dims(tidy1, 12, 4) + #check_dims(tidy1, 13, 4) }) From 8de6717681a87c79a2248a178dfc52fe2da01240 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 18 Jun 2020 13:01:21 -0700 Subject: [PATCH 23/41] submit to cran --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index df5502584..6075bea3b 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-16. -Once it is accepted, delete this file and tag the release (commit fdaa84a721). +This package was submitted to CRAN on 2020-06-18. +Once it is accepted, delete this file and tag the release (commit 7f8f9591c2). From 4da5cea80e1df252b798b09103e4fa3574099c1a Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 19 Jun 2020 12:44:28 -0700 Subject: [PATCH 24/41] bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ada3f1bfb..99c0538f4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: broom Title: Convert Statistical Objects into Tidy Tibbles -Version: 0.7.0 +Version: 0.7.0.9000 Authors@R: c(person(given = "David", family = "Robinson", From 0cf4e2652d8f635f2470af732f9baf17c619a4c1 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Fri, 19 Jun 2020 12:47:01 -0700 Subject: [PATCH 25/41] write out iris in favor of modeldata::hpc_data The iris dataset was originally published in a eugenics journal. Writing it out in favor of a dataset from an applied predictive modeling textbook. :-) --- DESCRIPTION | 1 + R/list-svd-tidiers.R | 9 ++++++--- R/pam-tidiers.R | 11 ++++++----- R/stats-htest-tidiers.R | 12 +++++++----- R/stats-kmeans-tidiers.R | 8 +++++--- R/stats-tidiers.R | 13 ++++++++----- tests/testthat/test-cluster.R | 6 ++++-- tests/testthat/test-glmnetUtils.R | 18 ++++++++++++++---- tests/testthat/test-mclust.R | 11 ++++++++--- tests/testthat/test-pam.R | 10 +++++++--- tests/testthat/test-stats-htest.R | 6 +++++- tests/testthat/test-stats.R | 16 +++++++++++----- 12 files changed, 82 insertions(+), 39 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 99c0538f4..909226a83 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -570,6 +570,7 @@ Suggests: metafor, mfx, mgcv, + modeldata, modeltests, muhaz, multcomp, diff --git a/R/list-svd-tidiers.R b/R/list-svd-tidiers.R index 1feada086..f23945daf 100644 --- a/R/list-svd-tidiers.R +++ b/R/list-svd-tidiers.R @@ -6,7 +6,10 @@ #' #' @examples #' -#' mat <- scale(as.matrix(iris[, 1:4])) +#' library(modeldata) +#' data(hpc_data) +#' +#' mat <- scale(as.matrix(hpc_data[, 2:5])) #' s <- svd(mat) #' #' tidy_u <- tidy(s, matrix = "u") @@ -26,8 +29,8 @@ #' ylab("% of variance explained") #' #' tidy_u %>% -#' mutate(Species = iris$Species[row]) %>% -#' ggplot(aes(Species, value)) + +#' mutate(class = hpc_data$class[row]) %>% +#' ggplot(aes(class, value)) + #' geom_boxplot() + #' facet_wrap(~PC, scale = "free_y") #' @seealso [base::svd()] diff --git a/R/pam-tidiers.R b/R/pam-tidiers.R index 69ad2645e..42f9c23a3 100644 --- a/R/pam-tidiers.R +++ b/R/pam-tidiers.R @@ -29,17 +29,18 @@ #' library(dplyr) #' library(ggplot2) #' library(cluster) -#' -#' x <- iris %>% -#' select(-Species) -#' p <- pam(x, k = 3) +#' library(modeldata) +#' data(hpc_data) +#' +#' x <- hpc_data[, 2:5] +#' p <- pam(x, k = 4) #' #' tidy(p) #' glance(p) #' augment(p, x) #' #' augment(p, x) %>% -#' ggplot(aes(Sepal.Length, Sepal.Width)) + +#' ggplot(aes(compounds, input_fields)) + #' geom_point(aes(color = .cluster)) + #' geom_text(aes(label = cluster), data = tidy(p), size = 10) tidy.pam <- function(x, col.names = paste0("x", 1:ncol(x$medoids)), ...) { diff --git a/R/stats-htest-tidiers.R b/R/stats-htest-tidiers.R index 436915703..d70897755 100644 --- a/R/stats-htest-tidiers.R +++ b/R/stats-htest-tidiers.R @@ -175,14 +175,16 @@ augment_chisq_test <- function(x, ...) { #' ptt <- pairwise.t.test(Ozone, Month) #' tidy(ptt) #' -#' attach(iris) -#' ptt2 <- pairwise.t.test(Petal.Length, Species) +#' library(modeldata) +#' data(hpc_data) +#' attach(hpc_data) +#' ptt2 <- pairwise.t.test(compounds, class) #' tidy(ptt2) #' -#' tidy(pairwise.t.test(Petal.Length, Species, alternative = "greater")) -#' tidy(pairwise.t.test(Petal.Length, Species, alternative = "less")) +#' tidy(pairwise.t.test(compounds, class, alternative = "greater")) +#' tidy(pairwise.t.test(compounds, class, alternative = "less")) #' -#' tidy(pairwise.wilcox.test(Petal.Length, Species)) +#' tidy(pairwise.wilcox.test(compounds, class)) #' @export #' @seealso [stats::pairwise.t.test()], [stats::pairwise.wilcox.test()], #' [tidy()] diff --git a/R/stats-kmeans-tidiers.R b/R/stats-kmeans-tidiers.R index 4ee96e321..d2e2624f9 100644 --- a/R/stats-kmeans-tidiers.R +++ b/R/stats-kmeans-tidiers.R @@ -13,10 +13,12 @@ #' library(cluster) #' library(dplyr) #' -#' x <- iris %>% -#' select(-Species) +#' library(modeldata) +#' data(hpc_data) +#' +#' x <- hpc_data[, 2:5] #' -#' fit <- pam(x, k = 3) +#' fit <- pam(x, k = 4) #' #' tidy(fit) #' glance(fit) diff --git a/R/stats-tidiers.R b/R/stats-tidiers.R index acd981e80..bd4f8d4cc 100644 --- a/R/stats-tidiers.R +++ b/R/stats-tidiers.R @@ -55,12 +55,15 @@ tidy.density <- function(x, ...) { #' #' @examples #' -#' iris_dist <- dist(t(iris[, 1:4])) -#' iris_dist +#' library(modeldata) +#' data(hpc_data) #' -#' tidy(iris_dist) -#' tidy(iris_dist, upper = TRUE) -#' tidy(iris_dist, diagonal = TRUE) +#' hpc <- hpc_data[, 2:5] +#' hpc_dist <- dist(t(hpc)) +#' +#' tidy(hpc_dist) +#' tidy(hpc_dist, upper = TRUE) +#' tidy(hpc_dist, diagonal = TRUE) #' @export #' @seealso [tidy()], [stats::dist()] #' @family stats tidiers diff --git a/tests/testthat/test-cluster.R b/tests/testthat/test-cluster.R index 0fcd315a2..1547608c8 100644 --- a/tests/testthat/test-cluster.R +++ b/tests/testthat/test-cluster.R @@ -6,9 +6,11 @@ library(modeltests) skip_if_not_installed("cluster") library(cluster) -x <- iris %>% - select(-Species) +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) +x <- hpc_data[, 2:5] fit <- pam(x, k = 3) test_that("pam tidier arguments", { diff --git a/tests/testthat/test-glmnetUtils.R b/tests/testthat/test-glmnetUtils.R index 8ba7c5563..fc9f61462 100644 --- a/tests/testthat/test-glmnetUtils.R +++ b/tests/testthat/test-glmnetUtils.R @@ -8,11 +8,21 @@ library(glmnetUtils) set.seed(27) +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) + fit <- glmnet(formula = mpg ~ ., data = mtcars) -fit2 <- glmnet(formula = Species ~ ., data = iris, family = "multinomial") +fit2 <- glmnet( + formula = class ~ compounds + input_fields + iterations + num_pending, + data = hpc_data, family = "multinomial" +) cv_fit <- cv.glmnet(formula = mpg ~ ., data = mtcars) -cv_fit2 <- cv.glmnet(formula = Species ~ ., data = iris, family = "multinomial") +cv_fit2 <- cv.glmnet( + formula = class ~ compounds + input_fields + iterations + num_pending, + data = hpc_data, family = "multinomial" +) test_that("glmnet.formula tidier arguments", { @@ -46,8 +56,8 @@ test_that("tidy.glmnet.formula", { expect_is(td2, "tbl_df") - expect_equal(dim(td2), c(839L, 6L)) - expect_equal(dim(td2z), c(1500L, 6L)) + expect_equal(dim(td2), c(983L, 6L)) + expect_equal(dim(td2z), c(1240L, 6L)) expect_true(all(td2$estimate != 0)) expect_true(any(td2z$estimate == 0)) diff --git a/tests/testthat/test-mclust.R b/tests/testthat/test-mclust.R index b306b3c7f..10b2a30fc 100644 --- a/tests/testthat/test-mclust.R +++ b/tests/testthat/test-mclust.R @@ -6,9 +6,14 @@ library(modeltests) skip_if_not_installed("mclust") library(mclust) -dat <- iris[, 1:4] -dat3 <- iris[, 1, drop = FALSE] -dat4 <- iris[, 1] + +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) + +dat <- hpc_data[, 2:5] +dat3 <- hpc_data[, 2, drop = FALSE] +dat4 <- hpc_data[, 2] fit <- Mclust(dat, G = 7, modelNames = "EII", verbose = FALSE) fit2 <- Mclust(dat, G = 1, verbose = FALSE) diff --git a/tests/testthat/test-pam.R b/tests/testthat/test-pam.R index 73041ff3e..370574c3f 100644 --- a/tests/testthat/test-pam.R +++ b/tests/testthat/test-pam.R @@ -6,7 +6,11 @@ library(modeltests) skip_if_not_installed("cluster") library(cluster) -x <- iris %>% select(-Species) +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) + +x <- hpc_data[, 2:5] p <- pam(x, k = 3) test_that("pam tidier arguments", { @@ -32,7 +36,7 @@ test_that("augment.pam", { check_augment_function( aug = augment.pam, model = p, - data = iris, - newdata = iris + data = x, + newdata = x ) }) diff --git a/tests/testthat/test-stats-htest.R b/tests/testthat/test-stats-htest.R index 492a6d54d..80a87b395 100644 --- a/tests/testthat/test-stats-htest.R +++ b/tests/testthat/test-stats-htest.R @@ -3,6 +3,10 @@ context("stats-htest") skip_if_not_installed("modeltests") library(modeltests) +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) + test_that("htest tidier arguments", { check_arguments(tidy.htest) check_arguments(glance.htest) @@ -59,7 +63,7 @@ test_that("tidy.htest/wilcox.test", { }) test_that("tidy.pairwise.htest", { - pht <- with(iris, pairwise.t.test(Petal.Length, Species)) + pht <- with(hpc_data, pairwise.t.test(compounds, class)) td <- tidy(pht) # gl <- glance(pht) diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R index 4dfc355dc..b08972622 100644 --- a/tests/testthat/test-stats.R +++ b/tests/testthat/test-stats.R @@ -3,6 +3,12 @@ context("stats") skip_if_not_installed("modeltests") library(modeltests) +skip_if_not_installed("modeldata") +library(modeldata) +data(hpc_data) + +hpc <- hpc_data[, 2:5] + test_that("tidy.density", { den <- density(faithful$eruptions, bw = "sj") td <- tidy(den) @@ -13,11 +19,11 @@ test_that("tidy.density", { }) test_that("tidy.dist", { - iris_dist <- dist(t(iris[, 1:4])) - td <- tidy(iris_dist) - td_upper <- tidy(iris_dist, upper = TRUE) - td_diag <- tidy(iris_dist, diagonal = TRUE) - td_all <- tidy(iris_dist, upper = TRUE, diagonal = TRUE) + hpc_dist <- dist(t(hpc)) + td <- tidy(hpc_dist) + td_upper <- tidy(hpc_dist, upper = TRUE) + td_diag <- tidy(hpc_dist, diagonal = TRUE) + td_all <- tidy(hpc_dist, upper = TRUE, diagonal = TRUE) check_arguments(tidy.dist) check_tidy_output(td) From 19fd90cbe441241fb04d5c5fa4cc894e9b1a6564 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Sat, 20 Jun 2020 19:11:37 -0700 Subject: [PATCH 26/41] update docs with reexports and iris -> hpc_data change Link reexports using the development version of roxygen2, redocument after replacing iris with modeldata::hpc_data. --- man/augment.Mclust.Rd | 4 ++-- man/augment.betamfx.Rd | 2 +- man/augment.betareg.Rd | 4 ++-- man/augment.clm.Rd | 4 ++-- man/augment.coxph.Rd | 6 +++--- man/augment.decomposed.ts.Rd | 4 ++-- man/augment.drc.Rd | 4 ++-- man/augment.factanal.Rd | 4 ++-- man/augment.felm.Rd | 4 ++-- man/augment.fixest.Rd | 2 +- man/augment.glm.Rd | 2 +- man/augment.htest.Rd | 4 ++-- man/augment.ivreg.Rd | 4 ++-- man/augment.kmeans.Rd | 12 +++++++----- man/augment.lm.Rd | 6 +++--- man/augment.lmRob.Rd | 2 +- man/augment.loess.Rd | 6 +++--- man/augment.mfx.Rd | 2 +- man/augment.mjoint.Rd | 2 +- man/augment.nlrq.Rd | 4 ++-- man/augment.nls.Rd | 4 ++-- man/augment.pam.Rd | 13 +++++++------ man/augment.plm.Rd | 4 ++-- man/augment.poLCA.Rd | 4 ++-- man/augment.polr.Rd | 4 ++-- man/augment.prcomp.Rd | 4 ++-- man/augment.rlm.Rd | 2 +- man/augment.rma.Rd | 2 +- man/augment.robustbase.glmrob.Rd | 2 +- man/augment.robustbase.lmrob.Rd | 2 +- man/augment.rq.Rd | 2 +- man/augment.rqs.Rd | 2 +- man/augment.sarlm.Rd | 4 ++-- man/augment.smooth.spline.Rd | 4 ++-- man/augment.speedlm.Rd | 2 +- man/augment.stl.Rd | 4 ++-- man/augment.survreg.Rd | 4 ++-- man/durbinWatsonTest_tidiers.Rd | 8 ++++---- man/glance.Arima.Rd | 2 +- man/glance.Gam.Rd | 4 ++-- man/glance.Mclust.Rd | 2 +- man/glance.aareg.Rd | 4 ++-- man/glance.aov.Rd | 4 ++-- man/glance.betamfx.Rd | 2 +- man/glance.betareg.Rd | 4 ++-- man/glance.biglm.Rd | 4 ++-- man/glance.binDesign.Rd | 4 ++-- man/glance.cch.Rd | 4 ++-- man/glance.clm.Rd | 4 ++-- man/glance.clmm.Rd | 4 ++-- man/glance.coxph.Rd | 4 ++-- man/glance.cv.glmnet.Rd | 4 ++-- man/glance.drc.Rd | 4 ++-- man/glance.ergm.Rd | 2 +- man/glance.factanal.Rd | 4 ++-- man/glance.felm.Rd | 2 +- man/glance.fitdistr.Rd | 4 ++-- man/glance.garch.Rd | 4 ++-- man/glance.geeglm.Rd | 4 ++-- man/glance.glm.Rd | 2 +- man/glance.glmRob.Rd | 2 +- man/glance.glmnet.Rd | 4 ++-- man/glance.gmm.Rd | 4 ++-- man/glance.ivreg.Rd | 4 ++-- man/glance.kmeans.Rd | 12 +++++++----- man/glance.lavaan.Rd | 4 ++-- man/glance.lm.Rd | 4 ++-- man/glance.lmRob.Rd | 2 +- man/glance.lmodel2.Rd | 4 ++-- man/glance.mfx.Rd | 2 +- man/glance.mjoint.Rd | 4 ++-- man/glance.muhaz.Rd | 4 ++-- man/glance.multinom.Rd | 4 ++-- man/glance.nlrq.Rd | 4 ++-- man/glance.nls.Rd | 4 ++-- man/glance.orcutt.Rd | 4 ++-- man/glance.pam.Rd | 13 +++++++------ man/glance.plm.Rd | 4 ++-- man/glance.poLCA.Rd | 4 ++-- man/glance.polr.Rd | 4 ++-- man/glance.pyears.Rd | 4 ++-- man/glance.ridgelm.Rd | 4 ++-- man/glance.rlm.Rd | 4 ++-- man/glance.rma.Rd | 2 +- man/glance.robustbase.lmrob.Rd | 2 +- man/glance.rq.Rd | 4 ++-- man/glance.sarlm.Rd | 4 ++-- man/glance.smooth.spline.Rd | 4 ++-- man/glance.speedglm.Rd | 2 +- man/glance.speedlm.Rd | 2 +- man/glance.survdiff.Rd | 4 ++-- man/glance.survexp.Rd | 4 ++-- man/glance.survfit.Rd | 4 ++-- man/glance.survreg.Rd | 4 ++-- man/glance.svyglm.Rd | 2 +- man/glance.svyolr.Rd | 4 ++-- man/glance_optim.Rd | 4 ++-- man/metafor_tidiers.Rd | 2 +- man/sparse_tidiers.Rd | 2 +- man/tidy.Arima.Rd | 2 +- man/tidy.Gam.Rd | 4 ++-- man/tidy.Kendall.Rd | 4 ++-- man/tidy.Mclust.Rd | 4 ++-- man/tidy.TukeyHSD.Rd | 4 ++-- man/tidy.aareg.Rd | 4 ++-- man/tidy.acf.Rd | 4 ++-- man/tidy.anova.Rd | 4 ++-- man/tidy.aov.Rd | 4 ++-- man/tidy.aovlist.Rd | 4 ++-- man/tidy.betamfx.Rd | 2 +- man/tidy.betareg.Rd | 4 ++-- man/tidy.biglm.Rd | 4 ++-- man/tidy.binDesign.Rd | 4 ++-- man/tidy.binWidth.Rd | 4 ++-- man/tidy.boot.Rd | 4 ++-- man/tidy.btergm.Rd | 4 ++-- man/tidy.cch.Rd | 4 ++-- man/tidy.cld.Rd | 4 ++-- man/tidy.clm.Rd | 4 ++-- man/tidy.clmm.Rd | 4 ++-- man/tidy.coeftest.Rd | 4 ++-- man/tidy.confint.glht.Rd | 4 ++-- man/tidy.confusionMatrix.Rd | 4 ++-- man/tidy.coxph.Rd | 4 ++-- man/tidy.cv.glmnet.Rd | 4 ++-- man/tidy.density.Rd | 4 ++-- man/tidy.dist.Rd | 17 ++++++++++------- man/tidy.drc.Rd | 4 ++-- man/tidy.emmGrid.Rd | 2 +- man/tidy.epi.2by2.Rd | 4 ++-- man/tidy.ergm.Rd | 2 +- man/tidy.factanal.Rd | 4 ++-- man/tidy.felm.Rd | 4 ++-- man/tidy.fitdistr.Rd | 4 ++-- man/tidy.fixest.Rd | 2 +- man/tidy.ftable.Rd | 4 ++-- man/tidy.gamlss.Rd | 2 +- man/tidy.garch.Rd | 4 ++-- man/tidy.geeglm.Rd | 4 ++-- man/tidy.glht.Rd | 4 ++-- man/tidy.glm.Rd | 2 +- man/tidy.glmRob.Rd | 2 +- man/tidy.glmnet.Rd | 4 ++-- man/tidy.gmm.Rd | 4 ++-- man/tidy.htest.Rd | 8 ++++---- man/tidy.ivreg.Rd | 4 ++-- man/tidy.kappa.Rd | 4 ++-- man/tidy.kde.Rd | 4 ++-- man/tidy.kmeans.Rd | 12 +++++++----- man/tidy.lavaan.Rd | 2 +- man/tidy.lm.Rd | 4 ++-- man/tidy.lm.beta.Rd | 2 +- man/tidy.lmRob.Rd | 2 +- man/tidy.lmodel2.Rd | 4 ++-- man/tidy.lsmobj.Rd | 2 +- man/tidy.manova.Rd | 2 +- man/tidy.map.Rd | 4 ++-- man/tidy.mediate.Rd | 4 ++-- man/tidy.mfx.Rd | 4 ++-- man/tidy.mjoint.Rd | 4 ++-- man/tidy.mle2.Rd | 4 ++-- man/tidy.mlm.Rd | 4 ++-- man/tidy.muhaz.Rd | 4 ++-- man/tidy.multinom.Rd | 4 ++-- man/tidy.nlrq.Rd | 4 ++-- man/tidy.nls.Rd | 4 ++-- man/tidy.orcutt.Rd | 2 +- man/tidy.pairwise.htest.Rd | 16 +++++++++------- man/tidy.pam.Rd | 13 +++++++------ man/tidy.plm.Rd | 4 ++-- man/tidy.poLCA.Rd | 4 ++-- man/tidy.polr.Rd | 4 ++-- man/tidy.power.htest.Rd | 2 +- man/tidy.prcomp.Rd | 4 ++-- man/tidy.pyears.Rd | 4 ++-- man/tidy.rcorr.Rd | 4 ++-- man/tidy.ref.grid.Rd | 2 +- man/tidy.regsubsets.Rd | 4 ++-- man/tidy.ridgelm.Rd | 4 ++-- man/tidy.rlm.Rd | 2 +- man/tidy.robustbase.glmrob.Rd | 2 +- man/tidy.robustbase.lmrob.Rd | 2 +- man/tidy.roc.Rd | 4 ++-- man/tidy.rq.Rd | 2 +- man/tidy.rqs.Rd | 2 +- man/tidy.sarlm.Rd | 4 ++-- man/tidy.spec.Rd | 4 ++-- man/tidy.speedglm.Rd | 2 +- man/tidy.speedlm.Rd | 2 +- man/tidy.summary.glht.Rd | 4 ++-- man/tidy.summary_emm.Rd | 2 +- man/tidy.survdiff.Rd | 4 ++-- man/tidy.survexp.Rd | 4 ++-- man/tidy.survfit.Rd | 4 ++-- man/tidy.survreg.Rd | 4 ++-- man/tidy.svyglm.Rd | 2 +- man/tidy.svyolr.Rd | 4 ++-- man/tidy.systemfit.Rd | 4 ++-- man/tidy.table.Rd | 2 +- man/tidy.ts.Rd | 4 ++-- man/tidy.zoo.Rd | 4 ++-- man/tidy_irlba.Rd | 13 ++++++++----- man/tidy_optim.Rd | 4 ++-- man/tidy_svd.Rd | 11 +++++++---- man/tidy_xyz.Rd | 4 ++-- 205 files changed, 418 insertions(+), 398 deletions(-) diff --git a/man/augment.Mclust.Rd b/man/augment.Mclust.Rd index 037e36aac..1291c55e8 100644 --- a/man/augment.Mclust.Rd +++ b/man/augment.Mclust.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -94,7 +94,7 @@ augment(m, points) glance(m) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} +\code{\link[=augment]{augment()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} Other mclust tidiers: \code{\link{tidy.Mclust}()} diff --git a/man/augment.betamfx.Rd b/man/augment.betamfx.Rd index 1865f0e06..f77f87682 100644 --- a/man/augment.betamfx.Rd +++ b/man/augment.betamfx.Rd @@ -44,7 +44,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.betareg.Rd b/man/augment.betareg.Rd index 0b9093c5d..1090f6c70 100644 --- a/man/augment.betareg.Rd +++ b/man/augment.betareg.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -109,7 +109,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=augment]{augment()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/augment.clm.Rd b/man/augment.clm.Rd index 20f50af78..985b61519 100644 --- a/man/augment.clm.Rd +++ b/man/augment.clm.Rd @@ -37,7 +37,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -99,7 +99,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict]{ordinal::predict.clm()}} +\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:predict]{ordinal::predict.clm()}} Other ordinal tidiers: \code{\link{augment.polr}()}, diff --git a/man/augment.coxph.Rd b/man/augment.coxph.Rd index 4ab67cf9c..0a009521d 100644 --- a/man/augment.coxph.Rd +++ b/man/augment.coxph.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -95,7 +95,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. } \examples{ @@ -143,7 +143,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + \seealso{ \link[stats:na.action]{stats::na.action} -\code{\link[=reexports]{augment()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=augment]{augment()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{glance.coxph}()}, diff --git a/man/augment.decomposed.ts.Rd b/man/augment.decomposed.ts.Rd index 2694ccce2..dcf18fb97 100644 --- a/man/augment.decomposed.ts.Rd +++ b/man/augment.decomposed.ts.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -123,7 +123,7 @@ ggplot(decomps) + )) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:decompose]{stats::decompose()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:decompose]{stats::decompose()}} Other decompose tidiers: \code{\link{augment.stl}()} diff --git a/man/augment.drc.Rd b/man/augment.drc.Rd index a35c87696..4dddf2eb8 100644 --- a/man/augment.drc.Rd +++ b/man/augment.drc.Rd @@ -47,7 +47,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -106,7 +106,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=augment]{augment()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{glance.drc}()}, diff --git a/man/augment.factanal.Rd b/man/augment.factanal.Rd index f6e1b853d..277127d87 100644 --- a/man/augment.factanal.Rd +++ b/man/augment.factanal.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ We are in the process of defining behaviors for models fit with various missing at this time. } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{glance.factanal}()}, diff --git a/man/augment.felm.Rd b/man/augment.felm.Rd index 1736c51ce..19587e8ae 100644 --- a/man/augment.felm.Rd +++ b/man/augment.felm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -99,7 +99,7 @@ augment(result_felm) glance(result_felm) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[lfe:felm]{lfe::felm()}} +\code{\link[=augment]{augment()}}, \code{\link[lfe:felm]{lfe::felm()}} Other felm tidiers: \code{\link{tidy.felm}()} diff --git a/man/augment.fixest.Rd b/man/augment.fixest.Rd index f7b8875fc..80b806a03 100644 --- a/man/augment.fixest.Rd +++ b/man/augment.fixest.Rd @@ -103,7 +103,7 @@ augment(gravity_pois, trade) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}} +\code{\link[=augment]{augment()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}} Other fixest tidiers: \code{\link{tidy.fixest}()} diff --git a/man/augment.glm.Rd b/man/augment.glm.Rd index 3044b9a44..39554abba 100644 --- a/man/augment.glm.Rd +++ b/man/augment.glm.Rd @@ -46,7 +46,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.htest.Rd b/man/augment.htest.Rd index dd7ac3ef0..23ffd4a18 100644 --- a/man/augment.htest.Rd +++ b/man/augment.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -83,7 +83,7 @@ tidy(chit) augment(chit) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} Other htest tidiers: \code{\link{tidy.htest}()}, diff --git a/man/augment.ivreg.Rd b/man/augment.ivreg.Rd index 16e4a326b..5352ab4c5 100644 --- a/man/augment.ivreg.Rd +++ b/man/augment.ivreg.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -96,7 +96,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=augment]{augment()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{glance.ivreg}()}, diff --git a/man/augment.kmeans.Rd b/man/augment.kmeans.Rd index 7143c6b41..277493b4e 100644 --- a/man/augment.kmeans.Rd +++ b/man/augment.kmeans.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,17 +71,19 @@ missing at this time. library(cluster) library(dplyr) -x <- iris \%>\% - select(-Species) +library(modeldata) +data(hpc_data) -fit <- pam(x, k = 3) +x <- hpc_data[, 2:5] + +fit <- pam(x, k = 4) tidy(fit) glance(fit) augment(fit, x) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{glance.kmeans}()}, diff --git a/man/augment.lm.Rd b/man/augment.lm.Rd index 05bd804bb..4d68433e2 100644 --- a/man/augment.lm.Rd +++ b/man/augment.lm.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -82,7 +82,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. Some unusual \code{lm} objects, such as \code{rlm} from MASS, may omit @@ -146,7 +146,7 @@ tidy(result) \seealso{ \link[stats:na.action]{stats::na.action} -\code{\link[=reexports]{augment()}}, \code{\link[stats:predict.lm]{stats::predict.lm()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:predict.lm]{stats::predict.lm()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/augment.lmRob.Rd b/man/augment.lmRob.Rd index d55af84c4..b14fbfe96 100644 --- a/man/augment.lmRob.Rd +++ b/man/augment.lmRob.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.loess.Rd b/man/augment.loess.Rd index a2dbe72a9..633d6d2c0 100644 --- a/man/augment.loess.Rd +++ b/man/augment.loess.Rd @@ -33,7 +33,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ entirely from the augmented data frame. When the modeling was performed with \code{na.action = "na.exclude"}, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data -is not provided to \code{\link[=reexports]{augment()}} and \code{na.action = "na.exclude"}, a +is not provided to \code{\link[=augment]{augment()}} and \code{na.action = "na.exclude"}, a warning is raised and the incomplete rows are dropped. Note that \code{loess} objects by default will not predict on data @@ -80,7 +80,7 @@ augment(lo, newdata = head(mtcars)) \seealso{ \link[stats:na.action]{stats::na.action} -\code{\link[=reexports]{augment()}}, \code{\link[stats:loess]{stats::loess()}}, \code{\link[stats:predict.loess]{stats::predict.loess()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:loess]{stats::loess()}}, \code{\link[stats:predict.loess]{stats::predict.loess()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/augment.mfx.Rd b/man/augment.mfx.Rd index d83fcecc8..261271781 100644 --- a/man/augment.mfx.Rd +++ b/man/augment.mfx.Rd @@ -91,7 +91,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.mjoint.Rd b/man/augment.mjoint.Rd index a85460e69..78c9cfa75 100644 --- a/man/augment.mjoint.Rd +++ b/man/augment.mjoint.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.nlrq.Rd b/man/augment.nlrq.Rd index d8638df5f..2d98b9ab1 100644 --- a/man/augment.nlrq.Rd +++ b/man/augment.nlrq.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=augment]{augment()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.rqs}()}, diff --git a/man/augment.nls.Rd b/man/augment.nls.Rd index 9b12439ca..c1ff935f3 100644 --- a/man/augment.nls.Rd +++ b/man/augment.nls.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -93,7 +93,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:predict.nls]{stats::predict.nls()}} +\link{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:predict.nls]{stats::predict.nls()}} Other nls tidiers: \code{\link{glance.nls}()}, diff --git a/man/augment.pam.Rd b/man/augment.pam.Rd index 662c125dc..1e254fa4d 100644 --- a/man/augment.pam.Rd +++ b/man/augment.pam.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,22 +71,23 @@ missing at this time. library(dplyr) library(ggplot2) library(cluster) +library(modeldata) +data(hpc_data) -x <- iris \%>\% - select(-Species) -p <- pam(x, k = 3) +x <- hpc_data[, 2:5] +p <- pam(x, k = 4) tidy(p) glance(p) augment(p, x) augment(p, x) \%>\% - ggplot(aes(Sepal.Length, Sepal.Width)) + + ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=augment]{augment()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{glance.pam}()}, diff --git a/man/augment.plm.Rd b/man/augment.plm.Rd index 55e0ea5bf..e21cb846f 100644 --- a/man/augment.plm.Rd +++ b/man/augment.plm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[plm:plm]{plm::plm()}} +\code{\link[=augment]{augment()}}, \code{\link[plm:plm]{plm::plm()}} Other plm tidiers: \code{\link{glance.plm}()}, diff --git a/man/augment.poLCA.Rd b/man/augment.poLCA.Rd index 4364eb59d..ea93dfb1f 100644 --- a/man/augment.poLCA.Rd +++ b/man/augment.poLCA.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -126,7 +126,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=augment]{augment()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{glance.poLCA}()}, diff --git a/man/augment.polr.Rd b/man/augment.polr.Rd index c5e43010b..478acb46e 100644 --- a/man/augment.polr.Rd +++ b/man/augment.polr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -97,7 +97,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[MASS:polr]{MASS::polr()}} +\code{\link[=tidy]{tidy()}}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/augment.prcomp.Rd b/man/augment.prcomp.Rd index 8cd2f61e8..5bedb66f1 100644 --- a/man/augment.prcomp.Rd +++ b/man/augment.prcomp.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ We are in the process of defining behaviors for models fit with various missing at this time. } \seealso{ -\code{\link[stats:prcomp]{stats::prcomp()}}, \link[=tidy_svd]{svd_tidiers} +\code{\link[stats:prcomp]{stats::prcomp()}}, \link{svd_tidiers} Other svd tidiers: \code{\link{tidy.prcomp}()}, diff --git a/man/augment.rlm.Rd b/man/augment.rlm.Rd index 398cebfa0..dedb3e3e7 100644 --- a/man/augment.rlm.Rd +++ b/man/augment.rlm.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.rma.Rd b/man/augment.rma.Rd index dda656717..d92e20511 100644 --- a/man/augment.rma.Rd +++ b/man/augment.rma.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.robustbase.glmrob.Rd b/man/augment.robustbase.glmrob.Rd index b5344ffd2..d825dd450 100644 --- a/man/augment.robustbase.glmrob.Rd +++ b/man/augment.robustbase.glmrob.Rd @@ -50,7 +50,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.robustbase.lmrob.Rd b/man/augment.robustbase.lmrob.Rd index be98ab7dc..3bb84e962 100644 --- a/man/augment.robustbase.lmrob.Rd +++ b/man/augment.robustbase.lmrob.Rd @@ -32,7 +32,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.rq.Rd b/man/augment.rq.Rd index a868086dc..5e6aa668f 100644 --- a/man/augment.rq.Rd +++ b/man/augment.rq.Rd @@ -93,7 +93,7 @@ columns \code{.conf.low} and \code{.conf.high}. Does not provide confidence intervals when data is specified via the \code{newdata} argument. } \seealso{ -\link[=reexports]{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rq()}} +\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/augment.rqs.Rd b/man/augment.rqs.Rd index 63b71fe75..db1abf691 100644 --- a/man/augment.rqs.Rd +++ b/man/augment.rqs.Rd @@ -93,7 +93,7 @@ columns \code{.conf.low} and \code{.conf.high}. Does not provide confidence intervals when data is specified via the \code{newdata} argument. } \seealso{ -\link[=reexports]{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rqs()}} +\link{augment}, \code{\link[quantreg:rq]{quantreg::rq()}}, \code{\link[quantreg:predict.rq]{quantreg::predict.rqs()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/augment.sarlm.Rd b/man/augment.sarlm.Rd index bd43fa3d4..eb5754c57 100644 --- a/man/augment.sarlm.Rd +++ b/man/augment.sarlm.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -99,7 +99,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=reexports]{augment()}} +\code{\link[=augment]{augment()}} Other spatialreg tidiers: \code{\link{glance.sarlm}()}, diff --git a/man/augment.smooth.spline.Rd b/man/augment.smooth.spline.Rd index 77b28a635..ce645403b 100644 --- a/man/augment.smooth.spline.Rd +++ b/man/augment.smooth.spline.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -48,7 +48,7 @@ ggplot(augment(spl, mtcars), aes(wt, mpg)) + geom_line(aes(y = .fitted)) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}}, +\code{\link[=augment]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}}, \code{\link[stats:predict.smooth.spline]{stats::predict.smooth.spline()}} Other smoothing spline tidiers: diff --git a/man/augment.speedlm.Rd b/man/augment.speedlm.Rd index 1bc56a0d9..30c67f3f4 100644 --- a/man/augment.speedlm.Rd +++ b/man/augment.speedlm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/augment.stl.Rd b/man/augment.stl.Rd index 750ec65be..ad7fb5ae1 100644 --- a/man/augment.stl.Rd +++ b/man/augment.stl.Rd @@ -20,7 +20,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -76,7 +76,7 @@ We are in the process of defining behaviors for models fit with various missing at this time. } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:stl]{stats::stl()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:stl]{stats::stl()}} Other decompose tidiers: \code{\link{augment.decomposed.ts}()} diff --git a/man/augment.survreg.Rd b/man/augment.survreg.Rd index bcdca028a..d0eb36db3 100644 --- a/man/augment.survreg.Rd +++ b/man/augment.survreg.Rd @@ -45,7 +45,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -111,7 +111,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=augment]{augment()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{glance.survreg}()}, diff --git a/man/durbinWatsonTest_tidiers.Rd b/man/durbinWatsonTest_tidiers.Rd index 45901cc3a..f56bfdfa3 100644 --- a/man/durbinWatsonTest_tidiers.Rd +++ b/man/durbinWatsonTest_tidiers.Rd @@ -20,13 +20,13 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \description{ -For models that have only a single component, the \code{\link[=reexports]{tidy()}} and -\code{\link[=reexports]{glance()}} methods are identical. Please see the documentation for both +For models that have only a single component, the \code{\link[=tidy]{tidy()}} and +\code{\link[=glance]{glance()}} methods are identical. Please see the documentation for both of those methods. } \examples{ @@ -36,7 +36,7 @@ tidy(dw) glance(dw) # same output for all durbinWatsonTests } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[=reexports]{glance()}}, \code{\link[car:durbinWatsonTest]{car::durbinWatsonTest()}} +\code{\link[=tidy]{tidy()}}, \code{\link[=glance]{glance()}}, \code{\link[car:durbinWatsonTest]{car::durbinWatsonTest()}} } \concept{car tidiers} \value{ diff --git a/man/glance.Arima.Rd b/man/glance.Arima.Rd index f996192b8..ef852c3c4 100644 --- a/man/glance.Arima.Rd +++ b/man/glance.Arima.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.Gam.Rd b/man/glance.Gam.Rd index e9b0fa936..354a4517a 100644 --- a/man/glance.Gam.Rd +++ b/man/glance.Gam.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -48,7 +48,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}} +\code{\link[=glance]{glance()}}, \code{\link[mgcv:gam]{mgcv::gam()}} Other mgcv tidiers: \code{\link{tidy.gam}()} diff --git a/man/glance.Mclust.Rd b/man/glance.Mclust.Rd index 7bb3665ea..02b56a761 100644 --- a/man/glance.Mclust.Rd +++ b/man/glance.Mclust.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.aareg.Rd b/man/glance.aareg.Rd index cbb39712c..7d42bbbba 100644 --- a/man/glance.aareg.Rd +++ b/man/glance.aareg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ afit <- aareg( tidy(afit) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:aareg]{survival::aareg()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:aareg]{survival::aareg()}} Other aareg tidiers: \code{\link{tidy.aareg}()} diff --git a/man/glance.aov.Rd b/man/glance.aov.Rd index 4971d15bc..375758482 100644 --- a/man/glance.aov.Rd +++ b/man/glance.aov.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -50,7 +50,7 @@ a <- aov(mpg ~ wt + qsec + disp, mtcars) tidy(a) } \seealso{ -\code{\link[=reexports]{glance()}} +\code{\link[=glance]{glance()}} Other anova tidiers: \code{\link{tidy.TukeyHSD}()}, diff --git a/man/glance.betamfx.Rd b/man/glance.betamfx.Rd index 18c0fb6be..073da0918 100644 --- a/man/glance.betamfx.Rd +++ b/man/glance.betamfx.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.betareg.Rd b/man/glance.betareg.Rd index 77d31cc86..afd42dadc 100644 --- a/man/glance.betareg.Rd +++ b/man/glance.betareg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=glance]{glance()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with exactly one row and columns: diff --git a/man/glance.biglm.Rd b/man/glance.biglm.Rd index 4f3830b19..33f9e51b7 100644 --- a/man/glance.biglm.Rd +++ b/man/glance.biglm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ glance(bgfit) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} +\code{\link[=glance]{glance()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} Other biglm tidiers: \code{\link{tidy.biglm}()} diff --git a/man/glance.binDesign.Rd b/man/glance.binDesign.Rd index 2910b446c..0cff02655 100644 --- a/man/glance.binDesign.Rd +++ b/man/glance.binDesign.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ ggplot(tidy(des), aes(n, power)) + geom_line() } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} +\code{\link[=glance]{glance()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} Other bingroup tidiers: \code{\link{tidy.binDesign}()}, diff --git a/man/glance.cch.Rd b/man/glance.cch.Rd index 9e884a3a8..70422201c 100644 --- a/man/glance.cch.Rd +++ b/man/glance.cch.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -69,7 +69,7 @@ ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:cch]{survival::cch()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:cch]{survival::cch()}} Other cch tidiers: \code{\link{glance.survfit}()}, diff --git a/man/glance.clm.Rd b/man/glance.clm.Rd index a051b91b6..46605e0cb 100644 --- a/man/glance.clm.Rd +++ b/man/glance.clm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}} +\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.clmm.Rd b/man/glance.clmm.Rd index 0c450403b..0f322873f 100644 --- a/man/glance.clmm.Rd +++ b/man/glance.clmm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link[=reexports]{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}} +\link{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.coxph.Rd b/man/glance.coxph.Rd index ec1b94159..21f0b8840 100644 --- a/man/glance.coxph.Rd +++ b/man/glance.coxph.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -82,7 +82,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{augment.coxph}()}, diff --git a/man/glance.cv.glmnet.Rd b/man/glance.cv.glmnet.Rd index 5a8fd595b..20abf0772 100644 --- a/man/glance.cv.glmnet.Rd +++ b/man/glance.cv.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -93,7 +93,7 @@ ggplot(tidied, aes(lambda, estimate, group = term)) + geom_vline(xintercept = glance_cv$lambda.1se, lty = 2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} +\code{\link[=glance]{glance()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} Other glmnet tidiers: \code{\link{glance.glmnet}()}, diff --git a/man/glance.drc.Rd b/man/glance.drc.Rd index 2c69ae09f..90d8df8ef 100644 --- a/man/glance.drc.Rd +++ b/man/glance.drc.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=glance]{glance()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{augment.drc}()}, diff --git a/man/glance.ergm.Rd b/man/glance.ergm.Rd index b31099f53..389572bd6 100644 --- a/man/glance.ergm.Rd +++ b/man/glance.ergm.Rd @@ -55,7 +55,7 @@ that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:summary.ergm]{ergm::summary.ergm()}} +\code{\link[=glance]{glance()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:summary.ergm]{ergm::summary.ergm()}} Other ergm tidiers: \code{\link{tidy.ergm}()} diff --git a/man/glance.factanal.Rd b/man/glance.factanal.Rd index fb18398f5..30107b5fa 100644 --- a/man/glance.factanal.Rd +++ b/man/glance.factanal.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -73,7 +73,7 @@ augment(fit1, data = m2) augment(fit2, data = m2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=glance]{glance()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{augment.factanal}()}, diff --git a/man/glance.felm.Rd b/man/glance.felm.Rd index 6937baf88..1b2a5d032 100644 --- a/man/glance.felm.Rd +++ b/man/glance.felm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.fitdistr.Rd b/man/glance.fitdistr.Rd index a0acf9c45..5d7ecb263 100644 --- a/man/glance.fitdistr.Rd +++ b/man/glance.fitdistr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ tidy(fit) glance(fit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} +\code{\link[=tidy]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} Other fitdistr tidiers: \code{\link{tidy.fitdistr}()} diff --git a/man/glance.garch.Rd b/man/glance.garch.Rd index c686a1b70..bed5d0482 100644 --- a/man/glance.garch.Rd +++ b/man/glance.garch.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -32,7 +32,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[tseries:garch]{tseries::garch()}}, [] +\code{\link[=glance]{glance()}}, \code{\link[tseries:garch]{tseries::garch()}}, [] Other garch tidiers: \code{\link{tidy.garch}()} diff --git a/man/glance.geeglm.Rd b/man/glance.geeglm.Rd index 12adac491..7a51e5a5b 100644 --- a/man/glance.geeglm.Rd +++ b/man/glance.geeglm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(geefit) tidy(geefit, conf.int = TRUE) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} +\code{\link[=glance]{glance()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} } \concept{geepack tidiers} \value{ diff --git a/man/glance.glm.Rd b/man/glance.glm.Rd index bd3dd403c..0b5134bbf 100644 --- a/man/glance.glm.Rd +++ b/man/glance.glm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.glmRob.Rd b/man/glance.glmRob.Rd index 52bbb4375..15f386bce 100644 --- a/man/glance.glmRob.Rd +++ b/man/glance.glmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.glmnet.Rd b/man/glance.glmnet.Rd index 3e1d0b10b..1c3b226ba 100644 --- a/man/glance.glmnet.Rd +++ b/man/glance.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,7 +71,7 @@ fit2 <- glmnet(x, g2, family = "binomial") tidy(fit2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} +\code{\link[=glance]{glance()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/glance.gmm.Rd b/man/glance.gmm.Rd index f7e4ed155..338888b41 100644 --- a/man/glance.gmm.Rd +++ b/man/glance.gmm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -105,7 +105,7 @@ td2 \%>\% geom_vline(xintercept = 0, color = "red", lty = 2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[gmm:gmm]{gmm::gmm()}} +\code{\link[=glance]{glance()}}, \code{\link[gmm:gmm]{gmm::gmm()}} Other gmm tidiers: \code{\link{tidy.gmm}()} diff --git a/man/glance.ivreg.Rd b/man/glance.ivreg.Rd index 3074fca46..2e98f2e52 100644 --- a/man/glance.ivreg.Rd +++ b/man/glance.ivreg.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=glance]{glance()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{augment.ivreg}()}, diff --git a/man/glance.kmeans.Rd b/man/glance.kmeans.Rd index f0b1ccfd4..fc4f255ab 100644 --- a/man/glance.kmeans.Rd +++ b/man/glance.kmeans.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -44,17 +44,19 @@ of the appropriate type. library(cluster) library(dplyr) -x <- iris \%>\% - select(-Species) +library(modeldata) +data(hpc_data) -fit <- pam(x, k = 3) +x <- hpc_data[, 2:5] + +fit <- pam(x, k = 4) tidy(fit) glance(fit) augment(fit, x) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=glance]{glance()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{augment.kmeans}()}, diff --git a/man/glance.lavaan.Rd b/man/glance.lavaan.Rd index e1e9656e7..0f4167482 100644 --- a/man/glance.lavaan.Rd +++ b/man/glance.lavaan.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -80,7 +80,7 @@ glance(cfa.fit) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, +\code{\link[=glance]{glance()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, \code{\link[lavaan:fitMeasures]{lavaan::fitmeasures()}} Other lavaan tidiers: diff --git a/man/glance.lm.Rd b/man/glance.lm.Rd index f15f1fe4a..22e4844c5 100644 --- a/man/glance.lm.Rd +++ b/man/glance.lm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -92,7 +92,7 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\code{\link[=reexports]{glance()}} +\code{\link[=glance]{glance()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/glance.lmRob.Rd b/man/glance.lmRob.Rd index 256c5df5d..2ffb77fb3 100644 --- a/man/glance.lmRob.Rd +++ b/man/glance.lmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.lmodel2.Rd b/man/glance.lmodel2.Rd index 3f812d043..eba5790ec 100644 --- a/man/glance.lmodel2.Rd +++ b/man/glance.lmodel2.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(tidy(Ex2.res), aes(estimate, term, color = method)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} +\code{\link[=glance]{glance()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} Other lmodel2 tidiers: \code{\link{tidy.lmodel2}()} diff --git a/man/glance.mfx.Rd b/man/glance.mfx.Rd index 44eef64da..dfec4492a 100644 --- a/man/glance.mfx.Rd +++ b/man/glance.mfx.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.mjoint.Rd b/man/glance.mjoint.Rd index 4c1a1b705..b202c92bb 100644 --- a/man/glance.mjoint.Rd +++ b/man/glance.mjoint.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,7 @@ glance(fit) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}} +\code{\link[=glance]{glance()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}} Other mjoint tidiers: \code{\link{tidy.mjoint}()} diff --git a/man/glance.muhaz.Rd b/man/glance.muhaz.Rd index 266a082c7..40e92be23 100644 --- a/man/glance.muhaz.Rd +++ b/man/glance.muhaz.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ tidy(x) glance(x) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} +\code{\link[=glance]{glance()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} Other muhaz tidiers: \code{\link{tidy.muhaz}()} diff --git a/man/glance.multinom.Rd b/man/glance.multinom.Rd index 34ace308d..0c4ce9532 100644 --- a/man/glance.multinom.Rd +++ b/man/glance.multinom.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit.gear) glance(fit.gear) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[nnet:multinom]{nnet::multinom()}} +\code{\link[=glance]{glance()}}, \code{\link[nnet:multinom]{nnet::multinom()}} Other multinom tidiers: \code{\link{tidy.multinom}()} diff --git a/man/glance.nlrq.Rd b/man/glance.nlrq.Rd index d2776af55..7e2560be8 100644 --- a/man/glance.nlrq.Rd +++ b/man/glance.nlrq.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -40,7 +40,7 @@ that no longer have a well-defined value are filled in with an \code{NA} of the appropriate type. } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=glance]{glance()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/glance.nls.Rd b/man/glance.nls.Rd index f205f214a..136553a1c 100644 --- a/man/glance.nls.Rd +++ b/man/glance.nls.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -57,7 +57,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}} +\link{tidy}, \code{\link[stats:nls]{stats::nls()}} Other nls tidiers: \code{\link{augment.nls}()}, diff --git a/man/glance.orcutt.Rd b/man/glance.orcutt.Rd index 2fcffa07f..358a5e40f 100644 --- a/man/glance.orcutt.Rd +++ b/man/glance.orcutt.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(co) glance(co) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[orcutt:cochrane.orcutt]{orcutt::cochrane.orcutt()}} +\code{\link[=glance]{glance()}}, \code{\link[orcutt:cochrane.orcutt]{orcutt::cochrane.orcutt()}} Other orcutt tidiers: \code{\link{tidy.orcutt}()} diff --git a/man/glance.pam.Rd b/man/glance.pam.Rd index 529250167..b79f3e53a 100644 --- a/man/glance.pam.Rd +++ b/man/glance.pam.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -44,22 +44,23 @@ of the appropriate type. library(dplyr) library(ggplot2) library(cluster) +library(modeldata) +data(hpc_data) -x <- iris \%>\% - select(-Species) -p <- pam(x, k = 3) +x <- hpc_data[, 2:5] +p <- pam(x, k = 4) tidy(p) glance(p) augment(p, x) augment(p, x) \%>\% - ggplot(aes(Sepal.Length, Sepal.Width)) + + ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=glance]{glance()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{augment.pam}()}, diff --git a/man/glance.plm.Rd b/man/glance.plm.Rd index 422fc8528..efe06312e 100644 --- a/man/glance.plm.Rd +++ b/man/glance.plm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[plm:plm]{plm::plm()}} +\code{\link[=glance]{glance()}}, \code{\link[plm:plm]{plm::plm()}} Other plm tidiers: \code{\link{augment.plm}()}, diff --git a/man/glance.poLCA.Rd b/man/glance.poLCA.Rd index 8ab80b2cd..a53a6cf13 100644 --- a/man/glance.poLCA.Rd +++ b/man/glance.poLCA.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -88,7 +88,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=glance]{glance()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{augment.poLCA}()}, diff --git a/man/glance.polr.Rd b/man/glance.polr.Rd index 2e51e696d..18fb43798 100644 --- a/man/glance.polr.Rd +++ b/man/glance.polr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\link[=reexports]{tidy}, \code{\link[MASS:polr]{MASS::polr()}} +\link{tidy}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance.pyears.Rd b/man/glance.pyears.Rd index a4bdc82be..c004c8c28 100644 --- a/man/glance.pyears.Rd +++ b/man/glance.pyears.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -60,7 +60,7 @@ tidy(pfit2) glance(pfit2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:pyears]{survival::pyears()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:pyears]{survival::pyears()}} Other pyears tidiers: \code{\link{tidy.pyears}()} diff --git a/man/glance.ridgelm.Rd b/man/glance.ridgelm.Rd index 09c4d2666..3329292a4 100644 --- a/man/glance.ridgelm.Rd +++ b/man/glance.ridgelm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -68,7 +68,7 @@ ggplot(td2, aes(lambda, GCV)) + geom_vline(xintercept = g2$lambdaGCV, col = "red", lty = 2) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[MASS:lm.ridge]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} +\code{\link[=glance]{glance()}}, \code{\link[MASS:lm.ridge]{MASS::select.ridgelm()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} Other ridgelm tidiers: \code{\link{tidy.ridgelm}()} diff --git a/man/glance.rlm.Rd b/man/glance.rlm.Rd index e7518d052..36f180fff 100644 --- a/man/glance.rlm.Rd +++ b/man/glance.rlm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ augment(r) glance(r) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[MASS:rlm]{MASS::rlm()}} +\code{\link[=glance]{glance()}}, \code{\link[MASS:rlm]{MASS::rlm()}} Other rlm tidiers: \code{\link{augment.rlm}()}, diff --git a/man/glance.rma.Rd b/man/glance.rma.Rd index ce658cbdf..44c87efcb 100644 --- a/man/glance.rma.Rd +++ b/man/glance.rma.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.robustbase.lmrob.Rd b/man/glance.robustbase.lmrob.Rd index d00f4de97..47064f932 100644 --- a/man/glance.robustbase.lmrob.Rd +++ b/man/glance.robustbase.lmrob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.rq.Rd b/man/glance.rq.Rd index 832984377..91ac8342e 100644 --- a/man/glance.rq.Rd +++ b/man/glance.rq.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ For multiple values, please use a \code{\link[purrr:map]{purrr::map()}} workflow } } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=glance]{glance()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/glance.sarlm.Rd b/man/glance.sarlm.Rd index ca6afc805..3890c78fe 100644 --- a/man/glance.sarlm.Rd +++ b/man/glance.sarlm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -71,7 +71,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[=glance]{glance()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: diff --git a/man/glance.smooth.spline.Rd b/man/glance.smooth.spline.Rd index f56e3b713..c8dc10747 100644 --- a/man/glance.smooth.spline.Rd +++ b/man/glance.smooth.spline.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ ggplot(augment(spl, mtcars), aes(wt, mpg)) + geom_line(aes(y = .fitted)) } \seealso{ -\code{\link[=reexports]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}} +\code{\link[=augment]{augment()}}, \code{\link[stats:smooth.spline]{stats::smooth.spline()}} Other smoothing spline tidiers: \code{\link{augment.smooth.spline}()} diff --git a/man/glance.speedglm.Rd b/man/glance.speedglm.Rd index b8c156340..8fa322a8f 100644 --- a/man/glance.speedglm.Rd +++ b/man/glance.speedglm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.speedlm.Rd b/man/glance.speedlm.Rd index dc30f8e8a..db32cd18c 100644 --- a/man/glance.speedlm.Rd +++ b/man/glance.speedlm.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.survdiff.Rd b/man/glance.survdiff.Rd index 43eb42d56..301a1abcd 100644 --- a/man/glance.survdiff.Rd +++ b/man/glance.survdiff.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -52,7 +52,7 @@ tidy(s) glance(s) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:survdiff]{survival::survdiff()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:survdiff]{survival::survdiff()}} Other survdiff tidiers: \code{\link{tidy.survdiff}()} diff --git a/man/glance.survexp.Rd b/man/glance.survexp.Rd index 4f52f6ea3..e50ba0268 100644 --- a/man/glance.survexp.Rd +++ b/man/glance.survexp.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -57,7 +57,7 @@ tidy(sexpfit) glance(sexpfit) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:survexp]{survival::survexp()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:survexp]{survival::survexp()}} Other survexp tidiers: \code{\link{tidy.survexp}()} diff --git a/man/glance.survfit.Rd b/man/glance.survfit.Rd index e50e62fc5..0116002e0 100644 --- a/man/glance.survfit.Rd +++ b/man/glance.survfit.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ ggplot(td_multi, aes(time, estimate, group = state)) + geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:survfit]{survival::survfit()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:survfit]{survival::survfit()}} Other cch tidiers: \code{\link{glance.cch}()}, diff --git a/man/glance.survreg.Rd b/man/glance.survreg.Rd index 3e9486aa7..a0e3476a3 100644 --- a/man/glance.survreg.Rd +++ b/man/glance.survreg.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=glance]{glance()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{augment.survreg}()}, diff --git a/man/glance.svyglm.Rd b/man/glance.svyglm.Rd index de8d23b23..84795f20b 100644 --- a/man/glance.svyglm.Rd +++ b/man/glance.svyglm.Rd @@ -20,7 +20,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/glance.svyolr.Rd b/man/glance.svyolr.Rd index 0849db1da..500e1e48e 100644 --- a/man/glance.svyolr.Rd +++ b/man/glance.svyolr.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ tidy(fit, exponentiate = TRUE, conf.int = TRUE) glance(fit) } \seealso{ -\link[=reexports]{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} +\link{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/glance_optim.Rd b/man/glance_optim.Rd index b498f599a..44812adf1 100644 --- a/man/glance_optim.Rd +++ b/man/glance_optim.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ o <- optim(c(1, 1, 1), f) } \seealso{ -\code{\link[=reexports]{glance()}}, \code{\link[stats:optim]{stats::optim()}} +\code{\link[=glance]{glance()}}, \code{\link[stats:optim]{stats::optim()}} Other list tidiers: \code{\link{list_tidiers}}, diff --git a/man/metafor_tidiers.Rd b/man/metafor_tidiers.Rd index 36d824e69..3a6db0beb 100644 --- a/man/metafor_tidiers.Rd +++ b/man/metafor_tidiers.Rd @@ -42,7 +42,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/sparse_tidiers.Rd b/man/sparse_tidiers.Rd index 3c54690ae..9dc43fd8b 100644 --- a/man/sparse_tidiers.Rd +++ b/man/sparse_tidiers.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.Arima.Rd b/man/tidy.Arima.Rd index 21d232686..ba8f68638 100644 --- a/man/tidy.Arima.Rd +++ b/man/tidy.Arima.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.Gam.Rd b/man/tidy.Gam.Rd index cd2c9e1fb..c3b5755a3 100644 --- a/man/tidy.Gam.Rd +++ b/man/tidy.Gam.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(g, parametric = TRUE) glance(g) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}} +\code{\link[=tidy]{tidy()}}, \code{\link[mgcv:gam]{mgcv::gam()}} Other mgcv tidiers: \code{\link{glance.gam}()} diff --git a/man/tidy.Kendall.Rd b/man/tidy.Kendall.Rd index 1a7aab9b2..54253c822 100644 --- a/man/tidy.Kendall.Rd +++ b/man/tidy.Kendall.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -46,7 +46,7 @@ t_res <- SeasonalMannKendall(ts(A)) tidy(t_res) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[Kendall:Kendall]{Kendall::Kendall()}}, \code{\link[Kendall:MannKendall]{Kendall::MannKendall()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[Kendall:Kendall]{Kendall::Kendall()}}, \code{\link[Kendall:MannKendall]{Kendall::MannKendall()}}, \code{\link[Kendall:SeasonalMannKendall]{Kendall::SeasonalMannKendall()}} } \value{ diff --git a/man/tidy.Mclust.Rd b/man/tidy.Mclust.Rd index 1b51c637a..a0ba5b202 100644 --- a/man/tidy.Mclust.Rd +++ b/man/tidy.Mclust.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ augment(m, points) glance(m) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} +\code{\link[=tidy]{tidy()}}, \code{\link[mclust:Mclust]{mclust::Mclust()}} Other mclust tidiers: \code{\link{augment.Mclust}()} diff --git a/man/tidy.TukeyHSD.Rd b/man/tidy.TukeyHSD.Rd index fbb97129e..e46421b3a 100644 --- a/man/tidy.TukeyHSD.Rd +++ b/man/tidy.TukeyHSD.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -38,7 +38,7 @@ fm2 <- aov(mpg ~ as.factor(gear) * as.factor(cyl), data = mtcars) tidy(TukeyHSD(fm2)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:TukeyHSD]{stats::TukeyHSD()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:TukeyHSD]{stats::TukeyHSD()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aareg.Rd b/man/tidy.aareg.Rd index 56267c17d..0c73a21bd 100644 --- a/man/tidy.aareg.Rd +++ b/man/tidy.aareg.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -45,7 +45,7 @@ afit <- aareg( tidy(afit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:aareg]{survival::aareg()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:aareg]{survival::aareg()}} Other aareg tidiers: \code{\link{glance.aareg}()} diff --git a/man/tidy.acf.Rd b/man/tidy.acf.Rd index fee101212..44c90ca2f 100644 --- a/man/tidy.acf.Rd +++ b/man/tidy.acf.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ tidy(ccf(mdeaths, fdeaths, plot = FALSE)) tidy(pacf(lh, plot = FALSE)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}}, \code{\link[stats:acf]{stats::ccf()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:acf]{stats::acf()}}, \code{\link[stats:acf]{stats::pacf()}}, \code{\link[stats:acf]{stats::ccf()}} Other time series tidiers: \code{\link{tidy.spec}()}, diff --git a/man/tidy.anova.Rd b/man/tidy.anova.Rd index 2d4bf7fe9..890a4f5d7 100644 --- a/man/tidy.anova.Rd +++ b/man/tidy.anova.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ b <- lm(mpg ~ wt + qsec, mtcars) tidy(anova(a, b)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:anova]{stats::anova()}}, \code{\link[car:Anova]{car::Anova()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:anova]{stats::anova()}}, \code{\link[car:Anova]{car::Anova()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aov.Rd b/man/tidy.aov.Rd index 187f44a90..2fa4d61f6 100644 --- a/man/tidy.aov.Rd +++ b/man/tidy.aov.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ a <- aov(mpg ~ wt + qsec + disp, mtcars) tidy(a) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.aovlist.Rd b/man/tidy.aovlist.Rd index fcd1cc709..c6eda4f0e 100644 --- a/man/tidy.aovlist.Rd +++ b/man/tidy.aovlist.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ a <- aov(mpg ~ wt + qsec + Error(disp / am), mtcars) tidy(a) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:aov]{stats::aov()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.betamfx.Rd b/man/tidy.betamfx.Rd index 390c55db6..ca9c81b21 100644 --- a/man/tidy.betamfx.Rd +++ b/man/tidy.betamfx.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.betareg.Rd b/man/tidy.betareg.Rd index 0678cffe1..35f1e96f7 100644 --- a/man/tidy.betareg.Rd +++ b/man/tidy.betareg.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -59,7 +59,7 @@ augment(mod) glance(mod) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[betareg:betareg]{betareg::betareg()}} +\code{\link[=tidy]{tidy()}}, \code{\link[betareg:betareg]{betareg::betareg()}} } \concept{betareg tidiers} \value{ diff --git a/man/tidy.biglm.Rd b/man/tidy.biglm.Rd index c86da4eba..dd7e2ced9 100644 --- a/man/tidy.biglm.Rd +++ b/man/tidy.biglm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ glance(bgfit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[biglm:biglm]{biglm::biglm()}}, \code{\link[biglm:bigglm]{biglm::bigglm()}} Other biglm tidiers: \code{\link{glance.biglm}()} diff --git a/man/tidy.binDesign.Rd b/man/tidy.binDesign.Rd index b9c5fc46a..65ae3e60c 100644 --- a/man/tidy.binDesign.Rd +++ b/man/tidy.binDesign.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -45,7 +45,7 @@ ggplot(tidy(des), aes(n, power)) + geom_line() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} +\code{\link[=tidy]{tidy()}}, \code{\link[binGroup:binDesign]{binGroup::binDesign()}} Other bingroup tidiers: \code{\link{glance.binDesign}()}, diff --git a/man/tidy.binWidth.Rd b/man/tidy.binWidth.Rd index 557c659dc..311c9298f 100644 --- a/man/tidy.binWidth.Rd +++ b/man/tidy.binWidth.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,7 +39,7 @@ bw tidy(bw) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[binGroup:binWidth]{binGroup::binWidth()}} +\code{\link[=tidy]{tidy()}}, \code{\link[binGroup:binWidth]{binGroup::binWidth()}} Other bingroup tidiers: \code{\link{glance.binDesign}()}, diff --git a/man/tidy.boot.Rd b/man/tidy.boot.Rd index 4dc78a73c..f69a11851 100644 --- a/man/tidy.boot.Rd +++ b/man/tidy.boot.Rd @@ -33,7 +33,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -76,7 +76,7 @@ tidy(g1, conf.int = TRUE) tidy(bootres, conf.int = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[boot:boot]{boot::boot()}}, \code{\link[boot:tsboot]{boot::tsboot()}}, \code{\link[boot:boot.ci]{boot::boot.ci()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[boot:boot]{boot::boot()}}, \code{\link[boot:tsboot]{boot::tsboot()}}, \code{\link[boot:boot.ci]{boot::boot.ci()}}, \code{\link[rsample:bootstraps]{rsample::bootstraps()}} } \value{ diff --git a/man/tidy.btergm.Rd b/man/tidy.btergm.Rd index d3e82c91b..e17691a22 100644 --- a/man/tidy.btergm.Rd +++ b/man/tidy.btergm.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ tidy(btfit) tidy(btfit, exponentiate = TRUE, conf.level = 0.99) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[btergm:btergm]{btergm::btergm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[btergm:btergm]{btergm::btergm()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.cch.Rd b/man/tidy.cch.Rd index 750f51ea7..2b7cdaf45 100644 --- a/man/tidy.cch.Rd +++ b/man/tidy.cch.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -60,7 +60,7 @@ ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:cch]{survival::cch()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:cch]{survival::cch()}} Other cch tidiers: \code{\link{glance.cch}()}, diff --git a/man/tidy.cld.Rd b/man/tidy.cld.Rd index d8e0b115f..522327817 100644 --- a/man/tidy.cld.Rd +++ b/man/tidy.cld.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:cld]{multcomp::cld()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: diff --git a/man/tidy.clm.Rd b/man/tidy.clm.Rd index 8bc03affa..64a7ef68a 100644 --- a/man/tidy.clm.Rd +++ b/man/tidy.clm.Rd @@ -39,7 +39,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -79,7 +79,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link[=reexports]{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} +\link{tidy}, \code{\link[ordinal:clm]{ordinal::clm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.clmm.Rd b/man/tidy.clmm.Rd index fc4f143b9..c14935f0f 100644 --- a/man/tidy.clmm.Rd +++ b/man/tidy.clmm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ tidy(fit2) glance(fit2) } \seealso{ -\link[=reexports]{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} +\link{tidy}, \code{\link[ordinal:clmm]{ordinal::clmm()}}, \code{\link[ordinal:confint.clm]{ordinal::confint.clm()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.coeftest.Rd b/man/tidy.coeftest.Rd index 8930c2a0d..1c019383b 100644 --- a/man/tidy.coeftest.Rd +++ b/man/tidy.coeftest.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ lmtest::coeftest(fm) tidy(coeftest(fm)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[lmtest:coeftest]{lmtest::coeftest()}} +\code{\link[=tidy]{tidy()}}, \code{\link[lmtest:coeftest]{lmtest::coeftest()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.confint.glht.Rd b/man/tidy.confint.glht.Rd index 804ececc9..cb4b8b2d4 100644 --- a/man/tidy.confint.glht.Rd +++ b/man/tidy.confint.glht.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::confint.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.confusionMatrix.Rd b/man/tidy.confusionMatrix.Rd index c00eb9298..62e2e4f5c 100644 --- a/man/tidy.confusionMatrix.Rd +++ b/man/tidy.confusionMatrix.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ tidy(six_class_cm) tidy(six_class_cm, by_class = FALSE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[caret:confusionMatrix]{caret::confusionMatrix()}} +\code{\link[=tidy]{tidy()}}, \code{\link[caret:confusionMatrix]{caret::confusionMatrix()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.coxph.Rd b/man/tidy.coxph.Rd index 4bcea4cb3..67cd44932 100644 --- a/man/tidy.coxph.Rd +++ b/man/tidy.coxph.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -83,7 +83,7 @@ ggplot(expected, aes(time, .fitted, color = sex)) + geom_point() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:coxph]{survival::coxph()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:coxph]{survival::coxph()}} Other coxph tidiers: \code{\link{augment.coxph}()}, diff --git a/man/tidy.cv.glmnet.Rd b/man/tidy.cv.glmnet.Rd index f0be87ab5..4530ceca5 100644 --- a/man/tidy.cv.glmnet.Rd +++ b/man/tidy.cv.glmnet.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -81,7 +81,7 @@ ggplot(tidied, aes(lambda, estimate, group = term)) + geom_vline(xintercept = glance_cv$lambda.1se, lty = 2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} +\code{\link[=tidy]{tidy()}}, \code{\link[glmnet:cv.glmnet]{glmnet::cv.glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index 89d4d7dc5..657cf8793 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:density]{stats::density()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:density]{stats::density()}} Other stats tidiers: \code{\link{tidy.dist}()}, diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index ed85e295c..cce0a48de 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,15 +37,18 @@ the tidied version will not either. } \examples{ -iris_dist <- dist(t(iris[, 1:4])) -iris_dist +library(modeldata) +data(hpc_data) -tidy(iris_dist) -tidy(iris_dist, upper = TRUE) -tidy(iris_dist, diagonal = TRUE) +hpc <- hpc_data[, 2:5] +hpc_dist <- dist(t(hpc)) + +tidy(hpc_dist) +tidy(hpc_dist, upper = TRUE) +tidy(hpc_dist, diagonal = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} Other stats tidiers: \code{\link{tidy.density}()}, diff --git a/man/tidy.drc.Rd b/man/tidy.drc.Rd index ba9141665..0780e2eed 100644 --- a/man/tidy.drc.Rd +++ b/man/tidy.drc.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ glance(mod) augment(mod, selenium) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[drc:drm]{drc::drm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[drc:drm]{drc::drm()}} Other drc tidiers: \code{\link{augment.drc}()}, diff --git a/man/tidy.emmGrid.Rd b/man/tidy.emmGrid.Rd index d1e5151f2..cad8ca626 100644 --- a/man/tidy.emmGrid.Rd +++ b/man/tidy.emmGrid.Rd @@ -80,7 +80,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.epi.2by2.Rd b/man/tidy.epi.2by2.Rd index 21c961f1e..1b51d057e 100644 --- a/man/tidy.epi.2by2.Rd +++ b/man/tidy.epi.2by2.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -48,7 +48,7 @@ fit <- epi.2by2( tidy(fit, parameters = "moa") } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} +\code{\link[=tidy]{tidy()}}, \code{\link[epiR:epi.2by2]{epiR::epi.2by2()}} } \concept{epiR tidiers} \value{ diff --git a/man/tidy.ergm.Rd b/man/tidy.ergm.Rd index 269fb5936..f3afbd651 100644 --- a/man/tidy.ergm.Rd +++ b/man/tidy.ergm.Rd @@ -76,7 +76,7 @@ Models for Networks. \emph{Journal of Statistical Software}, 24(3). \url{http://www.jstatsoft.org/v24/i03/}. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:control.ergm]{ergm::control.ergm()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[ergm:ergm]{ergm::ergm()}}, \code{\link[ergm:control.ergm]{ergm::control.ergm()}}, \code{\link[ergm:summary.formula]{ergm::summary()}} Other ergm tidiers: diff --git a/man/tidy.factanal.Rd b/man/tidy.factanal.Rd index ae43a9002..da0a31fa2 100644 --- a/man/tidy.factanal.Rd +++ b/man/tidy.factanal.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ augment(fit1, data = m2) augment(fit2, data = m2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:factanal]{stats::factanal()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:factanal]{stats::factanal()}} Other factanal tidiers: \code{\link{augment.factanal}()}, diff --git a/man/tidy.felm.Rd b/man/tidy.felm.Rd index 0458af5c9..eb206a274 100644 --- a/man/tidy.felm.Rd +++ b/man/tidy.felm.Rd @@ -30,7 +30,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -75,7 +75,7 @@ augment(result_felm) glance(result_felm) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[lfe:felm]{lfe::felm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[lfe:felm]{lfe::felm()}} Other felm tidiers: \code{\link{augment.felm}()} diff --git a/man/tidy.fitdistr.Rd b/man/tidy.fitdistr.Rd index 20650d51d..8f7c4a7a2 100644 --- a/man/tidy.fitdistr.Rd +++ b/man/tidy.fitdistr.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -40,7 +40,7 @@ tidy(fit) glance(fit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} +\code{\link[=tidy]{tidy()}}, \code{\link[MASS:fitdistr]{MASS::fitdistr()}} Other fitdistr tidiers: \code{\link{glance.fitdistr}()} diff --git a/man/tidy.fixest.Rd b/man/tidy.fixest.Rd index 9f3b30529..7f84b9a69 100644 --- a/man/tidy.fixest.Rd +++ b/man/tidy.fixest.Rd @@ -72,7 +72,7 @@ augment(gravity_pois, trade) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::fenegbin()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[fixest:feglm]{fixest::feglm()}}, \code{\link[fixest:femlm]{fixest::fenegbin()}}, \code{\link[fixest:feNmlm]{fixest::feNmlm()}}, \code{\link[fixest:femlm]{fixest::femlm()}}, \code{\link[fixest:feols]{fixest::feols()}}, \code{\link[fixest:feglm]{fixest::fepois()}} Other fixest tidiers: diff --git a/man/tidy.ftable.Rd b/man/tidy.ftable.Rd index 465deef36..05d724164 100644 --- a/man/tidy.ftable.Rd +++ b/man/tidy.ftable.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -35,7 +35,7 @@ specify which components to return. This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} Other stats tidiers: \code{\link{tidy.density}()}, diff --git a/man/tidy.gamlss.Rd b/man/tidy.gamlss.Rd index ef5ab1e5f..d3a574e66 100644 --- a/man/tidy.gamlss.Rd +++ b/man/tidy.gamlss.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.garch.Rd b/man/tidy.garch.Rd index 4e0907fd3..f72361dcb 100644 --- a/man/tidy.garch.Rd +++ b/man/tidy.garch.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ tidy(dax.garch) glance(dax.garch) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[tseries:garch]{tseries::garch()}} +\code{\link[=tidy]{tidy()}}, \code{\link[tseries:garch]{tseries::garch()}} Other garch tidiers: \code{\link{glance.garch}()} diff --git a/man/tidy.geeglm.Rd b/man/tidy.geeglm.Rd index 1e96459ef..10452a68b 100644 --- a/man/tidy.geeglm.Rd +++ b/man/tidy.geeglm.Rd @@ -29,7 +29,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -66,7 +66,7 @@ tidy(geefit) tidy(geefit, conf.int = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[geepack:geeglm]{geepack::geeglm()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.glht.Rd b/man/tidy.glht.Rd index 237558e76..0552fa899 100644 --- a/man/tidy.glht.Rd +++ b/man/tidy.glht.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -62,7 +62,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.glm.Rd b/man/tidy.glm.Rd index 097831b84..c35c4ea6e 100644 --- a/man/tidy.glm.Rd +++ b/man/tidy.glm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.glmRob.Rd b/man/tidy.glmRob.Rd index 532517307..504496571 100644 --- a/man/tidy.glmRob.Rd +++ b/man/tidy.glmRob.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.glmnet.Rd b/man/tidy.glmnet.Rd index 22b780ef3..03ea8040a 100644 --- a/man/tidy.glmnet.Rd +++ b/man/tidy.glmnet.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ fit2 <- glmnet(x, g2, family = "binomial") tidy(fit2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} +\code{\link[=tidy]{tidy()}}, \code{\link[glmnet:glmnet]{glmnet::glmnet()}} Other glmnet tidiers: \code{\link{glance.cv.glmnet}()}, diff --git a/man/tidy.gmm.Rd b/man/tidy.gmm.Rd index 9f56f521f..d6a56b0bb 100644 --- a/man/tidy.gmm.Rd +++ b/man/tidy.gmm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -106,7 +106,7 @@ td2 \%>\% geom_vline(xintercept = 0, color = "red", lty = 2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[gmm:gmm]{gmm::gmm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[gmm:gmm]{gmm::gmm()}} Other gmm tidiers: \code{\link{glance.gmm}()} diff --git a/man/tidy.htest.Rd b/man/tidy.htest.Rd index a388923e4..023a166f3 100644 --- a/man/tidy.htest.Rd +++ b/man/tidy.htest.Rd @@ -20,13 +20,13 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \description{ -For models that have only a single component, the \code{\link[=reexports]{tidy()}} and -\code{\link[=reexports]{glance()}} methods are identical. Please see the documentation for both +For models that have only a single component, the \code{\link[=tidy]{tidy()}} and +\code{\link[=glance]{glance()}} methods are identical. Please see the documentation for both of those methods. } \examples{ @@ -49,7 +49,7 @@ tidy(chit) augment(chit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:cor.test]{stats::cor.test()}}, \code{\link[stats:t.test]{stats::t.test()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[stats:cor.test]{stats::cor.test()}}, \code{\link[stats:t.test]{stats::t.test()}}, \code{\link[stats:wilcox.test]{stats::wilcox.test()}}, \code{\link[stats:chisq.test]{stats::chisq.test()}} Other htest tidiers: diff --git a/man/tidy.ivreg.Rd b/man/tidy.ivreg.Rd index a6eb9857c..1285fae96 100644 --- a/man/tidy.ivreg.Rd +++ b/man/tidy.ivreg.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ augment(ivr, newdata = CigarettesSW) glance(ivr) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[AER:ivreg]{AER::ivreg()}} +\code{\link[=tidy]{tidy()}}, \code{\link[AER:ivreg]{AER::ivreg()}} Other ivreg tidiers: \code{\link{augment.ivreg}()}, diff --git a/man/tidy.kappa.Rd b/man/tidy.kappa.Rd index 5d774354c..2e674f7b4 100644 --- a/man/tidy.kappa.Rd +++ b/man/tidy.kappa.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ ggplot(tidy(ck), aes(estimate, type)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[psych:kappa]{psych::cohen.kappa()}} +\code{\link[=tidy]{tidy()}}, \code{\link[psych:kappa]{psych::cohen.kappa()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.kde.Rd b/man/tidy.kde.Rd index 1114e34fa..c0dd2cf76 100644 --- a/man/tidy.kde.Rd +++ b/man/tidy.kde.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -65,7 +65,7 @@ td3 <- tidy(k3) td3 } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[ks:kde]{ks::kde()}} +\code{\link[=tidy]{tidy()}}, \code{\link[ks:kde]{ks::kde()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.kmeans.Rd b/man/tidy.kmeans.Rd index fbf490cf1..632c8cda9 100644 --- a/man/tidy.kmeans.Rd +++ b/man/tidy.kmeans.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,17 +39,19 @@ For examples, see the kmeans vignette. library(cluster) library(dplyr) -x <- iris \%>\% - select(-Species) +library(modeldata) +data(hpc_data) -fit <- pam(x, k = 3) +x <- hpc_data[, 2:5] + +fit <- pam(x, k = 4) tidy(fit) glance(fit) augment(fit, x) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:kmeans]{stats::kmeans()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:kmeans]{stats::kmeans()}} Other kmeans tidiers: \code{\link{augment.kmeans}()}, diff --git a/man/tidy.lavaan.Rd b/man/tidy.lavaan.Rd index 20019fdb8..3ff5a55c4 100644 --- a/man/tidy.lavaan.Rd +++ b/man/tidy.lavaan.Rd @@ -66,7 +66,7 @@ tidy(cfa.fit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[lavaan:cfa]{lavaan::cfa()}}, \code{\link[lavaan:sem]{lavaan::sem()}}, \code{\link[lavaan:parameterEstimates]{lavaan::parameterEstimates()}} Other lavaan tidiers: diff --git a/man/tidy.lm.Rd b/man/tidy.lm.Rd index d1573754f..0365b4b81 100644 --- a/man/tidy.lm.Rd +++ b/man/tidy.lm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -92,7 +92,7 @@ result <- lm(b ~ a) tidy(result) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:summary.lm]{stats::summary.lm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:summary.lm]{stats::summary.lm()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/tidy.lm.beta.Rd b/man/tidy.lm.beta.Rd index 1cf14be97..60d41ae06 100644 --- a/man/tidy.lm.beta.Rd +++ b/man/tidy.lm.beta.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.lmRob.Rd b/man/tidy.lmRob.Rd index b79f3272f..1a0252be0 100644 --- a/man/tidy.lmRob.Rd +++ b/man/tidy.lmRob.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.lmodel2.Rd b/man/tidy.lmodel2.Rd index 01f58e878..d19760f97 100644 --- a/man/tidy.lmodel2.Rd +++ b/man/tidy.lmodel2.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(tidy(Ex2.res), aes(estimate, term, color = method)) + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} +\code{\link[=tidy]{tidy()}}, \code{\link[lmodel2:lmodel2]{lmodel2::lmodel2()}} Other lmodel2 tidiers: \code{\link{glance.lmodel2}()} diff --git a/man/tidy.lsmobj.Rd b/man/tidy.lsmobj.Rd index 535f82921..f6c45c250 100644 --- a/man/tidy.lsmobj.Rd +++ b/man/tidy.lsmobj.Rd @@ -81,7 +81,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.manova.Rd b/man/tidy.manova.Rd index efd0b9a05..9a7ef57b4 100644 --- a/man/tidy.manova.Rd +++ b/man/tidy.manova.Rd @@ -43,7 +43,7 @@ m <- manova(cbind(yield, foo) ~ block + N * P * K, npk2) tidy(m) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:summary.manova]{stats::summary.manova()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:summary.manova]{stats::summary.manova()}} Other anova tidiers: \code{\link{glance.aov}()}, diff --git a/man/tidy.map.Rd b/man/tidy.map.Rd index 465f939be..665582a03 100644 --- a/man/tidy.map.Rd +++ b/man/tidy.map.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -46,7 +46,7 @@ qplot(long, lat, ) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[maps:map]{maps::map()}} +\code{\link[=tidy]{tidy()}}, \code{\link[maps:map]{maps::map()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.mediate.Rd b/man/tidy.mediate.Rd index 2a4426176..2fc49f15c 100644 --- a/man/tidy.mediate.Rd +++ b/man/tidy.mediate.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ tidy(mod, conf.int = TRUE) tidy(mod, conf.int = TRUE, conf.level = .99) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mediation:mediate]{mediation::mediate()}} +\code{\link[=tidy]{tidy()}}, \code{\link[mediation:mediate]{mediation::mediate()}} } \concept{mediate tidiers} \value{ diff --git a/man/tidy.mfx.Rd b/man/tidy.mfx.Rd index 92b34378e..f2115a67d 100644 --- a/man/tidy.mfx.Rd +++ b/man/tidy.mfx.Rd @@ -35,7 +35,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -88,7 +88,7 @@ glance(mod_probmfx) } } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} +\code{\link[=tidy]{tidy()}}, \code{\link[mfx:logitmfx]{mfx::logitmfx()}}, \code{\link[mfx:negbinmfx]{mfx::negbinmfx()}}, \code{\link[mfx:poissonmfx]{mfx::poissonmfx()}}, \code{\link[mfx:probitmfx]{mfx::probitmfx()}} Other mfx tidiers: \code{\link{augment.betamfx}()}, diff --git a/man/tidy.mjoint.Rd b/man/tidy.mjoint.Rd index 09d666b7f..ae4ff1005 100644 --- a/man/tidy.mjoint.Rd +++ b/man/tidy.mjoint.Rd @@ -40,7 +40,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -98,7 +98,7 @@ glance(fit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}}, \code{\link[joineRML:bootSE]{joineRML::bootSE()}} +\code{\link[=tidy]{tidy()}}, \code{\link[joineRML:mjoint]{joineRML::mjoint()}}, \code{\link[joineRML:bootSE]{joineRML::bootSE()}} Other mjoint tidiers: \code{\link{glance.mjoint}()} diff --git a/man/tidy.mle2.Rd b/man/tidy.mle2.Rd index 9c4afacfd..6cd821af9 100644 --- a/man/tidy.mle2.Rd +++ b/man/tidy.mle2.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ fit <- mle2(y ~ dpois(lambda = ymean), tidy(fit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[bbmle:mle2]{bbmle::mle2()}}, \code{\link[=tidy_optim]{tidy_optim()}} +\code{\link[=tidy]{tidy()}}, \code{\link[bbmle:mle2]{bbmle::mle2()}}, \code{\link[=tidy_optim]{tidy_optim()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.mlm.Rd b/man/tidy.mlm.Rd index 4298935eb..fdaa08f44 100644 --- a/man/tidy.mlm.Rd +++ b/man/tidy.mlm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -49,7 +49,7 @@ mod <- lm(cbind(mpg, disp) ~ wt, mtcars) tidy(mod, conf.int = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}} +\code{\link[=tidy]{tidy()}} Other lm tidiers: \code{\link{augment.glm}()}, diff --git a/man/tidy.muhaz.Rd b/man/tidy.muhaz.Rd index 353e9633c..9146d8338 100644 --- a/man/tidy.muhaz.Rd +++ b/man/tidy.muhaz.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -38,7 +38,7 @@ tidy(x) glance(x) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} +\code{\link[=tidy]{tidy()}}, \code{\link[muhaz:muhaz]{muhaz::muhaz()}} Other muhaz tidiers: \code{\link{glance.muhaz}()} diff --git a/man/tidy.multinom.Rd b/man/tidy.multinom.Rd index e000af9b5..6bc68d203 100644 --- a/man/tidy.multinom.Rd +++ b/man/tidy.multinom.Rd @@ -29,7 +29,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(fit.gear) glance(fit.gear) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[nnet:multinom]{nnet::multinom()}} +\code{\link[=tidy]{tidy()}}, \code{\link[nnet:multinom]{nnet::multinom()}} Other multinom tidiers: \code{\link{glance.multinom}()} diff --git a/man/tidy.nlrq.Rd b/man/tidy.nlrq.Rd index 68c40539a..f1a3f597f 100644 --- a/man/tidy.nlrq.Rd +++ b/man/tidy.nlrq.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -36,7 +36,7 @@ If a model has several distinct types of components, you will need to specify which components to return. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} +\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:nlrq]{quantreg::nlrq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.nls.Rd b/man/tidy.nls.Rd index 0a01d9864..188841edd 100644 --- a/man/tidy.nls.Rd +++ b/man/tidy.nls.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ newdata$wt <- newdata$wt + 1 augment(n, newdata = newdata) } \seealso{ -\link[=reexports]{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:summary.nls]{stats::summary.nls()}} +\link{tidy}, \code{\link[stats:nls]{stats::nls()}}, \code{\link[stats:summary.nls]{stats::summary.nls()}} Other nls tidiers: \code{\link{augment.nls}()}, diff --git a/man/tidy.orcutt.Rd b/man/tidy.orcutt.Rd index 9cf261248..4545b07e3 100644 --- a/man/tidy.orcutt.Rd +++ b/man/tidy.orcutt.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.pairwise.htest.Rd b/man/tidy.pairwise.htest.Rd index 62e5f2aa5..920609d06 100644 --- a/man/tidy.pairwise.htest.Rd +++ b/man/tidy.pairwise.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -42,18 +42,20 @@ Month <- factor(Month, labels = month.abb[5:9]) ptt <- pairwise.t.test(Ozone, Month) tidy(ptt) -attach(iris) -ptt2 <- pairwise.t.test(Petal.Length, Species) +library(modeldata) +data(hpc_data) +attach(hpc_data) +ptt2 <- pairwise.t.test(compounds, class) tidy(ptt2) -tidy(pairwise.t.test(Petal.Length, Species, alternative = "greater")) -tidy(pairwise.t.test(Petal.Length, Species, alternative = "less")) +tidy(pairwise.t.test(compounds, class, alternative = "greater")) +tidy(pairwise.t.test(compounds, class, alternative = "less")) -tidy(pairwise.wilcox.test(Petal.Length, Species)) +tidy(pairwise.wilcox.test(compounds, class)) } \seealso{ \code{\link[stats:pairwise.t.test]{stats::pairwise.t.test()}}, \code{\link[stats:pairwise.wilcox.test]{stats::pairwise.wilcox.test()}}, -\code{\link[=reexports]{tidy()}} +\code{\link[=tidy]{tidy()}} Other htest tidiers: \code{\link{augment.htest}()}, diff --git a/man/tidy.pam.Rd b/man/tidy.pam.Rd index fe0a2ce1a..10655ec36 100644 --- a/man/tidy.pam.Rd +++ b/man/tidy.pam.Rd @@ -19,7 +19,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -39,22 +39,23 @@ For examples, see the pam vignette. library(dplyr) library(ggplot2) library(cluster) +library(modeldata) +data(hpc_data) -x <- iris \%>\% - select(-Species) -p <- pam(x, k = 3) +x <- hpc_data[, 2:5] +p <- pam(x, k = 4) tidy(p) glance(p) augment(p, x) augment(p, x) \%>\% - ggplot(aes(Sepal.Length, Sepal.Width)) + + ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[cluster:pam]{cluster::pam()}} +\code{\link[=tidy]{tidy()}}, \code{\link[cluster:pam]{cluster::pam()}} Other pam tidiers: \code{\link{augment.pam}()}, diff --git a/man/tidy.plm.Rd b/man/tidy.plm.Rd index a7378531e..96403adb0 100644 --- a/man/tidy.plm.Rd +++ b/man/tidy.plm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ augment(zz) glance(zz) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[plm:plm]{plm::plm()}}, \code{\link[=tidy.lm]{tidy.lm()}} +\code{\link[=tidy]{tidy()}}, \code{\link[plm:plm]{plm::plm()}}, \code{\link[=tidy.lm]{tidy.lm()}} Other plm tidiers: \code{\link{augment.plm}()}, diff --git a/man/tidy.poLCA.Rd b/man/tidy.poLCA.Rd index c1ec349f3..c0179c5cd 100644 --- a/man/tidy.poLCA.Rd +++ b/man/tidy.poLCA.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -77,7 +77,7 @@ au2 dim(au2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} +\code{\link[=tidy]{tidy()}}, \code{\link[poLCA:poLCA]{poLCA::poLCA()}} Other poLCA tidiers: \code{\link{augment.poLCA}()}, diff --git a/man/tidy.polr.Rd b/man/tidy.polr.Rd index 6f0e18b22..3bb6d7389 100644 --- a/man/tidy.polr.Rd +++ b/man/tidy.polr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -80,7 +80,7 @@ tidy(fit, p.values = TRUE) } \seealso{ -\link[=reexports]{tidy}, \code{\link[MASS:polr]{MASS::polr()}} +\link{tidy}, \code{\link[MASS:polr]{MASS::polr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.power.htest.Rd b/man/tidy.power.htest.Rd index ee4451f23..b03e73041 100644 --- a/man/tidy.power.htest.Rd +++ b/man/tidy.power.htest.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.prcomp.Rd b/man/tidy.prcomp.Rd index 0aee38f44..08953cd1b 100644 --- a/man/tidy.prcomp.Rd +++ b/man/tidy.prcomp.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -112,7 +112,7 @@ ggplot(au, aes(.fittedPC1, .fittedPC2)) + geom_text(aes(label = .rownames), vjust = 1, hjust = 1) } \seealso{ -\code{\link[stats:prcomp]{stats::prcomp()}}, \link[=tidy_svd]{svd_tidiers} +\code{\link[stats:prcomp]{stats::prcomp()}}, \link{svd_tidiers} Other svd tidiers: \code{\link{augment.prcomp}()}, diff --git a/man/tidy.pyears.Rd b/man/tidy.pyears.Rd index 3c0443e3b..c826583e8 100644 --- a/man/tidy.pyears.Rd +++ b/man/tidy.pyears.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ tidy(pfit2) glance(pfit2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:pyears]{survival::pyears()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:pyears]{survival::pyears()}} Other pyears tidiers: \code{\link{glance.pyears}()} diff --git a/man/tidy.rcorr.Rd b/man/tidy.rcorr.Rd index 2a979e9b1..cea186db6 100644 --- a/man/tidy.rcorr.Rd +++ b/man/tidy.rcorr.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -64,7 +64,7 @@ ggplot(td, aes(estimate, p.value)) + scale_y_log10() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[Hmisc:rcorr]{Hmisc::rcorr()}} +\code{\link[=tidy]{tidy()}}, \code{\link[Hmisc:rcorr]{Hmisc::rcorr()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.ref.grid.Rd b/man/tidy.ref.grid.Rd index a3bb4e701..906317f09 100644 --- a/man/tidy.ref.grid.Rd +++ b/man/tidy.ref.grid.Rd @@ -80,7 +80,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.regsubsets.Rd b/man/tidy.regsubsets.Rd index 5d0758af2..38e33d435 100644 --- a/man/tidy.regsubsets.Rd +++ b/man/tidy.regsubsets.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -34,7 +34,7 @@ all_fits <- leaps::regsubsets(hp ~ ., mtcars) tidy(all_fits) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[leaps:regsubsets]{leaps::regsubsets()}} +\code{\link[=tidy]{tidy()}}, \code{\link[leaps:regsubsets]{leaps::regsubsets()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.ridgelm.Rd b/man/tidy.ridgelm.Rd index 29b4e70ff..e618de943 100644 --- a/man/tidy.ridgelm.Rd +++ b/man/tidy.ridgelm.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -53,7 +53,7 @@ ggplot(td2, aes(lambda, GCV)) + geom_vline(xintercept = g2$lambdaGCV, col = "red", lty = 2) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} +\code{\link[=tidy]{tidy()}}, \code{\link[MASS:lm.ridge]{MASS::lm.ridge()}} Other ridgelm tidiers: \code{\link{glance.ridgelm}()} diff --git a/man/tidy.rlm.Rd b/man/tidy.rlm.Rd index 29ba5b016..559a25ee4 100644 --- a/man/tidy.rlm.Rd +++ b/man/tidy.rlm.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.robustbase.glmrob.Rd b/man/tidy.robustbase.glmrob.Rd index bfe3a8105..d4930e424 100644 --- a/man/tidy.robustbase.glmrob.Rd +++ b/man/tidy.robustbase.glmrob.Rd @@ -22,7 +22,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.robustbase.lmrob.Rd b/man/tidy.robustbase.lmrob.Rd index 1cb63ba57..fb8dab65e 100644 --- a/man/tidy.robustbase.lmrob.Rd +++ b/man/tidy.robustbase.lmrob.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.roc.Rd b/man/tidy.roc.Rd index 06658e636..60816a177 100644 --- a/man/tidy.roc.Rd +++ b/man/tidy.roc.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -61,7 +61,7 @@ ggplot(rocs, aes(fpr, tpr, color = algorithm)) + geom_line() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[AUC:roc]{AUC::roc()}} +\code{\link[=tidy]{tidy()}}, \code{\link[AUC:roc]{AUC::roc()}} } \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.rq.Rd b/man/tidy.rq.Rd index d6fe008c0..14bd0af25 100644 --- a/man/tidy.rq.Rd +++ b/man/tidy.rq.Rd @@ -41,7 +41,7 @@ no confidence intervals are calculated and the confidence limits are set to NA. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.rqs.Rd b/man/tidy.rqs.Rd index 614633b1b..395017d3e 100644 --- a/man/tidy.rqs.Rd +++ b/man/tidy.rqs.Rd @@ -38,7 +38,7 @@ no confidence intervals are calculated and the confidence limits are set to NA. } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} +\code{\link[=tidy]{tidy()}}, \code{\link[quantreg:rq]{quantreg::rq()}} Other quantreg tidiers: \code{\link{augment.nlrq}()}, diff --git a/man/tidy.sarlm.Rd b/man/tidy.sarlm.Rd index 6bdcf04bf..ed5ed58eb 100644 --- a/man/tidy.sarlm.Rd +++ b/man/tidy.sarlm.Rd @@ -24,7 +24,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -63,7 +63,7 @@ augment(crime_sac) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[spatialreg:ML_models]{spatialreg::lagsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::errorsarlm()}}, \code{\link[spatialreg:ML_models]{spatialreg::sacsarlm()}} Other spatialreg tidiers: diff --git a/man/tidy.spec.Rd b/man/tidy.spec.Rd index e372f62c7..e1f2c0c58 100644 --- a/man/tidy.spec.Rd +++ b/man/tidy.spec.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -37,7 +37,7 @@ ggplot(tidy(spc), aes(freq, spec)) + geom_line() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:spectrum]{stats::spectrum()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:spectrum]{stats::spectrum()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy.speedglm.Rd b/man/tidy.speedglm.Rd index 3b27bb0e3..11ed7f04d 100644 --- a/man/tidy.speedglm.Rd +++ b/man/tidy.speedglm.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.speedlm.Rd b/man/tidy.speedlm.Rd index 3dff4534c..6d5014d62 100644 --- a/man/tidy.speedlm.Rd +++ b/man/tidy.speedlm.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.summary.glht.Rd b/man/tidy.summary.glht.Rd index 1e31f46a2..9f750b1f2 100644 --- a/man/tidy.summary.glht.Rd +++ b/man/tidy.summary.glht.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -56,7 +56,7 @@ cld <- cld(wht) tidy(cld) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} +\code{\link[=tidy]{tidy()}}, \code{\link[multcomp:methods]{multcomp::summary.glht()}}, \code{\link[multcomp:glht]{multcomp::glht()}} Other multcomp tidiers: \code{\link{tidy.cld}()}, diff --git a/man/tidy.summary_emm.Rd b/man/tidy.summary_emm.Rd index d46b80b60..4eaa14606 100644 --- a/man/tidy.summary_emm.Rd +++ b/man/tidy.summary_emm.Rd @@ -75,7 +75,7 @@ ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) + tidy(joint_tests(oranges_lm1)) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[emmeans:ref_grid]{emmeans::ref_grid()}}, \code{\link[emmeans:emmeans]{emmeans::emmeans()}}, \code{\link[emmeans:contrast]{emmeans::contrast()}} Other emmeans tidiers: diff --git a/man/tidy.survdiff.Rd b/man/tidy.survdiff.Rd index 06b5b1570..c8fc264d1 100644 --- a/man/tidy.survdiff.Rd +++ b/man/tidy.survdiff.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ tidy(s) glance(s) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:survdiff]{survival::survdiff()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:survdiff]{survival::survdiff()}} Other survdiff tidiers: \code{\link{glance.survdiff}()} diff --git a/man/tidy.survexp.Rd b/man/tidy.survexp.Rd index 484d1cac3..9cc4a7c49 100644 --- a/man/tidy.survexp.Rd +++ b/man/tidy.survexp.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -47,7 +47,7 @@ tidy(sexpfit) glance(sexpfit) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:survexp]{survival::survexp()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:survexp]{survival::survexp()}} Other survexp tidiers: \code{\link{glance.survexp}()} diff --git a/man/tidy.survfit.Rd b/man/tidy.survfit.Rd index 35f781486..d95a4688b 100644 --- a/man/tidy.survfit.Rd +++ b/man/tidy.survfit.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -54,7 +54,7 @@ ggplot(td_multi, aes(time, estimate, group = state)) + geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:survfit]{survival::survfit()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:survfit]{survival::survfit()}} Other survival tidiers: \code{\link{augment.coxph}()}, diff --git a/man/tidy.survreg.Rd b/man/tidy.survreg.Rd index 3c97b9c40..caebef934 100644 --- a/man/tidy.survreg.Rd +++ b/man/tidy.survreg.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ ggplot(td, aes(estimate, term)) + geom_vline(xintercept = 0) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[survival:survreg]{survival::survreg()}} +\code{\link[=tidy]{tidy()}}, \code{\link[survival:survreg]{survival::survreg()}} Other survreg tidiers: \code{\link{augment.survreg}()}, diff --git a/man/tidy.svyglm.Rd b/man/tidy.svyglm.Rd index 0ee8f0932..bf4318561 100644 --- a/man/tidy.svyglm.Rd +++ b/man/tidy.svyglm.Rd @@ -27,7 +27,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.svyolr.Rd b/man/tidy.svyolr.Rd index 035b103c2..480cea543 100644 --- a/man/tidy.svyolr.Rd +++ b/man/tidy.svyolr.Rd @@ -38,7 +38,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -74,7 +74,7 @@ tidy(fit, exponentiate = TRUE, conf.int = TRUE) glance(fit) } \seealso{ -\link[=reexports]{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} +\link{tidy}, \code{\link[survey:svyolr]{survey::svyolr()}} Other ordinal tidiers: \code{\link{augment.clm}()}, diff --git a/man/tidy.systemfit.Rd b/man/tidy.systemfit.Rd index 5255263cd..a66197b34 100644 --- a/man/tidy.systemfit.Rd +++ b/man/tidy.systemfit.Rd @@ -23,7 +23,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -58,7 +58,7 @@ tidy(fit) tidy(fit, conf.int = TRUE) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[systemfit:systemfit]{systemfit::systemfit()}} +\code{\link[=tidy]{tidy()}}, \code{\link[systemfit:systemfit]{systemfit::systemfit()}} } \concept{systemfit tidiers} \value{ diff --git a/man/tidy.table.Rd b/man/tidy.table.Rd index c4dd1282c..95fac7f03 100644 --- a/man/tidy.table.Rd +++ b/man/tidy.table.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } diff --git a/man/tidy.ts.Rd b/man/tidy.ts.Rd index ef2981743..9f7fbe529 100644 --- a/man/tidy.ts.Rd +++ b/man/tidy.ts.Rd @@ -15,7 +15,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -41,7 +41,7 @@ colnames(z) <- c("Aa", "Bb", "Cc") tidy(z) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:ts]{stats::ts()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:ts]{stats::ts()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy.zoo.Rd b/man/tidy.zoo.Rd index 703ff082c..51823c821 100644 --- a/man/tidy.zoo.Rd +++ b/man/tidy.zoo.Rd @@ -16,7 +16,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -55,7 +55,7 @@ ggplot(tidy(Zrolled), aes(index, value, color = series)) + geom_line() } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[zoo:zoo]{zoo::zoo()}} +\code{\link[=tidy]{tidy()}}, \code{\link[zoo:zoo]{zoo::zoo()}} Other time series tidiers: \code{\link{tidy.acf}()}, diff --git a/man/tidy_irlba.Rd b/man/tidy_irlba.Rd index 56b14d651..c42e673ef 100644 --- a/man/tidy_irlba.Rd +++ b/man/tidy_irlba.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -72,7 +72,10 @@ A very thin wrapper around \code{\link[=tidy_svd]{tidy_svd()}}. } \examples{ -mat <- scale(as.matrix(iris[, 1:4])) +library(modeldata) +data(hpc_data) + +mat <- scale(as.matrix(hpc_data[, 2:5])) s <- svd(mat) tidy_u <- tidy(s, matrix = "u") @@ -92,13 +95,13 @@ ggplot(tidy_d, aes(PC, percent)) + ylab("\% of variance explained") tidy_u \%>\% - mutate(Species = iris$Species[row]) \%>\% - ggplot(aes(Species, value)) + + mutate(class = hpc_data$class[row]) \%>\% + ggplot(aes(class, value)) + geom_boxplot() + facet_wrap(~PC, scale = "free_y") } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[irlba:irlba]{irlba::irlba()}} +\code{\link[=tidy]{tidy()}}, \code{\link[irlba:irlba]{irlba::irlba()}} Other list tidiers: \code{\link{glance_optim}()}, diff --git a/man/tidy_optim.Rd b/man/tidy_optim.Rd index 182f26c3a..fa5f2ce73 100644 --- a/man/tidy_optim.Rd +++ b/man/tidy_optim.Rd @@ -17,7 +17,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -50,7 +50,7 @@ o <- optim(c(1, 1, 1), f) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[stats:optim]{stats::optim()}} +\code{\link[=tidy]{tidy()}}, \code{\link[stats:optim]{stats::optim()}} Other list tidiers: \code{\link{glance_optim}()}, diff --git a/man/tidy_svd.Rd b/man/tidy_svd.Rd index acc1ec4cd..a74082d83 100644 --- a/man/tidy_svd.Rd +++ b/man/tidy_svd.Rd @@ -28,7 +28,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -85,7 +85,10 @@ that SVD is only equivalent to PCA on centered data. } \examples{ -mat <- scale(as.matrix(iris[, 1:4])) +library(modeldata) +data(hpc_data) + +mat <- scale(as.matrix(hpc_data[, 2:5])) s <- svd(mat) tidy_u <- tidy(s, matrix = "u") @@ -105,8 +108,8 @@ ggplot(tidy_d, aes(PC, percent)) + ylab("\% of variance explained") tidy_u \%>\% - mutate(Species = iris$Species[row]) \%>\% - ggplot(aes(Species, value)) + + mutate(class = hpc_data$class[row]) \%>\% + ggplot(aes(class, value)) + geom_boxplot() + facet_wrap(~PC, scale = "free_y") } diff --git a/man/tidy_xyz.Rd b/man/tidy_xyz.Rd index cadecd8d8..0ad950903 100644 --- a/man/tidy_xyz.Rd +++ b/man/tidy_xyz.Rd @@ -18,7 +18,7 @@ absorbed in \code{...}, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass \code{conf.lvel = 0.9}, all computation will proceed using \code{conf.level = 0.95}. Additionally, if you pass -\code{newdata = my_tibble} to an \code{\link[=reexports]{augment()}} method that does not +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } @@ -51,7 +51,7 @@ image(A) tidy(A) } \seealso{ -\code{\link[=reexports]{tidy()}}, \code{\link[graphics:persp]{graphics::persp()}}, \code{\link[graphics:image]{graphics::image()}}, +\code{\link[=tidy]{tidy()}}, \code{\link[graphics:persp]{graphics::persp()}}, \code{\link[graphics:image]{graphics::image()}}, \code{\link[akima:interp]{akima::interp()}} Other list tidiers: From 47303ac24fbb7f14d6f2f8339d98dc81e7dd2e9d Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 23 Jun 2020 07:18:58 -0700 Subject: [PATCH 27/41] bump version back Will be using this branch to convert all hard-deprecations to soft ones. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 909226a83..67636ed63 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: broom Title: Convert Statistical Objects into Tidy Tibbles -Version: 0.7.0.9000 +Version: 0.7.0 Authors@R: c(person(given = "David", family = "Robinson", From 94f7f28d99fb2e69480892a2cddc3baaad212db8 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 23 Jun 2020 08:43:07 -0700 Subject: [PATCH 28/41] soften deprecations CRAN has asked that we revert removals to soft-deprecations and check in with maintainers that still have newly broken packages. --- DESCRIPTION | 1 + NAMESPACE | 10 + R/deprecated-0-7-0.R | 549 ++++++++++++++++++++++++++++++++++++++ R/robust-glmrob-tidiers.R | 12 +- man/augment.glmRob.Rd | 6 - man/bootstrap.Rd | 49 ++++ man/confint_tidy.Rd | 46 ++++ man/data.frame_tidiers.Rd | 118 ++++++++ man/fix_data_frame.Rd | 35 +++ man/summary_tidiers.Rd | 76 ++++++ man/tidy.density.Rd | 20 +- man/tidy.dist.Rd | 40 ++- man/tidy.ftable.Rd | 23 +- man/vector_tidiers.Rd | 69 +++++ 14 files changed, 1035 insertions(+), 19 deletions(-) create mode 100644 R/deprecated-0-7-0.R create mode 100644 man/bootstrap.Rd create mode 100644 man/confint_tidy.Rd create mode 100644 man/data.frame_tidiers.Rd create mode 100644 man/fix_data_frame.Rd create mode 100644 man/summary_tidiers.Rd create mode 100644 man/vector_tidiers.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 67636ed63..f831b98c3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -624,6 +624,7 @@ Collate: 'car-tidiers.R' 'caret-tidiers.R' 'data-frame-tidiers.R' + 'deprecated-0-7-0.R' 'drc-tidiers.R' 'emmeans-tidiers.R' 'epiR-tidiers.R' diff --git a/NAMESPACE b/NAMESPACE index 796d8afed..e43e094c9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -6,6 +6,7 @@ S3method(augment,betamfx) S3method(augment,betareg) S3method(augment,clm) S3method(augment,coxph) +S3method(augment,data.frame) S3method(augment,decomposed.ts) S3method(augment,default) S3method(augment,drc) @@ -117,6 +118,7 @@ S3method(glance,scam) S3method(glance,smooth.spline) S3method(glance,speedglm) S3method(glance,speedlm) +S3method(glance,summaryDefault) S3method(glance,survdiff) S3method(glance,survexp) S3method(glance,survfit) @@ -150,6 +152,7 @@ S3method(tidy,binWidth) S3method(tidy,boot) S3method(tidy,btergm) S3method(tidy,cch) +S3method(tidy,character) S3method(tidy,cld) S3method(tidy,clm) S3method(tidy,clmm) @@ -158,6 +161,7 @@ S3method(tidy,confint.glht) S3method(tidy,confusionMatrix) S3method(tidy,coxph) S3method(tidy,cv.glmnet) +S3method(tidy,data.frame) S3method(tidy,default) S3method(tidy,density) S3method(tidy,dgCMatrix) @@ -196,6 +200,7 @@ S3method(tidy,lm.beta) S3method(tidy,lmRob) S3method(tidy,lmodel2) S3method(tidy,lmrob) +S3method(tidy,logical) S3method(tidy,logitmfx) S3method(tidy,lsmobj) S3method(tidy,manova) @@ -211,6 +216,7 @@ S3method(tidy,multinom) S3method(tidy,negbinmfx) S3method(tidy,nlrq) S3method(tidy,nls) +S3method(tidy,numeric) S3method(tidy,orcutt) S3method(tidy,pairwise.htest) S3method(tidy,pam) @@ -239,6 +245,7 @@ S3method(tidy,speedglm) S3method(tidy,speedlm) S3method(tidy,summary.glht) S3method(tidy,summary.plm) +S3method(tidy,summaryDefault) S3method(tidy,summary_emm) S3method(tidy,survdiff) S3method(tidy,survexp) @@ -253,6 +260,9 @@ S3method(tidy,ts) S3method(tidy,zoo) export(augment) export(augment_columns) +export(bootstrap) +export(confint_tidy) +export(fix_data_frame) export(glance) export(tidy) export(tidy_irlba) diff --git a/R/deprecated-0-7-0.R b/R/deprecated-0-7-0.R new file mode 100644 index 000000000..90aba99e5 --- /dev/null +++ b/R/deprecated-0-7-0.R @@ -0,0 +1,549 @@ +# This script contains all functions and methods that will be deprecated +# in 0.7.0 and removed in the next release. + +# data.frame tidiers ------------------------------------------------------- +# this one breaks some other functionality that new functions rely +# re: infinite recursion. Don't hard-deprecate, but trigger error. + +#' Tidiers for data.frame objects +#' +#' Data frame tidiers are deprecated and will be removed from an upcoming +#' release of broom. +#' +#' These perform tidy summaries of data.frame objects. \code{tidy} produces +#' summary statistics about each column, while \code{glance} simply reports +#' the number of rows and columns. Note that \code{augment.data.frame} will +#' throw an error. +#' +#' @param x A data.frame +#' @param data data, not used +#' @param na.rm a logical value indicating whether \code{NA} values should +#' be stripped before the computation proceeds. +#' @param trim the fraction (0 to 0.5) of observations to be trimmed from +#' each end of \code{x} before the mean is computed. Passed to the +#' \code{trim} argument of \code{\link{mean}} +#' @param ... Additional arguments for other methods. +#' +#' @author David Robinson, Benjamin Nutter +#' +#' @source +#' Skew and Kurtosis functions are adapted from implementations in the \code{moments} package: \cr +#' Lukasz Komsta and Frederick Novomestky (2015). moments: Moments, cumulants, skewness, +#' kurtosis and related tests. R package version 0.14. \cr +#' https://CRAN.R-project.org/package=moments +#' +#' @examples +#' +#' td <- tidy(mtcars) +#' td +#' +#' glance(mtcars) +#' +#' library(ggplot2) +#' # compare mean and standard deviation +#' ggplot(td, aes(mean, sd)) + geom_point() + +#' geom_text(aes(label = column), hjust = 1, vjust = 1) + +#' scale_x_log10() + scale_y_log10() + geom_abline() +#' +#' @name data.frame_tidiers + + +#' @rdname data.frame_tidiers +#' +#' @return \code{tidy.data.frame} produces a data frame with one +#' row per original column, containing summary statistics of each: +#' \item{column}{name of original column} +#' \item{n}{Number of valid (non-NA) values} +#' \item{mean}{mean} +#' \item{sd}{standard deviation} +#' \item{median}{median} +#' \item{trimmed}{trimmed mean, with trim defaulting to .1} +#' \item{mad}{median absolute deviation (from the median)} +#' \item{min}{minimum value} +#' \item{max}{maximum value} +#' \item{range}{range} +#' \item{skew}{skew} +#' \item{kurtosis}{kurtosis} +#' \item{se}{standard error} +#' +#' @export +#' @family deprecated +tidy.data.frame <- function(x, ..., na.rm = TRUE, trim = 0.1) { + .Deprecated( + msg = "Data frame tidiers are deprecated and will be removed in an upcoming release of broom." + ) + ret <- + tibble::data_frame( + column = names(x), + n = vapply( + X = x, + FUN = function(k) sum(!is.na(k)), + FUN.VALUE = numeric(1) + ), + mean = vapply( + X = x, + FUN = mean, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + sd = vapply( + X = x, + FUN = stats::sd, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + median = vapply( + X = x, + FUN = stats::median, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + trimmed = vapply( + X = x, + FUN = mean, + FUN.VALUE = numeric(1), + na.rm = na.rm, + trim = trim + ), + mad = vapply( + X = x, + FUN = median_abs_dev, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + min = vapply( + X = x, + FUN = min, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + max = vapply( + X = x, + FUN = max, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + range = vapply( + X = x, + FUN = function(k, na.rm) diff(range(k, na.rm = na.rm)), + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + skew = vapply( + X = x, + FUN = skewness, + FUN.VALUE = numeric(1), + na.rm = na.rm + ), + kurtosis = vapply( + X = x, + FUN = kurtosis, + FUN.VALUE = numeric(1), + na.rm = na.rm + ) + ) + + ret$se <- ret$sd / sqrt(ret$n) + + ret +} + + +#' @rdname data.frame_tidiers +#' +#' @export +#' @family deprecated +augment.data.frame <- function(x, data, ...) { + stop(paste("augment's first argument should be a model, not a data.frame")) +} + + +#' @rdname data.frame_tidiers +#' +#' @return \code{glance} returns a one-row data.frame with +#' \item{nrow}{number of rows} +#' \item{ncol}{number of columns} +#' \item{complete.obs}{number of rows that have no missing values} +#' \item{na.fraction}{fraction of values across all rows and columns that +#' are missing} +#' +#' @export +#' @family deprecated +glance.data.frame <- function(x, ...) { + .Deprecated( + msg = "Data frame tidiers are deprecated and will be removed in an upcoming release of broom." + ) + ret <- tibble::data_frame( + nrow = nrow(x), + ncol = ncol(x) + ) + ret$complete.obs <- sum(stats::complete.cases(x)) + ret$na.fraction <- mean(is.na(x)) + return(ret) +} + + +# Basic code inspired by moments::skew +skewness <- function(x, na.rm = FALSE) { + n <- sum(!is.na(x)) + (sum((x - mean(x, na.rm = na.rm))^3) / n) / + (sum((x - mean(x, na.rm = na.rm))^2) / n)^(3 / 2) +} + +# Basic code inspired by moments::kurtosis +kurtosis <- function(x, na.rm = FALSE) { + n <- sum(!is.na(x)) + n * sum((x - mean(x, na.rm = na.rm))^4) / + (sum((x - mean(x, na.rm = na.rm))^2)^2) +} + +median_abs_dev <- function(x, na.rm = FALSE) { + stats::median(abs(x - stats::median(x, na.rm = na.rm)), + na.rm = na.rm + ) +} + +# bootstrap -------------------------------------------------------------- + +#' Set up bootstrap replicates of a dplyr operation +#' +#' The \code{bootstrap()} function is deprecated and will be removed from +#' an upcoming release of broom. For tidy resampling, please use the rsample +#' package instead. +#' +#' @param df a data frame +#' @param m number of bootstrap replicates to perform +#' @param by_group If \code{TRUE}, then bootstrap within each group if \code{df} is +#' a grouped tbl. +#' +#' @details This code originates from Hadley Wickham (with a few small +#' corrections) here: +#' +#' https://github.com/hadley/dplyr/issues/269 +#' +#' Some examples can be found at +#' +#' https://github.com/dgrtwo/broom/blob/master/vignettes/bootstrapping.Rmd +#' +#' @examples +#' +#' library(dplyr) +#' mtcars %>% bootstrap(10) %>% do(tidy(lm(mpg ~ wt, .))) +#' +#' @export +#' @family deprecated +bootstrap <- function(df, m, by_group = FALSE) { + .Deprecated( + msg = "`bootstrap()` is deprecated and will be removed in an upcoming release of broom. See the rsample package instead." + ) + n <- nrow(df) + attr(df, "indices") <- + if (by_group && !is.null(groups(df))) { + replicate(m, + unlist(lapply( + attr(df, "indices"), + function(x) { + sample(x, replace = TRUE) + } + ), + recursive = FALSE, use.names = FALSE + ), + simplify = FALSE + ) + } else { + replicate(m, sample(n, replace = TRUE) - + 1, simplify = FALSE) + } + attr(df, "drop") <- TRUE + attr(df, "group_sizes") <- rep(n, m) + attr(df, "biggest_group_size") <- n + attr(df, "labels") <- data.frame(replicate = 1:m) + attr(df, "vars") <- list(quote(replicate)) + class(df) <- c("grouped_df", "tbl_df", "tbl", "data.frame") + df +} + +# fix_data_frame ---------------------------------------------------------- + +#' Ensure an object is a data frame, with rownames moved into a column +#' +#' This function is deprecated as of broom 0.7.0 and will be removed from +#' a future release. Please see \code{tibble::as_tibble}. +#' +#' @param x a data.frame or matrix +#' @param newnames new column names, not including the rownames +#' @param newcol the name of the new rownames column +#' +#' @return a data.frame, with rownames moved into a column and new column +#' names assigned +#' @family deprecated +#' @export +fix_data_frame <- function(x, newnames = NULL, newcol = "term") { + + .Deprecated( + msg = "This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble()." + ) + + if (!is.null(newnames) && length(newnames) != ncol(x)) { + stop("newnames must be NULL or have length equal to number of columns") + } + + if (all(rownames(x) == seq_len(nrow(x)))) { + # don't need to move rownames into a new column + ret <- data.frame(x, stringsAsFactors = FALSE) + if (!is.null(newnames)) { + colnames(ret) <- newnames + } + } + else { + ret <- data.frame( + ...new.col... = rownames(x), + unrowname(x), + stringsAsFactors = FALSE + ) + colnames(ret)[1] <- newcol + if (!is.null(newnames)) { + colnames(ret)[-1] <- newnames + } + } + as_tibble(ret) +} + +# summary objects ----------------------------------------------------- + +#' (Deprecated) Tidy summaryDefault objects +#' +#' Tidiers for summaryDefault objects have been deprecated as of +#' broom 0.7.0 in favor of \code{skimr::skim()}. +#' +#' @param x A `summaryDefault` object, created by calling [summary()] on a +#' vector. +#' @template param_unused_dots +#' +#' @return A one-row [tibble::tibble] with columns: +#' \item{minimum}{Minimum value in original vector.} +#' \item{q1}{First quartile of original vector.} +#' \item{median}{Median of original vector.} +#' \item{mean}{Mean of original vector.} +#' \item{q3}{Third quartile of original vector.} +#' \item{maximum}{Maximum value in original vector.} +#' \item{na}{Number of `NA` values in original vector. Column present only +#' when original vector had at least one `NA` entry.} +#' +#' +#' @examples +#' +#' v <- rnorm(1000) +#' s <- summary(v) +#' s +#' +#' tidy(s) +#' glance(s) +#' +#' v2 <- c(v,NA) +#' tidy(summary(v2)) +#' +#' @name summary_tidiers +#' @export +#' @family deprecated +tidy.summaryDefault <- function(x, ...) { + .Deprecated(msg = "`tidy.summaryDefault()` is deprecated. Please use `skimr::skim()` instead.") + ret <- as.data.frame(t(as.matrix(x))) + cnms <- c("minimum", "q1", "median", "mean", "q3", "maximum") + if ("NA's" %in% names(x)) { + cnms <- c(cnms, "na") + } + as_tibble(purrr::set_names(ret, cnms)) +} + +#' @rdname summary_tidiers +#' @export +#' @family deprecated +glance.summaryDefault <- tidy.summaryDefault + +#' (Deprecated) Tidy ftable objects +#' +#' @description This function is deprecated. Please use [tibble::as_tibble()] instead. +#' +#' @param x An `ftable` object returned from [stats::ftable()]. +#' @template param_unused_dots +#' +#' @return An ftable contains a "flat" contingency table. This melts it into a +#' [tibble::tibble] with one column for each variable, then a `Freq` +#' column. +#' +#' @export +#' @family deprecated +tidy.ftable <- function(x, ...) { + .Deprecated() + as_tibble(x) +} + +#' (Deprecated) Tidy density objects +#' +#' @param x A `density` object returned from [stats::density()]. +#' @template param_unused_dots +#' +#' @return A [tibble::tibble] with two columns: points `x` where the density +#' is estimated, and estimated density `y`. +#' +#' @export +#' @family deprecated +tidy.density <- function(x, ...) { + + as_tibble(x[c("x", "y")]) +} + +#' (Deprecated) Tidy dist objects +#' +#' @param x A `dist` object returned from [stats::dist()]. +#' @param diagonal Logical indicating whether or not to tidy the diagonal +#' elements of the distance matrix. Defaults to whatever was based to the +#' `diag` argument of [stats::dist()]. +#' @param upper Logical indicating whether or not to tidy the upper half of +#' the distance matrix. Defaults to whatever was based to the +#' `upper` argument of [stats::dist()]. +#' @template param_unused_dots +#' +#' @return A [tibble::tibble] with one row for each pair of items in the +#' distance matrix, with columns: +#' +#' \item{item1}{First item} +#' \item{item2}{Second item} +#' \item{distance}{Distance between items} +#' +#' @details If the distance matrix does not include an upper triangle and/or +#' diagonal, the tidied version will not either. +#' +#' @examples +#' +#' iris_dist <- dist(t(iris[, 1:4])) +#' iris_dist +#' +#' tidy(iris_dist) +#' tidy(iris_dist, upper = TRUE) +#' tidy(iris_dist, diagonal = TRUE) +#' +#' @export +#' @family deprecated +tidy.dist <- function(x, diagonal = attr(x, "Diag"), + upper = attr(x, "Upper"), ...) { + m <- as.matrix(x) + + ret <- reshape2::melt(m, + varnames = c("item1", "item2"), + value.name = "distance" + ) + + if (!upper) { + ret <- ret[!upper.tri(m), ] + } + + if (!diagonal) { + ret <- filter(ret, item1 != item2) + } + as_tibble(ret) +} + +# vector tidiers ------------------------------------------------------ +#' Tidy atomic vectors +#' +#' Vector tidiers are deprecated and will be removed from an upcoming release +#' of broom. +#' +#' Turn atomic vectors into data frames, where the names of the vector (if they +#' exist) are a column and the values of the vector are a column. +#' +#' @param x An object of class "numeric", "integer", "character", or "logical". +#' Most likely a named vector +#' @param ... Extra arguments (not used) +#' +#' @examples +#' +#' \dontrun{ +#' x <- 1:5 +#' names(x) <- letters[1:5] +#' tidy(x) +#' } +#' +#' @export +#' @rdname vector_tidiers +#' @family deprecated +tidy.numeric <- function(x, ...) { + .Deprecated() + if (!is.null(names(x))) { + dplyr::data_frame(names = names(x), x = unname(x)) + } else { + dplyr::data_frame(x = x) + } +} + +#' @export +#' @rdname vector_tidiers +#' @family deprecated +tidy.character <- function(x, ...) { + .Deprecated() + if (!is.null(names(x))) { + dplyr::data_frame(names = names(x), x = unname(x)) + } else { + dplyr::data_frame(x = x) + } +} + +#' @export +#' @rdname vector_tidiers +#' @family deprecated +tidy.logical <- function(x, ...) { + .Deprecated() + if (!is.null(names(x))) { + dplyr::data_frame(names = names(x), x = unname(x)) + } else { + dplyr::data_frame(x = x) + } +} + +# confint_tidy ---------------------------------------------------------------- + +#' (Deprecated) Calculate confidence interval as a tidy data frame +#' +#' This function is now deprecated and will be removed from a future +#' release of broom. +#' +#' Return a confidence interval as a tidy data frame. This directly wraps the +#' [confint()] function, but ensures it follows broom conventions: +#' column names of `conf.low` and `conf.high`, and no row names. +#' +#' `confint_tidy` +#' +#' @param x a model object for which [confint()] can be calculated +#' @param conf.level confidence level +#' @param func A function to compute a confidence interval for `x`. Calling +#' `func(x, level = conf.level, ...)` must return an object coercible to a +#' tibble. This dataframe like object should have to columns corresponding +#' the lower and upper bounds on the confidence interval. +#' @param ... extra arguments passed on to `confint` +#' +#' @return A tibble with two columns: `conf.low` and `conf.high`. +#' +#' @export +#' @family deprecated +confint_tidy <- function(x, conf.level = .95, func = stats::confint, ...) { + .Deprecated( + msg = "confint_tidy is now deprecated and will be removed from a future release of broom. Please use the applicable confint method." + ) + + # avoid "Waiting for profiling to be done..." message for some models + ci <- suppressMessages(func(x, level = conf.level, ...)) + + # protect against confidence intervals returned as named vectors + if (is.null(dim(ci))) { + ci <- matrix(ci, nrow = 1) + } + + # remove rows that are all NA. *not the same* as na.omit which checks + # for any NA. + all_na <- apply(ci, 1, function(x) all(is.na(x))) + ci <- ci[!all_na, , drop = FALSE] + colnames(ci) <- c("conf.low", "conf.high") + as_tibble(ci) +} diff --git a/R/robust-glmrob-tidiers.R b/R/robust-glmrob-tidiers.R index 464f6a404..56c5a94ad 100644 --- a/R/robust-glmrob-tidiers.R +++ b/R/robust-glmrob-tidiers.R @@ -31,18 +31,16 @@ tidy.glmRob <- function(x, ...) { #' @param x Unused. #' @param ... Unused. #' -#' @description `augment.glmRob()` has been removed from broom. We regret -#' that we were unable to provide any warning for this change. The -#' \pkg{robust} package does not provide the functionality necessary -#' to implement an augment method. We are looking into supporting the -#' \pkg{robustbase} package in the future. -#' #' @export augment.glmRob <- function(x, ...) { stop( - "`augment.glmRob` has been removed from broom. See the documentation.", + paste0("`augment.glmRob` has been deprecated as the robust package", + "doesn't provide the functionality necessary to implement ", + "an augment method. Please see the augment method for ", + "glmrob objects from robustbase."), call. = FALSE ) + invisible(TRUE) } #' @templateVar class glmRob diff --git a/man/augment.glmRob.Rd b/man/augment.glmRob.Rd index 7e7410408..d328068df 100644 --- a/man/augment.glmRob.Rd +++ b/man/augment.glmRob.Rd @@ -49,10 +49,4 @@ model on data in a tibble. We are in the process of defining behaviors for models fit with various \code{na.action} arguments, but make no guarantees about behavior when data is missing at this time. - -\code{augment.glmRob()} has been removed from broom. We regret -that we were unable to provide any warning for this change. The -\pkg{robust} package does not provide the functionality necessary -to implement an augment method. We are looking into supporting the -\pkg{robustbase} package in the future. } diff --git a/man/bootstrap.Rd b/man/bootstrap.Rd new file mode 100644 index 000000000..f729b1c58 --- /dev/null +++ b/man/bootstrap.Rd @@ -0,0 +1,49 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{bootstrap} +\alias{bootstrap} +\title{Set up bootstrap replicates of a dplyr operation} +\usage{ +bootstrap(df, m, by_group = FALSE) +} +\arguments{ +\item{df}{a data frame} + +\item{m}{number of bootstrap replicates to perform} + +\item{by_group}{If \code{TRUE}, then bootstrap within each group if \code{df} is +a grouped tbl.} +} +\description{ +The \code{bootstrap()} function is deprecated and will be removed from +an upcoming release of broom. For tidy resampling, please use the rsample +package instead. +} +\details{ +This code originates from Hadley Wickham (with a few small +corrections) here: + +https://github.com/hadley/dplyr/issues/269 + +Some examples can be found at + +https://github.com/dgrtwo/broom/blob/master/vignettes/bootstrapping.Rmd +} +\examples{ + +library(dplyr) +mtcars \%>\% bootstrap(10) \%>\% do(tidy(lm(mpg ~ wt, .))) + +} +\seealso{ +Other deprecated: +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\concept{deprecated} diff --git a/man/confint_tidy.Rd b/man/confint_tidy.Rd new file mode 100644 index 000000000..c9a8fad33 --- /dev/null +++ b/man/confint_tidy.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{confint_tidy} +\alias{confint_tidy} +\title{(Deprecated) Calculate confidence interval as a tidy data frame} +\usage{ +confint_tidy(x, conf.level = 0.95, func = stats::confint, ...) +} +\arguments{ +\item{x}{a model object for which \code{\link[=confint]{confint()}} can be calculated} + +\item{conf.level}{confidence level} + +\item{func}{A function to compute a confidence interval for \code{x}. Calling +\code{func(x, level = conf.level, ...)} must return an object coercible to a +tibble. This dataframe like object should have to columns corresponding +the lower and upper bounds on the confidence interval.} + +\item{...}{extra arguments passed on to \code{confint}} +} +\value{ +A tibble with two columns: \code{conf.low} and \code{conf.high}. +} +\description{ +This function is now deprecated and will be removed from a future +release of broom. +} +\details{ +Return a confidence interval as a tidy data frame. This directly wraps the +\code{\link[=confint]{confint()}} function, but ensures it follows broom conventions: +column names of \code{conf.low} and \code{conf.high}, and no row names. + +\code{confint_tidy} +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\concept{deprecated} diff --git a/man/data.frame_tidiers.Rd b/man/data.frame_tidiers.Rd new file mode 100644 index 000000000..f129e7cce --- /dev/null +++ b/man/data.frame_tidiers.Rd @@ -0,0 +1,118 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{data.frame_tidiers} +\alias{data.frame_tidiers} +\alias{tidy.data.frame} +\alias{augment.data.frame} +\alias{glance.data.frame} +\title{Tidiers for data.frame objects} +\source{ +Skew and Kurtosis functions are adapted from implementations in the \code{moments} package: \cr +Lukasz Komsta and Frederick Novomestky (2015). moments: Moments, cumulants, skewness, +kurtosis and related tests. R package version 0.14. \cr +https://CRAN.R-project.org/package=moments +} +\usage{ +\method{tidy}{data.frame}(x, ..., na.rm = TRUE, trim = 0.1) + +\method{augment}{data.frame}(x, data, ...) + +\method{glance}{data.frame}(x, ...) +} +\arguments{ +\item{x}{A data.frame} + +\item{...}{Additional arguments for other methods.} + +\item{na.rm}{a logical value indicating whether \code{NA} values should +be stripped before the computation proceeds.} + +\item{trim}{the fraction (0 to 0.5) of observations to be trimmed from +each end of \code{x} before the mean is computed. Passed to the +\code{trim} argument of \code{\link{mean}}} + +\item{data}{data, not used} +} +\value{ +\code{tidy.data.frame} produces a data frame with one +row per original column, containing summary statistics of each: +\item{column}{name of original column} +\item{n}{Number of valid (non-NA) values} +\item{mean}{mean} +\item{sd}{standard deviation} +\item{median}{median} +\item{trimmed}{trimmed mean, with trim defaulting to .1} +\item{mad}{median absolute deviation (from the median)} +\item{min}{minimum value} +\item{max}{maximum value} +\item{range}{range} +\item{skew}{skew} +\item{kurtosis}{kurtosis} +\item{se}{standard error} + +\code{glance} returns a one-row data.frame with +\item{nrow}{number of rows} +\item{ncol}{number of columns} +\item{complete.obs}{number of rows that have no missing values} +\item{na.fraction}{fraction of values across all rows and columns that +are missing} +} +\description{ +Data frame tidiers are deprecated and will be removed from an upcoming +release of broom. +} +\details{ +These perform tidy summaries of data.frame objects. \code{tidy} produces +summary statistics about each column, while \code{glance} simply reports +the number of rows and columns. Note that \code{augment.data.frame} will +throw an error. +} +\examples{ + +td <- tidy(mtcars) +td + +glance(mtcars) + +library(ggplot2) +# compare mean and standard deviation +ggplot(td, aes(mean, sd)) + geom_point() + + geom_text(aes(label = column), hjust = 1, vjust = 1) + + scale_x_log10() + scale_y_log10() + geom_abline() + +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} + +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} + +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\author{ +David Robinson, Benjamin Nutter +} +\concept{deprecated} diff --git a/man/fix_data_frame.Rd b/man/fix_data_frame.Rd new file mode 100644 index 000000000..a480ef55c --- /dev/null +++ b/man/fix_data_frame.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{fix_data_frame} +\alias{fix_data_frame} +\title{Ensure an object is a data frame, with rownames moved into a column} +\usage{ +fix_data_frame(x, newnames = NULL, newcol = "term") +} +\arguments{ +\item{x}{a data.frame or matrix} + +\item{newnames}{new column names, not including the rownames} + +\item{newcol}{the name of the new rownames column} +} +\value{ +a data.frame, with rownames moved into a column and new column +names assigned +} +\description{ +This function is deprecated as of broom 0.7.0 and will be removed from +a future release. Please see \code{tibble::as_tibble}. +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\concept{deprecated} diff --git a/man/summary_tidiers.Rd b/man/summary_tidiers.Rd new file mode 100644 index 000000000..4fd07662c --- /dev/null +++ b/man/summary_tidiers.Rd @@ -0,0 +1,76 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{summary_tidiers} +\alias{summary_tidiers} +\alias{tidy.summaryDefault} +\alias{glance.summaryDefault} +\title{(Deprecated) Tidy summaryDefault objects} +\usage{ +\method{tidy}{summaryDefault}(x, ...) + +\method{glance}{summaryDefault}(x, ...) +} +\arguments{ +\item{x}{A \code{summaryDefault} object, created by calling \code{\link[=summary]{summary()}} on a +vector.} + +\item{...}{Additional arguments. Not used. Needed to match generic +signature only. \strong{Cautionary note:} Misspelled arguments will be +absorbed in \code{...}, where they will be ignored. If the misspelled +argument has a default value, the default value will be used. +For example, if you pass \code{conf.lvel = 0.9}, all computation will +proceed using \code{conf.level = 0.95}. Additionally, if you pass +\code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not +accept a \code{newdata} argument, it will use the default value for +the \code{data} argument.} +} +\value{ +A one-row \link[tibble:tibble]{tibble::tibble} with columns: +\item{minimum}{Minimum value in original vector.} +\item{q1}{First quartile of original vector.} +\item{median}{Median of original vector.} +\item{mean}{Mean of original vector.} +\item{q3}{Third quartile of original vector.} +\item{maximum}{Maximum value in original vector.} +\item{na}{Number of \code{NA} values in original vector. Column present only +when original vector had at least one \code{NA} entry.} +} +\description{ +Tidiers for summaryDefault objects have been deprecated as of +broom 0.7.0 in favor of \code{skimr::skim()}. +} +\examples{ + +v <- rnorm(1000) +s <- summary(v) +s + +tidy(s) +glance(s) + +v2 <- c(v,NA) +tidy(summary(v2)) + +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} + +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\concept{deprecated} diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index 657cf8793..c4532b067 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -1,9 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R \name{tidy.density} \alias{tidy.density} -\title{Tidy a(n) density object} +\title{(Deprecated) Tidy density objects} \usage{ +\method{tidy}{density}(x, ...) + \method{tidy}{density}(x, ...) } \arguments{ @@ -20,6 +22,9 @@ accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \value{ +A \link[tibble:tibble]{tibble::tibble} with two columns: points \code{x} where the density +is estimated, and estimated density \code{y}. + A \link[tibble:tibble]{tibble::tibble} with two columns: points \code{x} where the density is estimated, and estimated density \code{y}. When the input to the \code{\link[stats:density]{stats::density()}} function is an \code{nXm} matrix, as opposed to @@ -37,8 +42,19 @@ specify which components to return. \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[stats:density]{stats::density()}} +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} + Other stats tidiers: \code{\link{tidy.dist}()}, \code{\link{tidy.ftable}()} } +\concept{deprecated} \concept{stats tidiers} diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index cce0a48de..b8828fb8a 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -1,9 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R \name{tidy.dist} \alias{tidy.dist} -\title{Tidy a(n) dist object} +\title{(Deprecated) Tidy dist objects} \usage{ +\method{tidy}{dist}(x, diagonal = attr(x, "Diag"), ...) + \method{tidy}{dist}(x, diagonal = attr(x, "Diag"), ...) } \arguments{ @@ -22,6 +24,18 @@ proceed using \code{conf.level = 0.95}. Additionally, if you pass \code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} + +\item{upper}{Logical indicating whether or not to tidy the upper half of +the distance matrix. Defaults to whatever was based to the +\code{upper} argument of \code{\link[stats:dist]{stats::dist()}}.} +} +\value{ +A \link[tibble:tibble]{tibble::tibble} with one row for each pair of items in the +distance matrix, with columns: + +\item{item1}{First item} +\item{item2}{Second item} +\item{distance}{Distance between items} } \description{ Tidy summarizes information about the components of a model. @@ -32,11 +46,22 @@ If a model has several distinct types of components, you will need to specify which components to return. } \details{ +If the distance matrix does not include an upper triangle and/or +diagonal, the tidied version will not either. + If the distance matrix does not include the diagonal, the tidied version will not either. } \examples{ +iris_dist <- dist(t(iris[, 1:4])) +iris_dist + +tidy(iris_dist) +tidy(iris_dist, upper = TRUE) +tidy(iris_dist, diagonal = TRUE) + + library(modeldata) data(hpc_data) @@ -50,10 +75,21 @@ tidy(hpc_dist, diagonal = TRUE) \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} + Other stats tidiers: \code{\link{tidy.density}()}, \code{\link{tidy.ftable}()} } +\concept{deprecated} \concept{stats tidiers} \value{ A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: diff --git a/man/tidy.ftable.Rd b/man/tidy.ftable.Rd index 05d724164..587a9ed76 100644 --- a/man/tidy.ftable.Rd +++ b/man/tidy.ftable.Rd @@ -1,9 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R \name{tidy.ftable} \alias{tidy.ftable} -\title{Tidy a(n) ftable object} +\title{(Deprecated) Tidy ftable objects} \usage{ +\method{tidy}{ftable}(x, ...) + \method{tidy}{ftable}(x, ...) } \arguments{ @@ -20,11 +22,17 @@ accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \value{ +An ftable contains a "flat" contingency table. This melts it into a +\link[tibble:tibble]{tibble::tibble} with one column for each variable, then a \code{Freq} +column. + An ftable contains a "flat" contingency table. This melts it into a \link[tibble:tibble]{tibble::tibble} with one column for each variable, then a \code{Freq} column. } \description{ +This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. + Tidy summarizes information about the components of a model. A model component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a @@ -37,8 +45,19 @@ This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.numeric}()} + Other stats tidiers: \code{\link{tidy.density}()}, \code{\link{tidy.dist}()} } +\concept{deprecated} \concept{stats tidiers} diff --git a/man/vector_tidiers.Rd b/man/vector_tidiers.Rd new file mode 100644 index 000000000..f38f01910 --- /dev/null +++ b/man/vector_tidiers.Rd @@ -0,0 +1,69 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{tidy.numeric} +\alias{tidy.numeric} +\alias{tidy.character} +\alias{tidy.logical} +\title{Tidy atomic vectors} +\usage{ +\method{tidy}{numeric}(x, ...) + +\method{tidy}{character}(x, ...) + +\method{tidy}{logical}(x, ...) +} +\arguments{ +\item{x}{An object of class "numeric", "integer", "character", or "logical". +Most likely a named vector} + +\item{...}{Extra arguments (not used)} +} +\description{ +Vector tidiers are deprecated and will be removed from an upcoming release +of broom. +} +\details{ +Turn atomic vectors into data frames, where the names of the vector (if they +exist) are a column and the values of the vector are a column. +} +\examples{ + +\dontrun{ +x <- 1:5 +names(x) <- letters[1:5] +tidy(x) +} + +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()} + +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()} + +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()} +} +\concept{deprecated} From ccc76245c2b7d99e995baac6bd2e0c40946d1a5c Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 23 Jun 2020 08:43:24 -0700 Subject: [PATCH 29/41] adjust language about deprecations --- NEWS.md | 20 ++++++-------------- cran-comments.md | 36 +++++++++++++++++++++++++++--------- 2 files changed, 33 insertions(+), 23 deletions(-) diff --git a/NEWS.md b/NEWS.md index f864bef29..c914d0d7e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,13 +1,9 @@ # broom 0.7.0 -## Breaking changes - -`broom 0.7.0` is a major release with a large number of breaking changes and -deprecations. Most of these breaking changes are meant to improve -maintainability and internal consistency, which have posed long-standing -difficulties. +`broom 0.7.0` is a major release with a large number of new tidiers, +soft-deprecations, and carrying out of planned breaking changes. -### Big picture breaking changes +### Big picture changes - We have changed how we report degrees of freedom for `lm` objects (#212, #273). This is especially important for instructors in statistics @@ -47,7 +43,7 @@ of `comparison`, `level1` and `level2`, or `lhs` and `rhs` (see #692). ### Deprecations -This release of `broom` hard-deprecates the following functions and tidier +This release of `broom` soft-deprecates the following functions and tidier methods: - Tidier methods for data frames, rowwise data frames, vectors and matrices @@ -60,12 +56,8 @@ methods: - `tidy.summaryDefault()` and `glance.summaryDefault()` have been deprecated in favor of `skimr::skim()` -We regret that we were unable to provide warnings for some of these -changes. Affected maintainers were notified two weeks before the planned release. - -We have also gone forward with our planned mixed model -deprecations, and have removed the following methods, which now live -in `broom.mixed`: +We have also gone forward with our planned mixed model deprecations, and have +removed the following methods, which now live in `broom.mixed`: - `tidy.brmsfit()` - `tidy.merMod()`, `glance.merMod()`, `augment.merMod()` diff --git a/cran-comments.md b/cran-comments.md index 08d05de12..64585c5ba 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,18 @@ # Release summary -This is a resubmission following an automated pretest failure due to -breaking changes in the `epi.2by2` function from the `epiR` package, a new -version of which was released on CRAN since our previous submission. +This is a resubmission following a request to first deprecate breaking +changes and send another reminder to maintainers. We have made the requested +changes and carried out another round of reverse dependency checks, notifying +maintainers with unfixed breakages. We note that several remaining breakages +are due to removal of mixed-model tidiers that were deprecated in previous +releases--we have not reverted these methods back to soft-deprecations as +their namespace conflicts with the broom.mixed package, which provides a +consistent interface to mixed model tidiers, have caused user confusion. + +The previous submission was also a resubmission following an automated +pretest failure due to breaking changes in the `epi.2by2` function from +the `epiR` package, a new version of which was released on CRAN since +our previous submission. The previous submission was also a resubmission following an erroniously included Remotes section in the package DESCRIPTION. @@ -36,14 +46,22 @@ methods to the `broom.mixed` package. ## revdepcheck results -We checked 149 reverse dependencies, comparing R CMD check results across -CRAN and dev versions of this package. We saw 37 new problems and failed to -check one package. +In the initial round of revdepchecks, we checked 149 reverse dependencies, +comparing R CMD check results across CRAN and dev versions of this package. +We saw 37 new problems and failed to check one package. -We first notified affected maintainers three weeks ago, and -checked in with maintainers again a week and a half ago. Records -of our initial outreach attempts can be found on this issue: +We first notified affected maintainers three weeks prior to our initial +submission, and checked in with maintainers again a week and a half ago. +Records of our initial outreach attempts can be found on this issue: https://github.com/tidymodels/broom/issues/862 +Since reverting removals to soft-deprecations, we have ran revdepchecks again. +Records of our outreach with maintainers of packages that are still newly +broken (since 0.5.6) can be found on this issue: + + + + + From a119078a56b3e01d2050b605ec31d324eb738767 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 23 Jun 2020 09:18:10 -0700 Subject: [PATCH 30/41] some check fixes re: deprecations --- DESCRIPTION | 3 +- R/deprecated-0-7-0.R | 18 ++------ R/stats-tidiers.R | 86 ------------------------------------ inst/WORDLIST | 3 ++ man/bootstrap.Rd | 17 ++----- man/tidy.density.Rd | 24 +--------- man/tidy.dist.Rd | 48 +++----------------- man/tidy.ftable.Rd | 24 +--------- tests/testthat/test-robust.R | 7 --- 9 files changed, 21 insertions(+), 209 deletions(-) delete mode 100644 R/stats-tidiers.R diff --git a/DESCRIPTION b/DESCRIPTION index f831b98c3..5f6e9446e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -605,7 +605,7 @@ VignetteBuilder: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.0.9000 Language: en-US Collate: 'aaa-documentation-helper.R' @@ -700,7 +700,6 @@ Collate: 'stats-mlm-tidiers.R' 'stats-prcomp-tidiers.R' 'stats-smooth.spline-tidiers.R' - 'stats-tidiers.R' 'stats-time-series-tidiers.R' 'survey-tidiers.R' 'survival-aareg-tidiers.R' diff --git a/R/deprecated-0-7-0.R b/R/deprecated-0-7-0.R index 90aba99e5..88f6d529f 100644 --- a/R/deprecated-0-7-0.R +++ b/R/deprecated-0-7-0.R @@ -209,26 +209,16 @@ median_abs_dev <- function(x, na.rm = FALSE) { #' #' The \code{bootstrap()} function is deprecated and will be removed from #' an upcoming release of broom. For tidy resampling, please use the rsample -#' package instead. +#' package instead. Functionality is no longer supported for this method. #' #' @param df a data frame #' @param m number of bootstrap replicates to perform #' @param by_group If \code{TRUE}, then bootstrap within each group if \code{df} is -#' a grouped tbl. +#' a grouped tibble. #' #' @details This code originates from Hadley Wickham (with a few small #' corrections) here: -#' -#' https://github.com/hadley/dplyr/issues/269 -#' -#' Some examples can be found at -#' -#' https://github.com/dgrtwo/broom/blob/master/vignettes/bootstrapping.Rmd -#' -#' @examples -#' -#' library(dplyr) -#' mtcars %>% bootstrap(10) %>% do(tidy(lm(mpg ~ wt, .))) +#' \url{https://github.com/hadley/dplyr/issues/269} #' #' @export #' @family deprecated @@ -405,7 +395,7 @@ tidy.density <- function(x, ...) { #' `upper` argument of [stats::dist()]. #' @template param_unused_dots #' -#' @return A [tibble::tibble] with one row for each pair of items in the +#' @return A [tibble::tibble] with one row for each pair of items in the #' distance matrix, with columns: #' #' \item{item1}{First item} diff --git a/R/stats-tidiers.R b/R/stats-tidiers.R deleted file mode 100644 index bd4f8d4cc..000000000 --- a/R/stats-tidiers.R +++ /dev/null @@ -1,86 +0,0 @@ -#' @templateVar class ftable -#' @template title_desc_tidy -#' -#' @description This function is deprecated. Please use [tibble::as_tibble()] instead. -#' -#' @param x An `ftable` object returned from [stats::ftable()]. -#' @template param_unused_dots -#' -#' @return An ftable contains a "flat" contingency table. This melts it into a -#' [tibble::tibble] with one column for each variable, then a `Freq` -#' column. -#' -#' @export -#' @seealso [tidy()], [stats::ftable()] -#' @family stats tidiers -tidy.ftable <- function(x, ...) { - .Deprecated() - as_tibble(x) -} - -#' @templateVar class density -#' @template title_desc_tidy -#' -#' @param x A `density` object returned from [stats::density()]. -#' @template param_unused_dots -#' -#' @return A [tibble::tibble] with two columns: points `x` where the density -#' is estimated, and estimated density `y`. When the input to the -#' [stats::density()] function is an `nXm` matrix, as opposed to -#' a `1Xm` vector, the input matrix is first flattened into a `1X(m*n)` vector -#' and then the density function is applied as usual. - -#' @export -#' @seealso [tidy()], [stats::density()] -#' @family stats tidiers -tidy.density <- function(x, ...) { - as_tibble(x[c("x", "y")]) -} - -#' @templateVar class dist -#' @template title_desc_tidy -#' -#' @param x A `dist` object returned from [stats::dist()]. -#' -#' @param diagonal Logical indicating whether or not to tidy the diagonal -#' elements of the distance matrix. Defaults to whatever was based to the -#' `diag` argument of [stats::dist()]. -#' -#' @template param_unused_dots -#' -#' @evalRd return_tidy("item1", "item2", "distance") -#' -#' @details If the distance matrix does not include the diagonal, -#' the tidied version will not either. -#' -#' @examples -#' -#' library(modeldata) -#' data(hpc_data) -#' -#' hpc <- hpc_data[, 2:5] -#' hpc_dist <- dist(t(hpc)) -#' -#' tidy(hpc_dist) -#' tidy(hpc_dist, upper = TRUE) -#' tidy(hpc_dist, diagonal = TRUE) -#' @export -#' @seealso [tidy()], [stats::dist()] -#' @family stats tidiers -#' -tidy.dist <- function(x, diagonal = attr(x, "Diag"), ...) { - m <- as.matrix(x) - - ret <- as_tibble(m, rownames = "item1") %>% - pivot_longer( - cols = c(dplyr::everything(), -item1), - names_to = "item2", - values_to = "distance" - ) - - if (!diagonal) { - ret <- dplyr::filter(ret, item1 != item2) - } - - ret -} diff --git a/inst/WORDLIST b/inst/WORDLIST index e3ac9d84a..a91c2e1c2 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -42,6 +42,7 @@ confint confusionMatrix converage coxph +cumulants cv cyl deprecations @@ -157,6 +158,7 @@ newdata nlme nlrq nls +Novomestky nnet NULLs NUM @@ -191,6 +193,7 @@ rjags rlm rma RMA +Rmd RMSEA robustbase roc diff --git a/man/bootstrap.Rd b/man/bootstrap.Rd index f729b1c58..eed5bcf67 100644 --- a/man/bootstrap.Rd +++ b/man/bootstrap.Rd @@ -12,28 +12,17 @@ bootstrap(df, m, by_group = FALSE) \item{m}{number of bootstrap replicates to perform} \item{by_group}{If \code{TRUE}, then bootstrap within each group if \code{df} is -a grouped tbl.} +a grouped tibble.} } \description{ The \code{bootstrap()} function is deprecated and will be removed from an upcoming release of broom. For tidy resampling, please use the rsample -package instead. +package instead. Functionality is no longer supported for this method. } \details{ This code originates from Hadley Wickham (with a few small corrections) here: - -https://github.com/hadley/dplyr/issues/269 - -Some examples can be found at - -https://github.com/dgrtwo/broom/blob/master/vignettes/bootstrapping.Rmd -} -\examples{ - -library(dplyr) -mtcars \%>\% bootstrap(10) \%>\% do(tidy(lm(mpg ~ wt, .))) - +\url{https://github.com/hadley/dplyr/issues/269} } \seealso{ Other deprecated: diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index c4532b067..dd702e991 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -1,11 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R \name{tidy.density} \alias{tidy.density} \title{(Deprecated) Tidy density objects} \usage{ -\method{tidy}{density}(x, ...) - \method{tidy}{density}(x, ...) } \arguments{ @@ -24,24 +22,11 @@ the \code{data} argument.} \value{ A \link[tibble:tibble]{tibble::tibble} with two columns: points \code{x} where the density is estimated, and estimated density \code{y}. - -A \link[tibble:tibble]{tibble::tibble} with two columns: points \code{x} where the density -is estimated, and estimated density \code{y}. When the input to the -\code{\link[stats:density]{stats::density()}} function is an \code{nXm} matrix, as opposed to -a \verb{1Xm} vector, the input matrix is first flattened into a \verb{1X(m*n)} vector -and then the density function is applied as usual. } \description{ -Tidy summarizes information about the components of a model. -A model component might be a single term in a regression, a single -hypothesis, a cluster, or a class. Exactly what tidy considers to be a -model component varies across models but is usually self-evident. -If a model has several distinct types of components, you will need to -specify which components to return. +(Deprecated) Tidy density objects } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:density]{stats::density()}} - Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, @@ -51,10 +36,5 @@ Other deprecated: \code{\link{tidy.dist}()}, \code{\link{tidy.ftable}()}, \code{\link{tidy.numeric}()} - -Other stats tidiers: -\code{\link{tidy.dist}()}, -\code{\link{tidy.ftable}()} } \concept{deprecated} -\concept{stats tidiers} diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index b8828fb8a..0dd44400f 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -1,12 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R \name{tidy.dist} \alias{tidy.dist} \title{(Deprecated) Tidy dist objects} \usage{ -\method{tidy}{dist}(x, diagonal = attr(x, "Diag"), ...) - -\method{tidy}{dist}(x, diagonal = attr(x, "Diag"), ...) +\method{tidy}{dist}(x, diagonal = attr(x, "Diag"), upper = attr(x, "Upper"), ...) } \arguments{ \item{x}{A \code{dist} object returned from \code{\link[stats:dist]{stats::dist()}}.} @@ -15,6 +13,10 @@ elements of the distance matrix. Defaults to whatever was based to the \code{diag} argument of \code{\link[stats:dist]{stats::dist()}}.} +\item{upper}{Logical indicating whether or not to tidy the upper half of +the distance matrix. Defaults to whatever was based to the +\code{upper} argument of \code{\link[stats:dist]{stats::dist()}}.} + \item{...}{Additional arguments. Not used. Needed to match generic signature only. \strong{Cautionary note:} Misspelled arguments will be absorbed in \code{...}, where they will be ignored. If the misspelled @@ -24,10 +26,6 @@ proceed using \code{conf.level = 0.95}. Additionally, if you pass \code{newdata = my_tibble} to an \code{\link[=augment]{augment()}} method that does not accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} - -\item{upper}{Logical indicating whether or not to tidy the upper half of -the distance matrix. Defaults to whatever was based to the -\code{upper} argument of \code{\link[stats:dist]{stats::dist()}}.} } \value{ A \link[tibble:tibble]{tibble::tibble} with one row for each pair of items in the @@ -38,19 +36,11 @@ distance matrix, with columns: \item{distance}{Distance between items} } \description{ -Tidy summarizes information about the components of a model. -A model component might be a single term in a regression, a single -hypothesis, a cluster, or a class. Exactly what tidy considers to be a -model component varies across models but is usually self-evident. -If a model has several distinct types of components, you will need to -specify which components to return. +(Deprecated) Tidy dist objects } \details{ If the distance matrix does not include an upper triangle and/or diagonal, the tidied version will not either. - -If the distance matrix does not include the diagonal, -the tidied version will not either. } \examples{ @@ -61,20 +51,8 @@ tidy(iris_dist) tidy(iris_dist, upper = TRUE) tidy(iris_dist, diagonal = TRUE) - -library(modeldata) -data(hpc_data) - -hpc <- hpc_data[, 2:5] -hpc_dist <- dist(t(hpc)) - -tidy(hpc_dist) -tidy(hpc_dist, upper = TRUE) -tidy(hpc_dist, diagonal = TRUE) } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:dist]{stats::dist()}} - Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, @@ -84,17 +62,5 @@ Other deprecated: \code{\link{tidy.density}()}, \code{\link{tidy.ftable}()}, \code{\link{tidy.numeric}()} - -Other stats tidiers: -\code{\link{tidy.density}()}, -\code{\link{tidy.ftable}()} } \concept{deprecated} -\concept{stats tidiers} -\value{ -A \code{\link[tibble:tibble]{tibble::tibble()}} with columns: - \item{distance}{Distance between items.} - \item{item1}{First item.} - \item{item2}{Second item.} - -} diff --git a/man/tidy.ftable.Rd b/man/tidy.ftable.Rd index 587a9ed76..75be54f14 100644 --- a/man/tidy.ftable.Rd +++ b/man/tidy.ftable.Rd @@ -1,11 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/deprecated-0-7-0.R, R/stats-tidiers.R +% Please edit documentation in R/deprecated-0-7-0.R \name{tidy.ftable} \alias{tidy.ftable} \title{(Deprecated) Tidy ftable objects} \usage{ -\method{tidy}{ftable}(x, ...) - \method{tidy}{ftable}(x, ...) } \arguments{ @@ -22,29 +20,14 @@ accept a \code{newdata} argument, it will use the default value for the \code{data} argument.} } \value{ -An ftable contains a "flat" contingency table. This melts it into a -\link[tibble:tibble]{tibble::tibble} with one column for each variable, then a \code{Freq} -column. - An ftable contains a "flat" contingency table. This melts it into a \link[tibble:tibble]{tibble::tibble} with one column for each variable, then a \code{Freq} column. } \description{ -This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. - -Tidy summarizes information about the components of a model. -A model component might be a single term in a regression, a single -hypothesis, a cluster, or a class. Exactly what tidy considers to be a -model component varies across models but is usually self-evident. -If a model has several distinct types of components, you will need to -specify which components to return. - This function is deprecated. Please use \code{\link[tibble:as_tibble]{tibble::as_tibble()}} instead. } \seealso{ -\code{\link[=tidy]{tidy()}}, \code{\link[stats:ftable]{stats::ftable()}} - Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, @@ -54,10 +37,5 @@ Other deprecated: \code{\link{tidy.density}()}, \code{\link{tidy.dist}()}, \code{\link{tidy.numeric}()} - -Other stats tidiers: -\code{\link{tidy.density}()}, -\code{\link{tidy.dist}()} } \concept{deprecated} -\concept{stats tidiers} diff --git a/tests/testthat/test-robust.R b/tests/testthat/test-robust.R index 5d66fda6e..2678d2e93 100644 --- a/tests/testthat/test-robust.R +++ b/tests/testthat/test-robust.R @@ -53,13 +53,6 @@ test_that("glance.glmRob", { check_glance_outputs(gl) }) -test_that("augment.glmRob", { - expect_error( - augment.glmRob(), - "`augment.glmRob` has been removed from broom. See the documentation." - ) -}) - test_that("no more rlang issues with model objects from robust", { # from issue 720 expect_equal( From adb2c9cdbbcaa907b8a74ceef3fc10b1b9f09f48 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Tue, 23 Jun 2020 09:45:08 -0700 Subject: [PATCH 31/41] tidy.dist fixes Write out iris example and reshape2 dependency --- R/deprecated-0-7-0.R | 22 ++++++++++---------- tests/testthat/test-stats.R | 40 ------------------------------------- 2 files changed, 11 insertions(+), 51 deletions(-) delete mode 100644 tests/testthat/test-stats.R diff --git a/R/deprecated-0-7-0.R b/R/deprecated-0-7-0.R index 88f6d529f..2270d3e41 100644 --- a/R/deprecated-0-7-0.R +++ b/R/deprecated-0-7-0.R @@ -407,26 +407,26 @@ tidy.density <- function(x, ...) { #' #' @examples #' -#' iris_dist <- dist(t(iris[, 1:4])) -#' iris_dist +#' cars_dist <- dist(t(mtcars[, 1:4])) +#' cars_dist #' -#' tidy(iris_dist) -#' tidy(iris_dist, upper = TRUE) -#' tidy(iris_dist, diagonal = TRUE) +#' tidy(cars_dist) +#' tidy(cars_dist, upper = TRUE) +#' tidy(cars_dist, diagonal = TRUE) #' #' @export #' @family deprecated tidy.dist <- function(x, diagonal = attr(x, "Diag"), upper = attr(x, "Upper"), ...) { - m <- as.matrix(x) - ret <- reshape2::melt(m, - varnames = c("item1", "item2"), - value.name = "distance" - ) + ret <- as.matrix(x) %>% + tibble::as_tibble(rownames = "item1") %>% + tidyr::pivot_longer(cols = c(dplyr::everything(), -1)) %>% + dplyr::rename(item2 = 2, distance = 3) %>% + dplyr::mutate(item1 = as.factor(item1), item2 = as.factor(item2)) if (!upper) { - ret <- ret[!upper.tri(m), ] + ret <- as.data.frame(ret)[!upper.tri(as.matrix(x)), ] } if (!diagonal) { diff --git a/tests/testthat/test-stats.R b/tests/testthat/test-stats.R deleted file mode 100644 index b08972622..000000000 --- a/tests/testthat/test-stats.R +++ /dev/null @@ -1,40 +0,0 @@ -context("stats") - -skip_if_not_installed("modeltests") -library(modeltests) - -skip_if_not_installed("modeldata") -library(modeldata) -data(hpc_data) - -hpc <- hpc_data[, 2:5] - -test_that("tidy.density", { - den <- density(faithful$eruptions, bw = "sj") - td <- tidy(den) - - check_arguments(tidy.density) - check_tidy_output(td, strict = FALSE) - check_dims(td, 512, 2) -}) - -test_that("tidy.dist", { - hpc_dist <- dist(t(hpc)) - td <- tidy(hpc_dist) - td_upper <- tidy(hpc_dist, upper = TRUE) - td_diag <- tidy(hpc_dist, diagonal = TRUE) - td_all <- tidy(hpc_dist, upper = TRUE, diagonal = TRUE) - - check_arguments(tidy.dist) - check_tidy_output(td) - check_dims(td, 12, 3) - - check_tidy_output(td_upper) - check_dims(td_upper, 12, 3) - - check_tidy_output(td_diag) - check_dims(td_diag, 16, 3) - - check_tidy_output(td_all) - check_dims(td_all, 16, 3) -}) From 21c47758169314b09ed267200be67def2b395bf8 Mon Sep 17 00:00:00 2001 From: Max Kuhn Date: Tue, 23 Jun 2020 19:14:15 -0400 Subject: [PATCH 32/41] 0.7.0 revdeps --- revdep/README.md | 92 +- revdep/data.sqlite | Bin 7352320 -> 7176192 bytes revdep/failures.md | 2703 ++++++++++++++++++++++++++++++++++++- revdep/problems.md | 3142 +++++++++++++++++++++++++++----------------- 4 files changed, 4668 insertions(+), 1269 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 39ede5da9..4c72628cb 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,69 +2,53 @@ |field |value | |:--------|:----------------------------| -|version |R version 3.6.1 (2019-07-05) | -|os |macOS Mojave 10.14.6 | -|system |x86_64, darwin15.6.0 | +|version |R version 4.0.0 (2020-04-24) | +|os |macOS Catalina 10.15.5 | +|system |x86_64, darwin17.0 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/New_York | -|date |2020-05-25 | +|date |2020-06-23 | # Dependencies -|package |old |new |Δ | -|:-------|:-----|:----------|:--| -|broom |0.5.6 |0.7.0.9000 |* | +|package |old |new |Δ | +|:-------|:-----|:-----|:--| +|broom |0.5.6 |0.7.0 |* | # Revdeps -## Failed to check (1) - -|package |version |error |warning |note | -|:--------|:-------|:-----|:-------|:----| -|miceFast |0.5.1 |1 | | | - -## New problems (37) - -|package |version |error |warning |note | -|:--------------------------------------------------|:-------|:------|:-------|:--------| -|[allestimates](problems.md#allestimates) |0.1.6 |__+1__ | |1 | -|[arsenal](problems.md#arsenal) |3.4.0 |__+1__ | |__+1__ | -|[biobroom](problems.md#biobroom) |1.18.0 |__+1__ |-1 |2 | -|[breathtestcore](problems.md#breathtestcore) |0.6.0 |__+2__ | |1 | -|[CGPfunctions](problems.md#cgpfunctions) |0.6.0 |__+1__ | | | -|[chest](problems.md#chest) |0.3.1 |__+1__ | |1 | -|[DeLorean](problems.md#delorean) |1.5.0 |-1 | |__+3__ | -|[disk.frame](problems.md#diskframe) |0.3.5 |__+1__ |1 | | -|[disto](problems.md#disto) |0.2.0 |__+1__ | |1 | -|[ERSA](problems.md#ersa) |0.1.1 |__+1__ | | | -|[eyetrackingR](problems.md#eyetrackingr) |0.1.8 |__+2__ | | | -|[forestmodel](problems.md#forestmodel) |0.5.0 |__+1__ | | | -|[GGally](problems.md#ggally) |1.5.0 |__+2__ | | | -|[ggasym](problems.md#ggasym) |0.1.3 |__+1__ | | | -|[glmmfields](problems.md#glmmfields) |0.1.3 | | |1 __+1__ | -|[gtsummary](problems.md#gtsummary) |1.3.0 |__+1__ | | | -|[jtools](problems.md#jtools) |2.0.5 |__+1__ | |1 | -|[konfound](problems.md#konfound) |0.2.1 |__+2__ | |1 | -|[merTools](problems.md#mertools) |0.5.0 |__+2__ |1 | | -|[mice](problems.md#mice) |3.9.0 |__+2__ | | | -|[moderndive](problems.md#moderndive) |0.4.0 |__+1__ | |1 | -|[NetworkExtinction](problems.md#networkextinction) |0.1.1 |__+1__ | | | -|[nlstimedist](problems.md#nlstimedist) |1.1.4 |__+2__ | | | -|[panelr](problems.md#panelr) |0.7.2 |__+2__ |1 | | -|[pixiedust](problems.md#pixiedust) |0.9.0 |__+1__ | | | -|[qgcomp](problems.md#qgcomp) |2.3.0 | | |__+1__ | -|[radiant.model](problems.md#radiantmodel) |1.3.10 |__+1__ |1 | | -|[RCT](problems.md#rct) |1.0.2 |__+2__ | | | -|[rstatix](problems.md#rstatix) |0.5.0 |__+1__ | | | -|[simglm](problems.md#simglm) |0.7.4 |__+2__ | | | -|[survminer](problems.md#survminer) |0.4.6 |__+1__ |1 |1 | -|[survutils](problems.md#survutils) |1.0.2 |__+1__ | | | -|[sweep](problems.md#sweep) |0.2.2 |__+2__ |__+1__ |1 | -|[SWMPrExtension](problems.md#swmprextension) |1.1.4 |__+1__ |1 |1 | -|[tadaatoolbox](problems.md#tadaatoolbox) |0.16.1 |__+2__ | |1 | -|[timetk](problems.md#timetk) |1.0.0 |__+2__ | |2 | -|[widyr](problems.md#widyr) |0.1.3 |__+2__ | | | +## Failed to check (2) + +|package |version |error |warning |note | +|:--------------------------------|:-------|:------|:-------|:----| +|[DeLorean](failures.md#delorean) |1.5.0 |__+1__ | |-3 | +|RBesT |1.6-1 |1 | | | + +## New problems (20) + +|package |version |error |warning |note | +|:-----------------------------------------|:-------|:------|:-------|:--------| +|[allestimates](problems.md#allestimates) |0.1.6 |__+1__ | |1 | +|[arsenal](problems.md#arsenal) |3.4.0 |__+1__ | | | +|[CGPfunctions](problems.md#cgpfunctions) |0.6.1 |__+1__ | | | +|[chest](problems.md#chest) |0.3.1 |__+1__ | |1 | +|[ERSA](problems.md#ersa) |0.1.1 |__+1__ | | | +|[eyetrackingR](problems.md#eyetrackingr) |0.1.8 |__+2__ | | | +|[forestmodel](problems.md#forestmodel) |0.5.0 |__+1__ | | | +|[ggasym](problems.md#ggasym) |0.1.4 |__+1__ | | | +|[glmmfields](problems.md#glmmfields) |0.1.3 | | |1 __+1__ | +|[konfound](problems.md#konfound) |0.2.1 |__+2__ | |1 | +|[lcsm](problems.md#lcsm) |0.1.1 |__+1__ | | | +|[mice](problems.md#mice) |3.9.0 |__+1__ | | | +|[moderndive](problems.md#moderndive) |0.4.0 |__+1__ | |1 | +|[nlstimedist](problems.md#nlstimedist) |1.1.4 |__+1__ | | | +|[qgcomp](problems.md#qgcomp) |2.3.0 | | |__+1__ | +|[radiant.model](problems.md#radiantmodel) |1.3.10 |__+1__ | | | +|[RCT](problems.md#rct) |1.0.2 |__+2__ | | | +|[survminer](problems.md#survminer) |0.4.7 |__+1__ | |1 | +|[survutils](problems.md#survutils) |1.0.2 |__+1__ | | | +|[sweep](problems.md#sweep) |0.2.2 |__+2__ |__+1__ |1 | diff --git a/revdep/data.sqlite b/revdep/data.sqlite index 40990b47030ae4f37de3662ad7e249811a501ecb..cd2146f5135dd5c9653d01a2a1f2aaa1711d91f2 100644 GIT binary patch delta 577553 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z`-$r};TH_(H+`$$yfQdkHK5?I^$8W6&x68)1~eRnO7jEKaL6M1BhYX#X!z;0nCLLo z;QKEad_M_kefMBApp9Qwzzk>;J2RkV%Z3`_NUb&$7NQMFr!C4y$iqM*l2KQ%O?BD{ VTS#~O&@E`P-V -* Version: 0.5.1 -* Source code: https://github.com/cran/miceFast -* URL: https://github.com/Polkas/miceFast -* BugReports: https://github.com/Polkas/miceFast/issues -* Date/Publication: 2019-08-19 22:50:02 UTC -* Number of recursive dependencies: 104 +* Version: 1.5.0 +* Source code: https://github.com/cran/DeLorean +* Date/Publication: 2018-10-17 22:30:16 UTC +* Number of recursive dependencies: 118 -Run `revdep_details(,"miceFast")` for more info +Run `revdep_details(,"DeLorean")` for more info -## In both +## Newly broken -* checking whether package ‘miceFast’ can be installed ... ERROR +* checking whether package ‘DeLorean’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/max/github/broom/revdep/checks.noindex/miceFast/new/miceFast.Rcheck/00install.out’ for details. + See ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/new/DeLorean.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 7.6Mb + sub-directories of 1Mb or more: + libs 4.9Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘lattice’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. ``` ## Installation @@ -26,48 +44,2645 @@ Run `revdep_details(,"miceFast")` for more info ### Devel ``` -* installing *source* package ‘miceFast’ ... -** package ‘miceFast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DeLorean’ ... +** package ‘DeLorean’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_funs.cpp -o R_funs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c corrData.cpp -o corrData.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c miceFast_additfunc.cpp -o miceFast_additfunc.o -clang: error: unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -make: *** [R_funs.o] Error 1 +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exact.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exactsizes.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowrank.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowranksizes.stan +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o +Wrote C++ file "stan_files/lowrank.cc" +Wrote C++ file "stan_files/exact.cc" +Wrote C++ file "stan_files/exactsizes.cc" +Wrote C++ file "stan_files/lowranksizes.cc" +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowrank.cc -o stan_files/lowrank.o +Error in readRDS("/var/folders/zh/nd9kmnyd2_d_xbwvbx5_7k_00000gn/T//RtmphfjD41/file91ed4d1f0548") : + error reading from connection +Calls: .Last -> readRDS +Execution halted +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exact.cc -o stan_files/exact.o +make: *** [stan_files/lowranksizes.cc] Error 1 make: *** Waiting for unfinished jobs.... -make: *** [miceFast_additfunc.o] Error 1 -make: *** [corrData.o] Error 1 -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘miceFast’ -* removing ‘/Users/max/github/broom/revdep/checks.noindex/miceFast/new/miceFast.Rcheck/miceFast’ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exact.cc:3: +stan_files/exact.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exact.hpp:714:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowrank.cc:3: +stan_files/lowrank.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowrank.hpp:864:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +28 warnings generated. +28 warnings generated. +rm stan_files/exact.cc stan_files/exactsizes.cc stan_files/lowranksizes.cc stan_files/lowrank.cc +ERROR: compilation failed for package ‘DeLorean’ +* removing ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/new/DeLorean.Rcheck/DeLorean’ ``` ### CRAN ``` -* installing *source* package ‘miceFast’ ... -** package ‘miceFast’ successfully unpacked and MD5 sums checked +* installing *source* package ‘DeLorean’ ... +** package ‘DeLorean’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_funs.cpp -o R_funs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c corrData.cpp -o corrData.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/max/github/broom/revdep/library.noindex/miceFast/Rcpp/include" -I"/Users/max/github/broom/revdep/library.noindex/miceFast/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c miceFast_additfunc.cpp -o miceFast_additfunc.o -clangclang: error: unsupported option '-fopenmp': clangclang -error: unsupported option '-fopenmp' -: error: error: unsupported option '-fopenmp' -: unsupported option '-fopenmp' -make: *** [RcppExports.o] Error 1 -make: *** Waiting for unfinished jobs.... -make: *** [miceFast_additfunc.o] Error 1 -make: *** [corrData.o] Error 1 -make: *** [R_funs.o] Error 1 -ERROR: compilation failed for package ‘miceFast’ -* removing ‘/Users/max/github/broom/revdep/checks.noindex/miceFast/old/miceFast.Rcheck/miceFast’ +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exact.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exactsizes.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowrank.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowranksizes.stan +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o +Wrote C++ file "stan_files/exactsizes.cc" +Wrote C++ file "stan_files/exact.cc" +Wrote C++ file "stan_files/lowranksizes.cc" +Wrote C++ file "stan_files/lowrank.cc" +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exactsizes.cc -o stan_files/exactsizes.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exact.cc -o stan_files/exact.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowranksizes.cc -o stan_files/lowranksizes.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowrank.cc -o stan_files/lowrank.o +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + #pragma clang diagnostic pop + ^ + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:In file included from 126stan_files/exact.cc::3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] +18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exact.cc:3: +stan_files/exact.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exact.hpp:714:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exactsizes.cc:3: +stan_files/exactsizes.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exactsizes.hpp:734:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowranksizes.cc:3: +stan_files/lowranksizes.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowranksizes.hpp:901:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowrank.cc:3: +stan_files/lowrank.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowrank.hpp:864:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +28 warnings generated. +28 warnings generated. +28 warnings generated. +28 warnings generated. +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DeLorean.so stan_files/exact.o stan_files/exactsizes.o stan_files/lowrank.o stan_files/lowranksizes.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +rm stan_files/exact.cc stan_files/exactsizes.cc stan_files/lowranksizes.cc stan_files/lowrank.cc +installing to /Users/max/github/broom/revdep/checks.noindex/DeLorean/old/DeLorean.Rcheck/00LOCK-DeLorean/00new/DeLorean/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (DeLorean) + +``` +# RBesT + +

+ +* Version: 1.6-1 +* Source code: https://github.com/cran/RBesT +* Date/Publication: 2020-05-28 09:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdep_details(,"RBesT")` for more info + +
+ +## In both + +* checking whether package ‘RBesT’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/max/github/broom/revdep/checks.noindex/RBesT/new/RBesT.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘RBesT’ ... +** package ‘RBesT’ successfully unpacked and MD5 sums checked +** using staged installation +DIAGNOSTIC(S) FROM PARSER: +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + beta ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ uniform(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ gamma(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ inv_gamma(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ lognormal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ cauchy(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ exponential(...) + +** libs + + +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include' -I/usr/local/include `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o + + +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include' -I/usr/local/include `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fPIC -Wall -g -O2 -c stanExports_gMAP.cc -o stanExports_gMAP.o +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/core.hpp:8: +/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/core/init_chainablestack.hpp:8:10: fatal error: 'tbb/task_scheduler_observer.h' file not found +#include + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +17 warnings and 1 error generated. +make: *** [stanExports_gMAP.o] Error 1 +ERROR: compilation failed for package ‘RBesT’ +* removing ‘/Users/max/github/broom/revdep/checks.noindex/RBesT/new/RBesT.Rcheck/RBesT’ + +``` +### CRAN + +``` +* installing *source* package ‘RBesT’ ... +** package ‘RBesT’ successfully unpacked and MD5 sums checked +** using staged installation +DIAGNOSTIC(S) FROM PARSER: +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + beta ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ normal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ uniform(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ gamma(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ inv_gamma(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ lognormal(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ cauchy(...) +Info: +Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. +If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. +Left-hand-side of sampling statement: + tau ~ exponential(...) + +** libs + + +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include' -I/usr/local/include `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o + + +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include' -I/usr/local/include `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fPIC -Wall -g -O2 -c stanExports_gMAP.cc -o stanExports_gMAP.o +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:30: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:31: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/RBesT/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stanExports_gMAP.cc:5: +In file included from ./stanExports_gMAP.h:15: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/core.hpp:8: +/Users/max/github/broom/revdep/library.noindex/RBesT/StanHeaders/include/stan/math/rev/core/init_chainablestack.hpp:8:10: fatal error: 'tbb/task_scheduler_observer.h' file not found +#include + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +17 warnings and 1 error generated. +make: *** [stanExports_gMAP.o] Error 1 +ERROR: compilation failed for package ‘RBesT’ +* removing ‘/Users/max/github/broom/revdep/checks.noindex/RBesT/old/RBesT.Rcheck/RBesT’ ``` diff --git a/revdep/problems.md b/revdep/problems.md index e07d1f760..095e12fd7 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -5,7 +5,7 @@ * Version: 0.1.6 * Source code: https://github.com/cran/allestimates * Date/Publication: 2020-02-05 16:30:12 UTC -* Number of recursive dependencies: 75 +* Number of recursive dependencies: 73 Run `revdep_details(,"allestimates")` for more info @@ -29,7 +29,6 @@ Run `revdep_details(,"allestimates")` for more info > results <- all_cox(crude = "Surv(t0, t1, Endpoint) ~ Diabetes", xlist = vlist, data = diab_df) Warning: Unknown or uninitialised column: `conf.low`. Warning: Unknown or uninitialised column: `conf.high`. - Warning: Unknown or uninitialised column: `n`. Error in data.frame(variables = "Crude", estimate, conf_low, conf_high, : arguments imply differing number of rows: 1, 0 Calls: all_cox -> data.frame @@ -54,7 +53,7 @@ Run `revdep_details(,"allestimates")` for more info * URL: https://github.com/eheinzen/arsenal, https://cran.r-project.org/package=arsenal, https://eheinzen.github.io/arsenal/ * BugReports: https://github.com/eheinzen/arsenal/issues * Date/Publication: 2020-02-15 19:10:03 UTC -* Number of recursive dependencies: 76 +* Number of recursive dependencies: 74 Run `revdep_details(,"arsenal")` for more info @@ -67,195 +66,33 @@ Run `revdep_details(,"arsenal")` for more info ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - 'confint_tidy' is not an exported object from 'namespace:broom' + > test_check("arsenal") + ── 1. Error: ordinal works (@test_modelsum.R#213) ───────────────────────────── + Must assign to rows with a valid subscript vector. + ℹ Logical subscripts must match the size of the indexed input. + ✖ Input has size 8 but subscript `coeffORTidy$coefficient_type == "zeta"` has size 0. Backtrace: 1. testthat::expect_identical(...) - 11. arsenal::modelsum(...) - 12. arsenal:::modelsum_guts(...) - 13. broom::confint_tidy - 14. base::getExportedValue(pkg, name) + 25. vctrs:::stop_indicator_size(...) ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 426 | SKIPPED: 12 | WARNINGS: 12 | FAILED: 2 ] + [ OK: 427 | SKIPPED: 12 | WARNINGS: 14 | FAILED: 1 ] 1. Error: ordinal works (@test_modelsum.R#213) - 2. Error: 08/01/2017: Beth Atkinson's subset problem (@test_modelsum.R#359) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Missing or unexported object: ‘broom::confint_tidy’ - ``` - -# biobroom - -
- -* Version: 1.18.0 -* Source code: https://github.com/cran/biobroom -* URL: https://github.com/StoreyLab/biobroom -* BugReports: https://github.com/StoreyLab/biobroom/issues -* Date/Publication: 2019-10-29 -* Number of recursive dependencies: 141 - -Run `revdep_details(,"biobroom")` for more info - -
- -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: -  1. generics::tidy(dds) -  2. biobroom::tidy.EList(dds) -  3. biobroom:::tidy_matrix(x$E) -  7. broom::fix_data_frame -  8. base::getExportedValue(pkg, name) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ] - 1. Error: limma tidier works as expected (@test-limma_tidiers.R#5) - 2. Error: voom tidier adds weight column (@test-limma_tidiers.R#26) - 3. Error: voomWithQualityWeights tidier adds weight and sample.weight columns (@test-limma_tidiers.R#49) - - Error: testthat unit tests failed - Execution halted - ``` - -## Newly fixed - -* checking whether package ‘biobroom’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘broom’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/biobroom/old/biobroom.Rcheck/00install.out’ for details. - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - 'library' or 'require' call to ‘DESeq2’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - Missing or unexported objects: - ‘broom::fix_data_frame’ ‘dplyr::tbl_dt’ - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - for ‘colData’ - tidy.deSet: no visible global function definition for ‘exprs<-’ - tidy.deSet: no visible binding for global variable ‘value’ - tidy.deSet: no visible binding for global variable ‘gene’ - tidy.deSet: no visible global function definition for ‘pData’ - tidy.qvalue: no visible binding for global variable ‘smoothed’ - tidy.qvalue: no visible binding for global variable ‘pi0’ - tidy.qvalue: no visible binding for global variable ‘lambda’ - tidy_matrix: no visible binding for global variable ‘value’ - tidy_matrix: no visible binding for global variable ‘gene’ - Undefined global functions or variables: - . DGEList calcNormFactors colData counts design end estimate - estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix - p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames - setNames smoothed start tbl_dt term value voom voomWithQualityWeights - Consider adding - importFrom("methods", "is") - importFrom("stats", "end", "model.matrix", "p.adjust", "setNames", - "start") - to your NAMESPACE file (and ensure that your DESCRIPTION Imports field - contains 'methods'). - ``` - -# breathtestcore - -
- -* Version: 0.6.0 -* Source code: https://github.com/cran/breathtestcore -* URL: https://github.com/dmenne/breathtestcore -* BugReports: https://github.com/dmenne/breathtestcore/issues -* Date/Publication: 2020-03-22 02:50:02 UTC -* Number of recursive dependencies: 88 - -Run `revdep_details(,"breathtestcore")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - > fit = nls_fit(data) - > coef_by_group(fit) - Error: `by` can't contain join column `lhs` which is missing from LHS - Backtrace: -  █ -  1. ├─breathtestcore::coef_by_group(fit) -  2. ├─breathtestcore:::coef_by_group.breathtestfit(fit) -  3. │ └─`%>%`(...) -  4. │ ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env)) -  5. │ └─base::eval(quote(`_fseq`(`_lhs`)), env, env) -  6. │ └─base::eval(quote(`_fseq`(`_lhs`)), env, env) -  7. │ └─breathtestcore:::`_fseq`(`_lhs`) -  8. │ └─magrittr::freduce(value, `_function_list`) -  9. │ └─function_list[[i]](value) -  10. │ ├─dplyr::do(...) -  11. │ └─dplyr:::do.grouped_df(...) -  12. │ └─rlang::eval_tidy(args[[j]], mask) -  13. └─`%>%`(...) -  14.  ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env)) - [ - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: -  24. dplyr:::common_by.list(by, x, y) -  25. dplyr:::bad_args(...) -  26. dplyr:::glubort(fmt_args(args), ..., .envir = .envir) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 333 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 6 ] - 1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#13) - 2. Error: Options digits is served (@test_coef_by_group.R#33) - 3. Error: Result with default parameters is tbl_df with required columns (@test_coef_diff_by_group.R#13) - 4. Error: Result with Dunnett contrast only returns 3 groups (@test_coef_diff_by_group.R#24) - 5. Error: Correct Dunnett contrast when reference value is given (@test_coef_diff_by_group.R#45) - 6. Error: Options digits is served (@test_coef_diff_by_group.R#67) Error: testthat unit tests failed Execution halted ``` -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘breathteststan’ - ``` - # CGPfunctions
-* Version: 0.6.0 +* Version: 0.6.1 * Source code: https://github.com/cran/CGPfunctions * URL: https://github.com/ibecav/CGPfunctions * BugReports: https://github.com/ibecav/CGPfunctions/issues -* Date/Publication: 2020-04-02 14:10:03 UTC -* Number of recursive dependencies: 174 +* Date/Publication: 2020-05-27 18:20:02 UTC +* Number of recursive dependencies: 161 Run `revdep_details(,"CGPfunctions")` for more info @@ -296,7 +133,7 @@ Run `revdep_details(,"CGPfunctions")` for more info * Version: 0.3.1 * Source code: https://github.com/cran/chest * Date/Publication: 2020-01-29 12:20:02 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 75 Run `revdep_details(,"chest")` for more info @@ -307,26 +144,26 @@ Run `revdep_details(,"chest")` for more info * checking examples ... ERROR ``` ... - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - Warning: Unknown or uninitialised column: `n`. - - Error in data.frame(out, p, n) : + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.high`. + Warning: Unknown or uninitialised column: `conf.low`. + Warning: Unknown or uninitialised column: `conf.high`. + Error in data.frame(variables, est, lb, ub, Change) : arguments imply differing number of rows: 8, 0 - Calls: chest_clogit -> data.frame + Calls: chest_cox -> data.frame Execution halted ``` @@ -353,11 +190,19 @@ Run `revdep_details(,"DeLorean")` for more info ## Newly broken +* checking whether package ‘DeLorean’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/new/DeLorean.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + * checking installed package size ... NOTE ``` - installed size is 7.7Mb + installed size is 7.6Mb sub-directories of 1Mb or more: - libs 5.0Mb + libs 4.9Mb ``` * checking dependencies in R code ... NOTE @@ -371,116 +216,1834 @@ Run `revdep_details(,"DeLorean")` for more info GNU make is a SystemRequirements. ``` -## Newly fixed - -* checking whether package ‘DeLorean’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/old/DeLorean.Rcheck/00install.out’ for details. - ``` - -# disk.frame - -
- -* Version: 0.3.5 -* Source code: https://github.com/cran/disk.frame -* URL: https://diskframe.com -* BugReports: https://github.com/xiaodaigh/disk.frame/issues -* Date/Publication: 2020-05-08 13:10:10 UTC -* Number of recursive dependencies: 105 - -Run `revdep_details(,"disk.frame")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - + # only run in interactive() - + setup_disk.frame(gui = TRUE) - + } - > - > # set the number workers to 2 - > setup_disk.frame(2) - Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : - port 37400 cannot be opened - Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : - Failed to launch and connect to R worker on local machine ‘localhost’ from local machine ‘imp.atlanticbb.net’. - * The error produced by socketConnection() was: ‘cannot open the connection’ - * In addition, socketConnection() produced 1 warning(s): - - Warning #1: ‘port 37400 cannot be opened’ (which suggests that this port is either already occupied by another process or blocked by the firewall on your local machine) - * The localhost socket connection that failed to connect to the R worker used port 37400 using a communication timeout of 120 seconds and a connection timeout of 120 seconds. - * Worker launch call: '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e '#label=UNKNOWN:56671:imp.atlanticbb.net:max' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/lb/xhxqmcrd7gv302_b1pdfykh80000gn/T//RtmpqhMLhX/future.parent=56671.dd5f59ec707e.pid")), silent = TRUE)' -e 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=37400 OUT=/dev/null TIMEOUT=120 XDR=TRUE. - * Worker (PID 57088) was successfully killed: TRUE - * Troubleshooting suggestions: - - Suggestion #1: Set 'verbose=TRUE' to see more details. - - Suggestion #2: Set 'outfile=NULL' to see output from worker. - Calls: setup_disk.frame ... tryCatchList -> tryCatchOne -> -> - Execution halted - ``` - -## In both - -* checking whether package ‘disk.frame’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘purrr’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/disk.frame/new/disk.frame.Rcheck/00install.out’ for details. - ``` - -# disto - -
- -* Version: 0.2.0 -* Source code: https://github.com/cran/disto -* URL: https://github.com/talegari/disto -* BugReports: https://github.com/talegari/disto/issues -* Date/Publication: 2018-08-02 12:50:02 UTC -* Number of recursive dependencies: 122 - -Run `revdep_details(,"disto")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘disto-Ex.R’ failed - The error most likely occurred in: - - > ### Name: summary.disto - > ### Title: Summary method for dist class - > ### Aliases: summary.disto - > - > ### ** Examples - > - > temp <- stats::dist(iris[,1:4]) - > dio <- disto(objectname = "temp") - > dio - disto with backend: dist - size: 150 - > summary(dio) - Warning: 'tidy.table' is deprecated. - See help("Deprecated") - Error in dimnames(x) <- dnx : 'dimnames' applied to non-array - Calls: summary ... eval -> eval -> data.frame -> do.call -> provideDimnames - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘dplyr’ ‘proxy’ - All declared Imports should be used. - ``` - +## Installation + +### Devel + +``` +* installing *source* package ‘DeLorean’ ... +** package ‘DeLorean’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exact.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exactsizes.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowrank.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowranksizes.stan +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o +Wrote C++ file "stan_files/lowrank.cc" +Wrote C++ file "stan_files/exact.cc" +Wrote C++ file "stan_files/exactsizes.cc" +Wrote C++ file "stan_files/lowranksizes.cc" +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowrank.cc -o stan_files/lowrank.o +Error in readRDS("/var/folders/zh/nd9kmnyd2_d_xbwvbx5_7k_00000gn/T//RtmphfjD41/file91ed4d1f0548") : + error reading from connection +Calls: .Last -> readRDS +Execution halted +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exact.cc -o stan_files/exact.o +make: *** [stan_files/lowranksizes.cc] Error 1 +make: *** Waiting for unfinished jobs.... +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exact.cc:3: +stan_files/exact.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exact.hpp:714:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowrank.cc:3: +stan_files/lowrank.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowrank.hpp:864:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +28 warnings generated. +28 warnings generated. +rm stan_files/exact.cc stan_files/exactsizes.cc stan_files/lowranksizes.cc stan_files/lowrank.cc +ERROR: compilation failed for package ‘DeLorean’ +* removing ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/new/DeLorean.Rcheck/DeLorean’ + +``` +### CRAN + +``` +* installing *source* package ‘DeLorean’ ... +** package ‘DeLorean’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exact.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/exactsizes.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowrank.stan +"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lowranksizes.stan +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o +Wrote C++ file "stan_files/exactsizes.cc" +Wrote C++ file "stan_files/exact.cc" +Wrote C++ file "stan_files/lowranksizes.cc" +Wrote C++ file "stan_files/lowrank.cc" +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exactsizes.cc -o stan_files/exactsizes.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/exact.cc -o stan_files/exact.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowranksizes.cc -o stan_files/lowranksizes.o +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/BH/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/Rcpp/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include' -I'/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/lowrank.cc -o stan_files/lowrank.o +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:1: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Core:535: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:2: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/LU:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Jacobi:29: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Cholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/QR:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Householder:27: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:5: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SVD:48: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Geometry:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Dense:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Eigenvalues:58: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + #pragma clang diagnostic pop + ^ + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:26: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCore:66: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:27: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/OrderingMethods:71: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:29: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseCholesky:43: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/SparseQR:35: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:11: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/version.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/Sparse:33: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:32: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/CholmodSupport:45: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:39: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/Polynomials:135: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:22: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigen.h:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/RcppEigenForward.h:40: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:283: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] + int n = G.rows(); // number of states + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:17: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] + inline static double square(double x) { return square(x); } + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:In file included from 126stan_files/exact.cc::3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] +18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:70: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] + const size_t coupled_size = cvodes_data.coupled_ode_.size(); + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exact.cc:3: +In file included from stan_files/exact.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exact.cc:3: +stan_files/exact.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exact.hpp:714:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/exactsizes.cc:3: +In file included from stan_files/exactsizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/exactsizes.cc:3: +stan_files/exactsizes.hpp:390:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/exactsizes.hpp:734:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowranksizes.cc:3: +In file included from stan_files/lowranksizes.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowranksizes.cc:3: +stan_files/lowranksizes.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowranksizes.hpp:901:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:46: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] +static void set_zero_all_adjoints() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:6: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core.hpp:47: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] +static void set_zero_all_adjoints_nested() { + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:278: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] + using T_partials_vec = typename Eigen::Matrix; + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:12: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat.hpp:328: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] + using T_alpha_val = typename std::conditional_t< + ^ +In file included from stan_files/lowrank.cc:3: +In file included from stan_files/lowrank.hpp:25: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/rstaninc.hpp:3: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/rstan/include/rstan/stan_fit.hpp:35: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/test_gradients.hpp:7: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: +In file included from /Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat.hpp:51: +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +/Users/max/github/broom/revdep/library.noindex/DeLorean/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] + using idx_t = typename index_type::type; + ^ +In file included from stan_files/lowrank.cc:3: +stan_files/lowrank.hpp:485:30: warning: unused typedef 'fun_return_scalar_t__' [-Wunused-local-typedef] + typedef local_scalar_t__ fun_return_scalar_t__; + ^ +stan_files/lowrank.hpp:864:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] + typedef double local_scalar_t__; + ^ +28 warnings generated. +28 warnings generated. +28 warnings generated. +28 warnings generated. +clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DeLorean.so stan_files/exact.o stan_files/exactsizes.o stan_files/lowrank.o stan_files/lowranksizes.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +rm stan_files/exact.cc stan_files/exactsizes.cc stan_files/lowranksizes.cc stan_files/lowrank.cc +installing to /Users/max/github/broom/revdep/checks.noindex/DeLorean/old/DeLorean.Rcheck/00LOCK-DeLorean/00new/DeLorean/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** checking absolute paths in shared objects and dynamic libraries +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (DeLorean) + +``` # ERSA
@@ -522,7 +2085,7 @@ Run `revdep_details(,"ERSA")` for more info * URL: http://eyetracking-r.com * BugReports: https://github.com/jwdink/eyetrackingR/issues * Date/Publication: 2018-12-03 22:00:39 UTC -* Number of recursive dependencies: 82 +* Number of recursive dependencies: 80 Run `revdep_details(,"eyetrackingR")` for more info @@ -570,7 +2133,7 @@ Run `revdep_details(,"eyetrackingR")` for more info  18. broom:::tidy.default(res_err_warn$res, effects = "fixed") ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 27 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ] + [ OK: 27 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ] 1. Error: (unknown) (@test_analyze_time_bins.R#98) 2. Error: (unknown) (@test_cluster_analysis.R#88) @@ -585,7 +2148,7 @@ Run `revdep_details(,"eyetrackingR")` for more info * Version: 0.5.0 * Source code: https://github.com/cran/forestmodel * Date/Publication: 2018-04-25 07:53:06 UTC -* Number of recursive dependencies: 61 +* Number of recursive dependencies: 59 Run `revdep_details(,"forestmodel")` for more info @@ -619,73 +2182,16 @@ Run `revdep_details(,"forestmodel")` for more info Execution halted ``` -# GGally - -
- -* Version: 1.5.0 -* Source code: https://github.com/cran/GGally -* URL: https://ggobi.github.io/ggally, https://github.com/ggobi/ggally -* BugReports: https://github.com/ggobi/ggally/issues -* Date/Publication: 2020-03-25 18:20:15 UTC -* Number of recursive dependencies: 133 - -Run `revdep_details(,"GGally")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GGally-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggally_nostic_se_fit - > ### Title: ggnostic - fitted value standard error - > ### Aliases: ggally_nostic_se_fit - > - > ### ** Examples - > - > dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars)) - > ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit)) - Error in FUN(X[[i]], ...) : object '.se.fit' not found - Calls: ... -> f -> scales_add_defaults -> lapply -> FUN - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("GGally") - ── 1. Error: ggnostic mtcars (@test-ggnostic.R#64)  ──────────────────────────── - Columns in 'columnsY' not found in data: c('.se.fit'). Choices: c('.rownames', 'mpg', 'wt', 'qsec', 'am', '.fitted', '.resid', '.std.resid', '.hat', '.sigma', '.cooksd') - Backtrace: -  1. GGally::ggnostic(...) -  2. GGally::ggduo(...) -  3. GGally:::fix_column_values(...) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 757 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ] - 1. Error: ggnostic mtcars (@test-ggnostic.R#64) - - Error: testthat unit tests failed - Execution halted - ``` - # ggasym
-* Version: 0.1.3 +* Version: 0.1.4 * Source code: https://github.com/cran/ggasym * URL: https://github.com/jhrcook/ggasym https://jhrcook.github.io/ggasym/ * BugReports: https://github.com/jhrcook/ggasym/issues -* Date/Publication: 2020-04-03 20:10:02 UTC -* Number of recursive dependencies: 101 +* Date/Publication: 2020-05-31 11:50:02 UTC +* Number of recursive dependencies: 99 Run `revdep_details(,"ggasym")` for more info @@ -697,19 +2203,17 @@ Run `revdep_details(,"ggasym")` for more info ``` ERROR Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: + Complete output: + > library(testthat) + > library(ggasym) > > test_check("ggasym") - Error : No tidy method for objects of class character - ── 1. Error: stats asymmetrization works (@test-asymmetrise_stats.R#13)  ─────── - Could not handle input data; try turning into a tibble using the broom package - Backtrace: -  1. testthat::expect_warning(prepare_data(grps)) -  6. ggasym::prepare_data(grps) + ── 1. Failure: stats asymmetrization works (@test-asymmetrise_stats.R#13)  ───── + `prepare_data(grps)` did not throw an error. ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 260 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] - 1. Error: stats asymmetrization works (@test-asymmetrise_stats.R#13) + [ OK: 266 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ] + 1. Failure: stats asymmetrization works (@test-asymmetrise_stats.R#13) Error: testthat unit tests failed Execution halted @@ -744,95 +2248,6 @@ Run `revdep_details(,"glmmfields")` for more info GNU make is a SystemRequirements. ``` -# gtsummary - -
- -* Version: 1.3.0 -* Source code: https://github.com/cran/gtsummary -* URL: https://github.com/ddsjoberg/gtsummary, http://www.danieldsjoberg.com/gtsummary/ -* BugReports: https://github.com/ddsjoberg/gtsummary/issues -* Date/Publication: 2020-04-17 08:00:02 UTC -* Number of recursive dependencies: 151 - -Run `revdep_details(,"gtsummary")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - > ### Title: Vetted tidy models - > ### Aliases: vetted_models - > ### Keywords: internal - > - > ### ** Examples - > - > my_tidy <- function(x, exponentiate = FALSE, conf.level = 0.95, ...) { - + tidy <- - + dplyr::bind_cols( - + broom::tidy(x, conf.int = FALSE), - + broom::confint_tidy(x, func = stats::confint.default, conf.level = conf.level) - + ) - + # exponentiating, if requested - + if (exponentiate == TRUE) - + tidy <- dplyr::mutate_at(vars(estimate, conf.low, conf.high), exp) - + } - > - > lm(age ~ grade + response, trial) %>% - + my_tidy() - Error: 'confint_tidy' is not an exported object from 'namespace:broom' - Execution halted - ``` - -# jtools - -
- -* Version: 2.0.5 -* Source code: https://github.com/cran/jtools -* URL: https://jtools.jacob-long.com -* BugReports: https://github.com/jacob-long/jtools/issues -* Date/Publication: 2020-04-21 12:20:12 UTC -* Number of recursive dependencies: 125 - -Run `revdep_details(,"jtools")` for more info - -
- -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: -  4. jtools::plot_summs(regmodel, scale = T) -  6. jtools::plot_coefs(...) -  7. jtools:::make_tidies(...) -  10. jtools:::tidy.summ(...) -  14. broom:::tidy.svyglm(...) -  15. broom:::broom_confint_terms(x, level = conf.level, ...) -  17. ellipsis:::action_dots(...) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 358 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 2 ] - 1. Error: plot_summs works with svyglm (@test-export-summs.R#211) - 2. Error: plot_summs accepts summ args with svyglm (@test-export-summs.R#216) - - Error: testthat unit tests failed - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘wec’, ‘interactions’, ‘piecewiseSEM’ - ``` - # konfound
@@ -842,7 +2257,7 @@ Run `revdep_details(,"jtools")` for more info * URL: https://github.com/jrosen48/konfound * BugReports: https://github.com/jrosen48/konfound/issues * Date/Publication: 2020-02-26 14:50:02 UTC -* Number of recursive dependencies: 113 +* Number of recursive dependencies: 112 Run `revdep_details(,"konfound")` for more info @@ -853,6 +2268,7 @@ Run `revdep_details(,"konfound")` for more info * checking examples ... ERROR ``` ... + To sustain an inference, 80.978% of the estimate would have to be due to bias. This is based on a threshold of 0.013 for statistical significance (alpha = 0.05). To sustain an inference, 17334 of the cases with 0 effect would have to be replaced with cases at the threshold of inference. See Frank et al. (2013) for a description of the method Citation: Frank, K.A., Maroulis, S., Duong, M., and Kelcey, B. 2013. What would it take to change an inference? Using Rubin's causal model to interpret the robustness of causal inferences. Education, Evaluation and Policy Analysis, 35 437-460. @@ -870,7 +2286,6 @@ Run `revdep_details(,"konfound")` for more info + konfound(m3, Days) + } Loading required namespace: lme4 - Warning: package ‘lme4’ was built under R version 3.6.2 Loading required package: Matrix Error: No tidy method for objects of class lmerMod Execution halted @@ -890,7 +2305,7 @@ Run `revdep_details(,"konfound")` for more info  4. broom:::tidy.default(model_object) ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 0 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ] + [ OK: 0 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ] 1. Error: (unknown) (@test-mkonfound.r#12) 2. Error: (unknown) (@test-pkonfound.R#11) @@ -906,17 +2321,18 @@ Run `revdep_details(,"konfound")` for more info All declared Imports should be used. ``` -# merTools +# lcsm
-* Version: 0.5.0 -* Source code: https://github.com/cran/merTools -* BugReports: https://www.github.com/jknowles/merTools -* Date/Publication: 2019-05-13 12:30:06 UTC -* Number of recursive dependencies: 131 +* Version: 0.1.1 +* Source code: https://github.com/cran/lcsm +* URL: https://milanwiedemann.github.io/lcsm/ +* BugReports: https://github.com/milanwiedemann/lcsm/issues +* Date/Publication: 2020-06-05 10:40:03 UTC +* Number of recursive dependencies: 148 -Run `revdep_details(,"merTools")` for more info +Run `revdep_details(,"lcsm")` for more info
@@ -924,58 +2340,30 @@ Run `revdep_details(,"merTools")` for more info * checking examples ... ERROR ``` - Running examples in ‘merTools-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lmerModList - > ### Title: Apply a multilevel model to a list of data frames - > ### Aliases: lmerModList blmerModList glmerModList bglmerModList - > - > ### ** Examples + ... + + beta = TRUE, + + phi = FALSE), + + model_y = list(alpha_constant = TRUE, + + beta = TRUE, + + phi = TRUE), + + coupling = list(delta_lag_xy = TRUE, + + xi_lag_yx = TRUE) + + ) + Warning in lav_model_vcov(lavmodel = lavmodel, lavsamplestats = lavsamplestats, : + lavaan WARNING: + The variance-covariance matrix of the estimated parameters (vcov) + does not appear to be positive definite! The smallest eigenvalue + (= 3.695231e-16) is close to zero. This may be a symptom that the + model is not identified. > - > sim_list <- replicate(n = 10, - + expr = sleepstudy[sample(row.names(sleepstudy), 180),], - + simplify=FALSE) - > fml <- "Reaction ~ Days + (Days | Subject)" - > mod <- lmerModList(fml, data = sim_list) - > summary(mod) - Error: No tidy method for objects of class lmerMod + > # Now extract fit statistics + > extract_fit(bi_lcsm_01) + Error in lavInspect(x, "converged") : + could not find function "lavInspect" + Calls: extract_fit ... bind_cols -> list2 -> tibble -> tibble_quos -> eval_tidy Execution halted ``` -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat-a_p.R’ failed. - Last 13 lines of output: - ── 1. Error: print methods work for merModList (@test-merModList.R#58)  ──────── - No tidy method for objects of class lmerMod - Backtrace: -  1. base::summary(g1) -  2. merTools:::summary.merModList(g1) -  3. merTools::modelFixedEff(modList) -  4. base::lapply(modList, tidy, effects = "fixed", ...) -  6. broom:::tidy.default(X[[i]], ...) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 285 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] - 1. Error: print methods work for merModList (@test-merModList.R#58) - - Error: testthat unit tests failed - Execution halted - ``` - -## In both - -* checking whether package ‘merTools’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘arm’ was built under R version 3.6.2 - Warning: package ‘MASS’ was built under R version 3.6.2 - Warning: package ‘lme4’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/merTools/new/merTools.Rcheck/00install.out’ for details. - ``` - # mice
@@ -985,7 +2373,7 @@ Run `revdep_details(,"merTools")` for more info * URL: https://github.com/stefvanbuuren/mice, https://stefvanbuuren.name/mice/, https://stefvanbuuren.name/fimd/ * BugReports: https://github.com/stefvanbuuren/mice/issues * Date/Publication: 2020-05-14 15:20:03 UTC -* Number of recursive dependencies: 85 +* Number of recursive dependencies: 84 Run `revdep_details(,"mice")` for more info @@ -993,44 +2381,23 @@ Run `revdep_details(,"mice")` for more info ## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘mice-Ex.R’ failed - The error most likely occurred in: - - > ### Name: D3 - > ### Title: Compare two nested models using D3-statistic - > ### Aliases: D3 - > - > ### ** Examples - > - > # Compare two linear models: - > imp <- mice(nhanes2, seed = 51009, print = FALSE) - > mi1 <- with(data = imp, expr = lm(bmi ~ age + hyp + chl)) - > mi0 <- with(data = imp, expr = lm(bmi ~ age + hyp)) - > D3(mi1, mi0) - Error in eval_tidy(xs[[j]], mask) : object 'fstatistic' not found - Calls: D3 ... with.default -> eval -> eval -> tibble -> tibble_quos -> eval_tidy - Execution halted - ``` - * checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: -  19. broom:::glance.lm(X[[i]], ...) -  21. base::with.default(...) -  22. [ base::eval(...) ] with 1 more call -  24. tibble::tibble(...) -  25. tibble:::tibble_quos(xs[!is_null], .rows, .name_repair) -  26. rlang::eval_tidy(xs[[j]], mask) + Backtrace: +  1. mice::parlmice(nhanes, n.core = 2, n.imp.core = 4) +  2. parallel::makeCluster(n.core, type = cl.type) +  3. parallel::makePSOCKcluster(names = spec, ...) +  4. base::serverSocket(port = port) ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 280 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ] - 1. Error: (unknown) (@test-D3.R#10) - 2. Error: anova.mira() produces silent D1 and D3 (@test-anova.R#9) - 3. Error: anova.mira() produces warnings on D2 (@test-anova.R#14) + [ OK: 277 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ] + 1. Error: (unknown) (@test-D3.R#58) + 2. Error: Warning and Imputations between mice and parlmice are unequal (@test-parlmice.R#5) + 3. Error: Imputations are equal between mice and parlmice (@test-parlmice.R#13) + 4. Error: (unknown) (@test-parlmice.R#19) Error: testthat unit tests failed Execution halted @@ -1045,7 +2412,7 @@ Run `revdep_details(,"mice")` for more info * URL: https://github.com/ModernDive/moderndive_package * BugReports: https://github.com/ModernDive/moderndive_package/issues * Date/Publication: 2019-11-04 05:40:02 UTC -* Number of recursive dependencies: 120 +* Number of recursive dependencies: 119 Run `revdep_details(,"moderndive")` for more info @@ -1066,7 +2433,7 @@ Run `revdep_details(,"moderndive")` for more info `get_regression_points(mpg_mlr_model2, newdata = newcars)` produced warnings. ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 33 | SKIPPED: 11 | WARNINGS: 3 | FAILED: 1 ] + [ OK: 33 | SKIPPED: 11 | WARNINGS: 1 | FAILED: 1 ] 1. Failure: README code works (@test-get_regression_functions.R#91) Error: testthat unit tests failed @@ -1080,43 +2447,6 @@ Run `revdep_details(,"moderndive")` for more info Package unavailable to check Rd xrefs: ‘openintro’ ``` -# NetworkExtinction - -
- -* Version: 0.1.1 -* Source code: https://github.com/cran/NetworkExtinction -* URL: https://derek-corcoran-barrios.github.io/NetworkExtintion/ -* Date/Publication: 2019-10-27 22:20:02 UTC -* Number of recursive dependencies: 85 - -Run `revdep_details(,"NetworkExtinction")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetworkExtinction-Ex.R’ failed - The error most likely occurred in: - - > ### Name: degree_distribution - > ### Title: Degree distribution of the network - > ### Aliases: degree_distribution - > - > ### ** Examples - > - > library(NetworkExtinction) - > data("net") - > degree_distribution(net, name = "Test") - Warning: Unknown or uninitialised column: `.resid`. - Error in ks.test(augment(exp.model)$.resid, y = "pnorm", alternative = "two.sided") : - not enough 'x' data - Calls: degree_distribution -> ifelse -> tidy -> ks.test - Execution halted - ``` - # nlstimedist
@@ -1126,7 +2456,7 @@ Run `revdep_details(,"NetworkExtinction")` for more info * URL: https://github.com/nathaneastwood/nlstimedist * BugReports: https://github.com/nathaneastwood/nlstimedist/issues * Date/Publication: 2019-05-15 21:40:03 UTC -* Number of recursive dependencies: 72 +* Number of recursive dependencies: 70 Run `revdep_details(,"nlstimedist")` for more info @@ -1134,32 +2464,6 @@ Run `revdep_details(,"nlstimedist")` for more info ## Newly broken -* checking examples ... ERROR - ``` - ... - > tdTilia <- tdData(tilia, x = "Day", y = "Trees") - > model <- timedist(data = tdTilia, x = "Day", y = "propMax", r = 0.1, c = 0.5, - + t = 120) - > tdCdfPlot(model) - Error: Can't subset columns that don't exist. - ✖ Column `.resid` doesn't exist. - Backtrace: -  █ -  1. ├─nlstimedist::tdCdfPlot(model) -  2. │ ├─data[, c(nameMod, ".fitted", ".resid")] -  3. │ └─tibble:::`[.tbl_df`(data, , c(nameMod, ".fitted", ".resid")) -  4. │ └─tibble:::tbl_subset_col(x, j = j, j_arg) -  5. │ └─tibble:::vectbl_as_col_index(j, x, j_arg = j_arg) -  6. │ └─tibble:::vectbl_as_col_location(...) -  7. │ ├─tibble:::subclass_col_index_errors(...) -  8. │ │ ├─base::tryCatch(...) -  9. │ │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers) -  10. │ │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) -  11. │ │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler) -  12. │ - Execution halted - ``` - * checking tests ... ``` ERROR @@ -1175,121 +2479,13 @@ Run `revdep_details(,"nlstimedist")` for more info Component 9: Mean relative difference: 0.9308432 ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] + [ OK: 6 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ] 1. Failure: Ensure the glance method is returning expected values (@test-glance.timedist.R#17) Error: testthat unit tests failed Execution halted ``` -# panelr - -
- -* Version: 0.7.2 -* Source code: https://github.com/cran/panelr -* URL: https://panelr.jacob-long.com -* BugReports: https://github.com/jacob-long/panelr -* Date/Publication: 2020-03-08 22:10:02 UTC -* Number of recursive dependencies: 168 - -Run `revdep_details(,"panelr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘panelr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tidy.wbm - > ### Title: Tidy methods for 'wbm' models - > ### Aliases: tidy.wbm glance.wbm glance.summ.wbm tidy.summ.wbm - > - > ### ** Examples - > - > data("WageData") - > wages <- panel_data(WageData, id = id, wave = t) - > model <- wbm(lwage ~ lag(union) + wks, data = wages) - > if (requireNamespace("broom")) { - + broom::tidy(model) - + } - Error: No tidy method for objects of class lmerMod - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("panelr") - ── 1. Error: tidy works (@test-utils.R#341)  ─────────────────────────────────── - No tidy method for objects of class lmerMod - Backtrace: -  1. testthat::expect_is(tidy.wbm(wb), "tbl_df") -  4. panelr:::tidy.wbm(wb) -  6. broom:::tidy.default(...) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 291 | SKIPPED: 0 | WARNINGS: 2436 | FAILED: 1 ] - 1. Error: tidy works (@test-utils.R#341) - - Error: testthat unit tests failed - Execution halted - ``` - -## In both - -* checking whether package ‘panelr’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘lme4’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/panelr/new/panelr.Rcheck/00install.out’ for details. - ``` - -# pixiedust - -
- -* Version: 0.9.0 -* Source code: https://github.com/cran/pixiedust -* URL: https://github.com/nutterb/pixiedust -* BugReports: https://github.com/nutterb/pixiedust/issues -* Date/Publication: 2020-05-15 05:50:10 UTC -* Number of recursive dependencies: 65 - -Run `revdep_details(,"pixiedust")` for more info - -
- -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("pixiedust") - ── 1. Error: dust runs when passed a data frame with tidy_df = TRUE (@test-dust. - No tidy method for objects of class data.frame - Backtrace: -  1. testthat::expect_warning(dust(mtcars, tidy_df = TRUE)) -  7. pixiedust:::dust.default(mtcars, tidy_df = TRUE) -  10. broom:::tidy.default(object, ...) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 512 | SKIPPED: 120 | WARNINGS: 0 | FAILED: 1 ] - 1. Error: dust runs when passed a data frame with tidy_df = TRUE (@test-dust.R#52) - - Error: testthat unit tests failed - Execution halted - ``` - # qgcomp
@@ -1319,7 +2515,7 @@ Run `revdep_details(,"qgcomp")` for more info * URL: https://github.com/radiant-rstats/radiant.model, https://radiant-rstats.github.io/radiant.model, https://radiant-rstats.github.io/docs * BugReports: https://github.com/radiant-rstats/radiant.model/issues * Date/Publication: 2020-03-24 09:50:03 UTC -* Number of recursive dependencies: 155 +* Number of recursive dependencies: 156 Run `revdep_details(,"radiant.model")` for more info @@ -1333,6 +2529,9 @@ Run `revdep_details(,"radiant.model")` for more info Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: + x[23]: "Nr obs: 2,999" + y[23]: "Nr obs: 3,000" + SI1 9 114304.420 104924.680 123684.159 9379.739 sex|male 0.080 -92.0% -2.522 0.163 -15.447 < .001 *** 2nd female 0.779 0.712 0.833 @@ -1343,22 +2542,9 @@ Run `revdep_details(,"radiant.model")` for more info 1. Failure: regress (@test_stats.R#23) Error: testthat unit tests failed - In addition: Warning messages: - 1: package 'lubridate' was built under R version 3.6.2 - 2: package 'tidyr' was built under R version 3.6.2 Execution halted ``` -## In both - -* checking whether package ‘radiant.model’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘lubridate’ was built under R version 3.6.2 - Warning: package ‘tidyr’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/radiant.model/new/radiant.model.Rcheck/00install.out’ for details. - ``` - # RCT
@@ -1366,7 +2552,7 @@ Run `revdep_details(,"radiant.model")` for more info * Version: 1.0.2 * Source code: https://github.com/cran/RCT * Date/Publication: 2020-05-13 06:20:10 UTC -* Number of recursive dependencies: 80 +* Number of recursive dependencies: 78 Run `revdep_details(,"RCT")` for more info @@ -1377,26 +2563,26 @@ Run `revdep_details(,"RCT")` for more info * checking examples ... ERROR ``` ... - > ### Title: Impact Evaluation of Treatment Effects - > ### Aliases: impact_eval - > - > ### ** Examples - > - > data <- data.frame(y_1 = rnorm(n = 100, mean = 100, sd = 15), - + y_2 = rnorm(n = 100, mean = 8, sd = 2), - + treat = rep(c(0,1,2,3), each = 25), - + heterogenous_var1 = rep(c("X_Q1", "X_Q2", "X_Q3", "X_Q4"), times = 25), - + cluster_var1 = rep(c(1:5), times = 20), - + fixed_effect_var1 = rep(c(1,2), times = 50), - + control_var1 = rnorm(n = 100, mean = 20, sd = 1)) - > > evaluation<-impact_eval(data = data, + endogenous_vars = c("y_1", "y_2"), + treatment = "treat", + heterogenous_vars = c("heterogenous_var1"), + cluster_vars = "cluster_var1", fixed_effect_vars = c("fixed_effect_var1"), + control_vars = c("control_var1")) - Error: No tidy method for objects of class rowwise_df + Warning: Data frame tidiers are deprecated and will be removed in an upcoming release of broom. + Warning: `data_frame()` is deprecated as of tibble 1.1.0. + Please use `tibble()` instead. + This warning is displayed once every 8 hours. + Call `lifecycle::last_warnings()` to see where this warning was generated. + Warning in mean.default(X[[i]], ...) : + argument is not numeric or logical: returning NA + Warning in mean.default(X[[i]], ...) : + argument is not numeric or logical: returning NA + Warning in var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) : + NAs introduced by coercion + Error in var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) : + is.atomic(x) is not TRUE + Calls: impact_eval ... tibble_quos -> eval_tidy -> vapply -> FUN -> var -> stopifnot Execution halted ``` @@ -1405,139 +2591,33 @@ Run `revdep_details(,"RCT")` for more info ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - No tidy method for objects of class rowwise_df + ── 1. Error: (unknown) (@test_impact_eval.R#64)  ─────────────────────────────── + is.atomic(x) is not TRUE Backtrace:  1. RCT::impact_eval(...) -  2. purrr::map2(...) -  3. RCT:::.f(.x[[1L]], .y[[1L]], ...) -  4. dplyr::group_by(., !!rlang::sym(x)) -  4. dplyr::do(., fit = lfe::felm(stats::as.formula(y), data = .)) -  12. broom::tidy(., fit) +  18. base::vapply(...) +  19. stats:::FUN(X[[i]], ...) +  20. stats::var(...) +  21. base::stopifnot(is.atomic(x)) ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] + [ OK: 79 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 1 ] 1. Error: (unknown) (@test_impact_eval.R#64) Error: testthat unit tests failed Execution halted ``` -# rstatix - -
- -* Version: 0.5.0 -* Source code: https://github.com/cran/rstatix -* URL: https://rpkgs.datanovia.com/rstatix/ -* BugReports: https://github.com/kassambara/rstatix/issues -* Date/Publication: 2020-04-28 10:40:02 UTC -* Number of recursive dependencies: 127 - -Run `revdep_details(,"rstatix")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - Running examples in ‘rstatix-Ex.R’ failed - The error most likely occurred in: - - > ### Name: emmeans_test - > ### Title: Pairwise Comparisons of Estimated Marginal Means - > ### Aliases: emmeans_test get_emmeans - > - > ### ** Examples - > - > # Data preparation - > df <- ToothGrowth - > df$dose <- as.factor(df$dose) - > - > # Pairwise comparisons - > res <- df %>% - + group_by(supp) %>% - + emmeans_test(len ~ dose, p.adjust.method = "bonferroni") - Error in summary.emmGrid(x, ...) : - formal argument "infer" matched by multiple actual arguments - Calls: %>% ... -> tidy -> tidy.emmGrid -> tidy_emmeans -> summary - Execution halted - ``` - -# simglm - -
- -* Version: 0.7.4 -* Source code: https://github.com/cran/simglm -* Date/Publication: 2019-05-31 17:10:03 UTC -* Number of recursive dependencies: 90 - -Run `revdep_details(,"simglm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - > with_err_gen <- 'rnorm' - > data_str <- "long" - > pow_param <- c('time', 'diff', 'act', 'actClust') - > alpha <- .01 - > pow_dist <- "z" - > pow_tail <- 2 - > replicates <- 1 - > power_out <- sim_pow(fixed = fixed, random = random, random3 = random3, - + fixed_param = fixed_param, - + random_param = random_param, - + random_param3 = random_param3, - + cov_param = cov_param, - + k = k, n = n, p = p, - + error_var = error_var, with_err_gen = "rnorm", - + data_str = data_str, - + unbal = list(level3 = FALSE, level2 = FALSE), - + pow_param = pow_param, alpha = alpha, - + pow_dist = pow_dist, pow_tail = pow_tail, - + replicates = replicates, raw_power = FALSE) - Error: No tidy method for objects of class lmerMod - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: -  7. simglm:::FUN(X[[i]], ...) -  10. simglm::sim_pow_glm_nested3(...) -  12. broom:::tidy.default(temp_mod, effects = "fixed") - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 125 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ] - 1. Error: three level power continuous (@test_power_struc.r#169) - 2. Error: two level power dich (@test_power_struc.r#203) - 3. Error: three level power dich (@test_power_struc.r#238) - 4. Error: three level power continuous (@test_power_vary.r#91) - 5. Error: two level power dich (@test_power_vary.r#128) - 6. Error: three level power dich (@test_power_vary.r#166) - - Error: testthat unit tests failed - Execution halted - ``` - # survminer
-* Version: 0.4.6 +* Version: 0.4.7 * Source code: https://github.com/cran/survminer * URL: http://www.sthda.com/english/rpkgs/survminer/ * BugReports: https://github.com/kassambara/survminer/issues -* Date/Publication: 2019-09-03 23:00:02 UTC -* Number of recursive dependencies: 119 +* Date/Publication: 2020-05-28 11:40:02 UTC +* Number of recursive dependencies: 118 Run `revdep_details(,"survminer")` for more info @@ -1547,7 +2627,6 @@ Run `revdep_details(,"survminer")` for more info * checking examples ... ERROR ``` - ... Running examples in ‘survminer-Ex.R’ failed The error most likely occurred in: @@ -1559,7 +2638,6 @@ Run `revdep_details(,"survminer")` for more info > > require("survival") Loading required package: survival - Warning: package ‘survival’ was built under R version 3.6.2 > model <- coxph( Surv(time, status) ~ sex + rx + adhere, + data = colon ) > ggforest(model) @@ -1573,18 +2651,11 @@ Run `revdep_details(,"survminer")` for more info ## In both -* checking whether package ‘survminer’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘ggpubr’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/survminer/new/survminer.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 5.6Mb + installed size is 5.3Mb sub-directories of 1Mb or more: - doc 5.1Mb + doc 4.8Mb ``` # survutils @@ -1596,7 +2667,7 @@ Run `revdep_details(,"survminer")` for more info * URL: https://github.com/tinyheero/survutils * BugReports: https://github.com/tinyheero/survutils/issues * Date/Publication: 2018-07-22 17:50:02 UTC -* Number of recursive dependencies: 61 +* Number of recursive dependencies: 59 Run `revdep_details(,"survutils")` for more info @@ -1619,7 +2690,7 @@ Run `revdep_details(,"survutils")` for more info Component 6: target is character, current is numeric ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] + [ OK: 6 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ] 1. Failure: get_cox_res runs univariate Cox regression on a single feature (@test_get_cox_res.R#48) Error: testthat unit tests failed @@ -1635,7 +2706,7 @@ Run `revdep_details(,"survutils")` for more info * URL: https://github.com/business-science/sweep * BugReports: https://github.com/business-science/sweep/issues * Date/Publication: 2019-10-08 13:50:02 UTC -* Number of recursive dependencies: 142 +* Number of recursive dependencies: 143 Run `revdep_details(,"sweep")` for more info @@ -1646,13 +2717,13 @@ Run `revdep_details(,"sweep")` for more info * checking examples ... ERROR ``` ... + filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > library(forecast) - Warning: package ‘forecast’ was built under R version 3.6.2 > library(sweep) > > fit_arima <- WWWusage %>% @@ -1674,18 +2745,18 @@ Run `revdep_details(,"sweep")` for more info ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: +  1. sweep::sw_glance(fit_robets)  2. sweep:::sw_glance.robets(fit_robets)  6. broom::finish_glance  7. base::getExportedValue(pkg, name) ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 143 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 6 ] - 1. Error: sw_sweep test returns tibble with correct rows and columns. (@test_sw_sweep.R#156) - 2. Error: sw_*.Arima test returns tibble with correct rows and columns. (@test_tidiers_arima.R#19) - 3. Error: sw_*.ets test returns tibble with correct rows and columns. (@test_tidiers_ets.R#19) - 4. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#22) - 5. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#32) - 6. Error: sw_*.robets test returns tibble with correct rows and columns. (@test_tidiers_robets.R#19) + [ OK: 146 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 5 ] + 1. Error: sw_*.Arima test returns tibble with correct rows and columns. (@test_tidiers_arima.R#19) + 2. Error: sw_*.ets test returns tibble with correct rows and columns. (@test_tidiers_ets.R#19) + 3. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#22) + 4. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#32) + 5. Error: sw_*.robets test returns tibble with correct rows and columns. (@test_tidiers_robets.R#19) Error: testthat unit tests failed Execution halted @@ -1709,274 +2780,3 @@ Run `revdep_details(,"sweep")` for more info Missing or unexported object: ‘broom::finish_glance’ ``` -# SWMPrExtension - -
- -* Version: 1.1.4 -* Source code: https://github.com/cran/SWMPrExtension -* BugReports: https://github.com/NOAA-OCM/SWMPrExtension/issues -* Date/Publication: 2020-05-04 15:10:11 UTC -* Number of recursive dependencies: 120 - -Run `revdep_details(,"SWMPrExtension")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SWMPrExtension-Ex.R’ failed - The error most likely occurred in: - - > ### Name: seasonal_dot - > ### Title: Seasonal Dot Plot - > ### Aliases: seasonal_dot seasonal_dot.swmpr - > - > ### ** Examples - > - > dat_wq <- elksmwq - > #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00')) - > dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5)) - > - > x <- - + seasonal_dot(dat_wq, param = 'do_mgl' - + , lm_trend = TRUE - + , lm_lab = TRUE - + , plot_title = TRUE) - Error: No tidy method for objects of class rowwise_df - Execution halted - ``` - -## In both - -* checking whether package ‘SWMPrExtension’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: package ‘zoo’ was built under R version 3.6.2 - See ‘/Users/max/github/broom/revdep/checks.noindex/SWMPrExtension/new/SWMPrExtension.Rcheck/00install.out’ for details. - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘rgeos’ - All declared Imports should be used. - ``` - -# tadaatoolbox - -
- -* Version: 0.16.1 -* Source code: https://github.com/cran/tadaatoolbox -* URL: https://github.com/tadaadata/tadaatoolbox -* BugReports: https://github.com/tadaadata/tadaatoolbox/issues -* Date/Publication: 2018-11-23 11:20:04 UTC -* Number of recursive dependencies: 118 - -Run `revdep_details(,"tadaatoolbox")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... -  6 jahrgang:… 13:Männlich-11… 0 1.16 -0.190 2.51 0.138 -  7 jahrgang:… 11:Weiblich-11… 0 1.58 0.478 2.68 0.000736 -  8 jahrgang:… 12:Weiblich-11… 0 0.940 -0.162 2.04 0.143 -  9 jahrgang:… 13:Weiblich-11… 0 2.76 1.41 4.11 0.000000207 - 10 jahrgang:… 13:Männlich-12… 0 0.420 -0.930 1.77 0.948 - 11 jahrgang:… 11:Weiblich-12… 0 0.840 -0.262 1.94 0.246 - 12 jahrgang:… 12:Weiblich-12… 0 0.200 -0.902 1.30 0.995 - 13 jahrgang:… 13:Weiblich-12… 0 2.02 0.670 3.37 0.000354 - 14 jahrgang:… 11:Weiblich-13… 0 0.420 -0.930 1.77 0.948 - 15 jahrgang:… 12:Weiblich-13… 0 -0.220 -1.57 1.13 0.997 - 16 jahrgang:… 13:Weiblich-13… 0 1.60 0.0415 3.16 0.0404 - 17 jahrgang:… 12:Weiblich-11… 0 -0.640 -1.74 0.462 0.554 - 18 jahrgang:… 13:Weiblich-11… 0 1.18 -0.170 2.53 0.125 - 19 jahrgang:… 13:Weiblich-12… 0 1.82 0.470 3.17 0.00190 - > tadaa_pairwise_tukey(data = ngo, deutsch, jahrgang, print = "console") - Error in tadaa_pairwise_tukey(data = ngo, deutsch, jahrgang, print = "console") : - 1 assertions failed: - * The following variable names are not found in the dust table: - * comparison - Calls: tadaa_pairwise_tukey ... -> sprinkle_colnames.default -> - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: -  6. tibble:::`$<-.tbl_df`(...) -  7. tibble:::tbl_subassign(...) -  8. tibble:::vectbl_recycle_rhs(...) -  9. base::tryCatch(...) -  10. base:::tryCatchList(expr, classes, parentenv, handlers) -  11. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) -  12. value[[3L]](cond) - - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 153 | SKIPPED: 1 | WARNINGS: 32 | FAILED: 2 ] - 1. Error: Pairwise tukey returns correct data structure (@test-pairwise_tests.R#50) - 2. Error: tadaa_pairwise_tukey produces plot (@test-plots.R#27) - - Error: testthat unit tests failed - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 3 marked UTF-8 strings - ``` - -# timetk - -
- -* Version: 1.0.0 -* Source code: https://github.com/cran/timetk -* URL: https://github.com/business-science/timetk -* BugReports: https://github.com/business-science/timetk/issues -* Date/Publication: 2020-04-19 17:50:02 UTC -* Number of recursive dependencies: 150 - -Run `revdep_details(,"timetk")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - Business Science offers a 1-hour course - Learning Lab #9: Performance Analysis & Portfolio Optimization with tidyquant! -  Learn more at: https://university.business-science.io/p/learning-labs-pro  - - Attaching package: ‘tidyquant’ - - The following objects are masked from ‘package:timetk’: - - summarise_by_time, summarize_by_time - - > library(timetk) - > - > # Filter values in January 1st through end of February, 2013 - > FANG %>% - + group_by(symbol) %>% - + filter_by_time(date, "start", "2013-02") %>% - + plot_time_series(date, adjusted, .facet_ncol = 2, .interactive = FALSE) - Warning: 'tidy.table' is deprecated. - See help("Deprecated") - Error in dimnames(x) <- dnx : 'dimnames' applied to non-array - Calls: %>% ... eval -> eval -> data.frame -> do.call -> provideDimnames - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 233 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 10 ] - 1. Error: tk_get_timeseries_summary(datetime) test returns correct format. (@test_tk_get_timeseries.R#79) - 2. Error: tk_get_timeseries_summary(date) test returns correct format. (@test_tk_get_timeseries.R#91) - 3. Error: tk_get_timeseries_summary(yearmon) test returns correct format. (@test_tk_get_timeseries.R#103) - 4. Error: tk_get_timeseries_summary(yearqtr) test returns correct format. (@test_tk_get_timeseries.R#116) - 5. Error: tk_make_future_timeseries(datetime) test returns correct format. (@test_tk_make_future_timeseries.R#12) - 6. Error: tk_make_future_timeseries(date) test returns correct format. (@test_tk_make_future_timeseries.R#53) - 7. Error: tk_make_future_timeseries(predict_every_two) test returns correct format. (@test_tk_make_future_timeseries.R#309) - 8. Error: tk_make_future_timeseries(predict_every_three) test returns correct format. (@test_tk_make_future_timeseries.R#348) - 9. Error: tk_make_future_timeseries(predict_every_four) test returns correct format. (@test_tk_make_future_timeseries.R#386) - 10. Error: tk_make_future_timeseries(predict_random) test returns correct format. (@test_tk_make_future_timeseries.R#430) - - Error: testthat unit tests failed - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - doc 5.1Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 2750 marked UTF-8 strings - ``` - -# widyr - -
- -* Version: 0.1.3 -* Source code: https://github.com/cran/widyr -* URL: http://github.com/dgrtwo/widyr -* BugReports: http://github.com/dgrtwo/widyr/issues -* Date/Publication: 2020-04-12 06:00:02 UTC -* Number of recursive dependencies: 113 - -Run `revdep_details(,"widyr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - ... - The following objects are masked from ‘package:stats’: - - filter, lag - - The following objects are masked from ‘package:base’: - - intersect, setdiff, setequal, union - - > dat <- tibble(group = rep(1:5, each = 2), - + letter = c("a", "b", - + "a", "c", - + "a", "c", - + "b", "e", - + "b", "f")) - > - > # count the number of times two letters appear together - > pairwise_count(dat, letter, group) - Error in `colnames<-`(`*tmp*`, value = c("item1", "item2", "value")) : - attempt to set 'colnames' on an object with less than two dimensions - Calls: pairwise_count ... freduce -> -> custom_melt -> colnames<- - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ testthat results ═══════════════════════════════════════════════════════════ - [ OK: 38 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 10 ] - 1. Error: pairing and counting works (@test-pairwise-count.R#16) - 2. Error: We can count with a weight column (@test-pairwise-count.R#63) - 3. Error: Counts co-occurrences of words in Pride & Prejudice (@test-pairwise-count.R#79) - 4. Error: Can count within groups (@test-pairwise-count.R#104) - 5. Error: Can count within groups (@test-pairwise-count.R#103) - 6. Error: (unknown) (@test-pairwise-count.R#103) - 7. Error: pairwise_similarity computes pairwise cosine similarity (@test-pairwise-similarity.R#14) - 8. Error: pairwise_similarity retains factor levels (@test-pairwise-similarity.R#29) - 9. Failure: Can perform 'squarely' operations on pairs of items (@test-squarely.R#14) - 10. Failure: Can perform 'squarely' within groups (@test-squarely.R#25) - - Error: testthat unit tests failed - Execution halted - ``` - From 85b5e8c0bbe0648c280b8769ee4a316312521613 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 07:21:31 -0700 Subject: [PATCH 33/41] /dontrun examples with longest runtime --- R/pam-tidiers.R | 3 +++ R/stats-kmeans-tidiers.R | 2 ++ man/augment.kmeans.Rd | 2 ++ man/augment.pam.Rd | 3 +++ man/glance.kmeans.Rd | 2 ++ man/glance.pam.Rd | 3 +++ man/tidy.dist.Rd | 10 +++++----- man/tidy.kmeans.Rd | 2 ++ man/tidy.pam.Rd | 3 +++ 9 files changed, 25 insertions(+), 5 deletions(-) diff --git a/R/pam-tidiers.R b/R/pam-tidiers.R index 42f9c23a3..c792ace5b 100644 --- a/R/pam-tidiers.R +++ b/R/pam-tidiers.R @@ -26,6 +26,7 @@ #' @family pam tidiers #' @examples #' +#' \dontrun{ #' library(dplyr) #' library(ggplot2) #' library(cluster) @@ -43,6 +44,8 @@ #' ggplot(aes(compounds, input_fields)) + #' geom_point(aes(color = .cluster)) + #' geom_text(aes(label = cluster), data = tidy(p), size = 10) +#' } +#' tidy.pam <- function(x, col.names = paste0("x", 1:ncol(x$medoids)), ...) { as_tibble(x$clusinfo) %>% mutate( diff --git a/R/stats-kmeans-tidiers.R b/R/stats-kmeans-tidiers.R index d2e2624f9..de2e836b4 100644 --- a/R/stats-kmeans-tidiers.R +++ b/R/stats-kmeans-tidiers.R @@ -10,6 +10,7 @@ #' #' @examples #' +#' \dontrun{ #' library(cluster) #' library(dplyr) #' @@ -23,6 +24,7 @@ #' tidy(fit) #' glance(fit) #' augment(fit, x) +#' } #' @details For examples, see the kmeans vignette. #' #' @aliases kmeans_tidiers diff --git a/man/augment.kmeans.Rd b/man/augment.kmeans.Rd index 277493b4e..dcfcbe3df 100644 --- a/man/augment.kmeans.Rd +++ b/man/augment.kmeans.Rd @@ -68,6 +68,7 @@ missing at this time. } \examples{ +\dontrun{ library(cluster) library(dplyr) @@ -82,6 +83,7 @@ tidy(fit) glance(fit) augment(fit, x) } +} \seealso{ \code{\link[=augment]{augment()}}, \code{\link[stats:kmeans]{stats::kmeans()}} diff --git a/man/augment.pam.Rd b/man/augment.pam.Rd index 1e254fa4d..a56027705 100644 --- a/man/augment.pam.Rd +++ b/man/augment.pam.Rd @@ -68,6 +68,7 @@ missing at this time. } \examples{ +\dontrun{ library(dplyr) library(ggplot2) library(cluster) @@ -85,6 +86,8 @@ augment(p, x) \%>\% ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) +} + } \seealso{ \code{\link[=augment]{augment()}}, \code{\link[cluster:pam]{cluster::pam()}} diff --git a/man/glance.kmeans.Rd b/man/glance.kmeans.Rd index fc4f255ab..8c1e1bdba 100644 --- a/man/glance.kmeans.Rd +++ b/man/glance.kmeans.Rd @@ -41,6 +41,7 @@ of the appropriate type. } \examples{ +\dontrun{ library(cluster) library(dplyr) @@ -55,6 +56,7 @@ tidy(fit) glance(fit) augment(fit, x) } +} \seealso{ \code{\link[=glance]{glance()}}, \code{\link[stats:kmeans]{stats::kmeans()}} diff --git a/man/glance.pam.Rd b/man/glance.pam.Rd index b79f3e53a..42a1f7944 100644 --- a/man/glance.pam.Rd +++ b/man/glance.pam.Rd @@ -41,6 +41,7 @@ of the appropriate type. } \examples{ +\dontrun{ library(dplyr) library(ggplot2) library(cluster) @@ -58,6 +59,8 @@ augment(p, x) \%>\% ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) +} + } \seealso{ \code{\link[=glance]{glance()}}, \code{\link[cluster:pam]{cluster::pam()}} diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index 0dd44400f..f29f207c5 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -44,12 +44,12 @@ diagonal, the tidied version will not either. } \examples{ -iris_dist <- dist(t(iris[, 1:4])) -iris_dist +cars_dist <- dist(t(mtcars[, 1:4])) +cars_dist -tidy(iris_dist) -tidy(iris_dist, upper = TRUE) -tidy(iris_dist, diagonal = TRUE) +tidy(cars_dist) +tidy(cars_dist, upper = TRUE) +tidy(cars_dist, diagonal = TRUE) } \seealso{ diff --git a/man/tidy.kmeans.Rd b/man/tidy.kmeans.Rd index 632c8cda9..e44374674 100644 --- a/man/tidy.kmeans.Rd +++ b/man/tidy.kmeans.Rd @@ -36,6 +36,7 @@ For examples, see the kmeans vignette. } \examples{ +\dontrun{ library(cluster) library(dplyr) @@ -50,6 +51,7 @@ tidy(fit) glance(fit) augment(fit, x) } +} \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[stats:kmeans]{stats::kmeans()}} diff --git a/man/tidy.pam.Rd b/man/tidy.pam.Rd index 10655ec36..f8c6cff22 100644 --- a/man/tidy.pam.Rd +++ b/man/tidy.pam.Rd @@ -36,6 +36,7 @@ For examples, see the pam vignette. } \examples{ +\dontrun{ library(dplyr) library(ggplot2) library(cluster) @@ -53,6 +54,8 @@ augment(p, x) \%>\% ggplot(aes(compounds, input_fields)) + geom_point(aes(color = .cluster)) + geom_text(aes(label = cluster), data = tidy(p), size = 10) +} + } \seealso{ \code{\link[=tidy]{tidy()}}, \code{\link[cluster:pam]{cluster::pam()}} From 8960c101c080dd85b076d69c1f1e2c80d9e22cf2 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 07:59:31 -0700 Subject: [PATCH 34/41] update cran comments with new revdepchecks records --- cran-comments.md | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 64585c5ba..14cc8f24b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -42,7 +42,10 @@ methods to the `broom.mixed` package. ## R CMD check results -0 NOTES, 0 WARNINGS, 0 ERRORS +0 NOTES, 0 WARNINGS, 0 ERRORS, aside from a Note_to_CRAN_Maintainers with +the following message: + +> Maintainer: 'Alex Hayes ' ## revdepcheck results @@ -51,17 +54,22 @@ comparing R CMD check results across CRAN and dev versions of this package. We saw 37 new problems and failed to check one package. We first notified affected maintainers three weeks prior to our initial -submission, and checked in with maintainers again a week and a half ago. +submission, and checked in with maintainers again a week and a half prior. Records of our initial outreach attempts can be found on this issue: https://github.com/tidymodels/broom/issues/862 -Since reverting removals to soft-deprecations, we have ran revdepchecks again. -Records of our outreach with maintainers of packages that are still newly -broken (since 0.5.6) can be found on this issue: - - - - - +Since being asked to revert removals to soft-deprecations by the CRAN team on +23 June 2020, we +have ran revdepchecks again. 20 issues remained, and after fixing 3 of them by +reverting removals to soft-deprecations, 17 remain. Of the 17 remaining issues, +9 of them have been fixed in development versions and are waiting on the release +of `broom` 0.7.0 to submit. I've reached out to maintainers for all remaining issues, +besides `eyetrackingR`, which currently does not have a maintainer. The majority of +remaining issues are due to the planned deprecation of mixed model tidiers to +`broom.mixed`, initially announced with the release of broom 0.5.0 two years ago. +Records of our most recent revdepchecks, and attempts to reach out to maintainers, +can be found on this issue: + +https://github.com/tidymodels/broom/issues/885 From 48331df4bfd65660b52987dec5d631f1c95e9887 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 08:04:25 -0700 Subject: [PATCH 35/41] restore finish_glance --- NAMESPACE | 1 + NEWS.md | 1 + R/deprecated-0-7-0.R | 40 ++++++++++++++++++++++++++++++++++++++ man/bootstrap.Rd | 1 + man/confint_tidy.Rd | 1 + man/data.frame_tidiers.Rd | 3 +++ man/finish_glance.Rd | 41 +++++++++++++++++++++++++++++++++++++++ man/fix_data_frame.Rd | 1 + man/summary_tidiers.Rd | 2 ++ man/tidy.density.Rd | 1 + man/tidy.dist.Rd | 1 + man/tidy.ftable.Rd | 1 + man/vector_tidiers.Rd | 3 +++ 13 files changed, 97 insertions(+) create mode 100644 man/finish_glance.Rd diff --git a/NAMESPACE b/NAMESPACE index e43e094c9..fb7dfb566 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -262,6 +262,7 @@ export(augment) export(augment_columns) export(bootstrap) export(confint_tidy) +export(finish_glance) export(fix_data_frame) export(glance) export(tidy) diff --git a/NEWS.md b/NEWS.md index c914d0d7e..900073b78 100644 --- a/NEWS.md +++ b/NEWS.md @@ -50,6 +50,7 @@ methods: - `bootstrap()` - `confint_tidy()` - `fix_data_frame()` +- `finish_glance()` - `augment.glmRob()` - `tidy.table()` and `tidy.ftable()` have been deprecated in favor of `tibble::as_tibble()` diff --git a/R/deprecated-0-7-0.R b/R/deprecated-0-7-0.R index 2270d3e41..8cc89e8f1 100644 --- a/R/deprecated-0-7-0.R +++ b/R/deprecated-0-7-0.R @@ -537,3 +537,43 @@ confint_tidy <- function(x, conf.level = .95, func = stats::confint, ...) { colnames(ci) <- c("conf.low", "conf.high") as_tibble(ci) } + +# finish_glance ------------------------------------------------------- +#' (Deprecated) Add logLik, AIC, BIC, and other common measurements to a +#' glance of a prediction +#' +#' This function is now deprecated in favor of using custom logic and +#' the appropriate \code{nobs()} method. +#' +#' +#' @param ret a one-row data frame (a partially complete glance) +#' @param x the prediction model +#' +#' @return a one-row data frame with additional columns added, such as +#' \item{logLik}{log likelihoods} +#' \item{AIC}{Akaike Information Criterion} +#' \item{BIC}{Bayesian Information Criterion} +#' \item{deviance}{deviance} +#' \item{df.residual}{residual degrees of freedom} +#' +#' Each of these are produced by the corresponding generics +#' +#' @export +#' @family deprecated +finish_glance <- function(ret, x) { + ret$logLik <- tryCatch(as.numeric(stats::logLik(x)), error = function(e) NULL) + ret$AIC <- tryCatch(stats::AIC(x), error = function(e) NULL) + ret$BIC <- tryCatch(stats::BIC(x), error = function(e) NULL) + + # special case for REML objects (better way?) + if (inherits(x, "lmerMod")) { + ret$deviance <- tryCatch(stats::deviance(x, REML = FALSE), + error = function(e) NULL + ) + } else { + ret$deviance <- tryCatch(stats::deviance(x), error = function(e) NULL) + } + ret$df.residual <- tryCatch(df.residual(x), error = function(e) NULL) + + as_tibble(ret, rownames = NULL) +} diff --git a/man/bootstrap.Rd b/man/bootstrap.Rd index eed5bcf67..6dc90d845 100644 --- a/man/bootstrap.Rd +++ b/man/bootstrap.Rd @@ -28,6 +28,7 @@ corrections) here: Other deprecated: \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, diff --git a/man/confint_tidy.Rd b/man/confint_tidy.Rd index c9a8fad33..3707df3f2 100644 --- a/man/confint_tidy.Rd +++ b/man/confint_tidy.Rd @@ -36,6 +36,7 @@ column names of \code{conf.low} and \code{conf.high}, and no row names. Other deprecated: \code{\link{bootstrap}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, diff --git a/man/data.frame_tidiers.Rd b/man/data.frame_tidiers.Rd index f129e7cce..e19d9e307 100644 --- a/man/data.frame_tidiers.Rd +++ b/man/data.frame_tidiers.Rd @@ -85,6 +85,7 @@ ggplot(td, aes(mean, sd)) + geom_point() + Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, @@ -95,6 +96,7 @@ Other deprecated: Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, @@ -105,6 +107,7 @@ Other deprecated: Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, diff --git a/man/finish_glance.Rd b/man/finish_glance.Rd new file mode 100644 index 000000000..d3124f3dd --- /dev/null +++ b/man/finish_glance.Rd @@ -0,0 +1,41 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprecated-0-7-0.R +\name{finish_glance} +\alias{finish_glance} +\title{(Deprecated) Add logLik, AIC, BIC, and other common measurements to a +glance of a prediction} +\usage{ +finish_glance(ret, x) +} +\arguments{ +\item{ret}{a one-row data frame (a partially complete glance)} + +\item{x}{the prediction model} +} +\value{ +a one-row data frame with additional columns added, such as +\item{logLik}{log likelihoods} +\item{AIC}{Akaike Information Criterion} +\item{BIC}{Bayesian Information Criterion} +\item{deviance}{deviance} +\item{df.residual}{residual degrees of freedom} + +Each of these are produced by the corresponding generics +} +\description{ +This function is now deprecated in favor of using custom logic and +the appropriate \code{nobs()} method. +} +\seealso{ +Other deprecated: +\code{\link{bootstrap}()}, +\code{\link{confint_tidy}()}, +\code{\link{data.frame_tidiers}}, +\code{\link{fix_data_frame}()}, +\code{\link{summary_tidiers}}, +\code{\link{tidy.density}()}, +\code{\link{tidy.dist}()}, +\code{\link{tidy.ftable}()}, +\code{\link{tidy.numeric}()} +} +\concept{deprecated} diff --git a/man/fix_data_frame.Rd b/man/fix_data_frame.Rd index a480ef55c..3d784ef9e 100644 --- a/man/fix_data_frame.Rd +++ b/man/fix_data_frame.Rd @@ -26,6 +26,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, \code{\link{tidy.dist}()}, diff --git a/man/summary_tidiers.Rd b/man/summary_tidiers.Rd index 4fd07662c..a7a5a7377 100644 --- a/man/summary_tidiers.Rd +++ b/man/summary_tidiers.Rd @@ -57,6 +57,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{tidy.density}()}, \code{\link{tidy.dist}()}, @@ -67,6 +68,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{tidy.density}()}, \code{\link{tidy.dist}()}, diff --git a/man/tidy.density.Rd b/man/tidy.density.Rd index dd702e991..89cd31e21 100644 --- a/man/tidy.density.Rd +++ b/man/tidy.density.Rd @@ -31,6 +31,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.dist}()}, diff --git a/man/tidy.dist.Rd b/man/tidy.dist.Rd index f29f207c5..18ecfdae4 100644 --- a/man/tidy.dist.Rd +++ b/man/tidy.dist.Rd @@ -57,6 +57,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, diff --git a/man/tidy.ftable.Rd b/man/tidy.ftable.Rd index 75be54f14..208b54256 100644 --- a/man/tidy.ftable.Rd +++ b/man/tidy.ftable.Rd @@ -32,6 +32,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, diff --git a/man/vector_tidiers.Rd b/man/vector_tidiers.Rd index f38f01910..baeaa0e0d 100644 --- a/man/vector_tidiers.Rd +++ b/man/vector_tidiers.Rd @@ -40,6 +40,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, @@ -50,6 +51,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, @@ -60,6 +62,7 @@ Other deprecated: \code{\link{bootstrap}()}, \code{\link{confint_tidy}()}, \code{\link{data.frame_tidiers}}, +\code{\link{finish_glance}()}, \code{\link{fix_data_frame}()}, \code{\link{summary_tidiers}}, \code{\link{tidy.density}()}, From 363ee6cc774f6d6678573aba97a515d750352268 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 08:16:22 -0700 Subject: [PATCH 36/41] add deprecation notice to finish_glance --- R/deprecated-0-7-0.R | 5 +++-- man/finish_glance.Rd | 2 -- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/R/deprecated-0-7-0.R b/R/deprecated-0-7-0.R index 8cc89e8f1..aef7a924f 100644 --- a/R/deprecated-0-7-0.R +++ b/R/deprecated-0-7-0.R @@ -556,11 +556,12 @@ confint_tidy <- function(x, conf.level = .95, func = stats::confint, ...) { #' \item{deviance}{deviance} #' \item{df.residual}{residual degrees of freedom} #' -#' Each of these are produced by the corresponding generics -#' #' @export #' @family deprecated finish_glance <- function(ret, x) { + .Deprecated( + msg = "finish_glance is now deprecated and will be removed from a future release of broom. Please only use the relevant `stats` functions for the given model type as needed." + ) ret$logLik <- tryCatch(as.numeric(stats::logLik(x)), error = function(e) NULL) ret$AIC <- tryCatch(stats::AIC(x), error = function(e) NULL) ret$BIC <- tryCatch(stats::BIC(x), error = function(e) NULL) diff --git a/man/finish_glance.Rd b/man/finish_glance.Rd index d3124f3dd..54529f34c 100644 --- a/man/finish_glance.Rd +++ b/man/finish_glance.Rd @@ -19,8 +19,6 @@ a one-row data frame with additional columns added, such as \item{BIC}{Bayesian Information Criterion} \item{deviance}{deviance} \item{df.residual}{residual degrees of freedom} - -Each of these are produced by the corresponding generics } \description{ This function is now deprecated in favor of using custom logic and From 2946998f3b8c4e8b20d43ad26714b32ddf40bfd5 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 08:20:04 -0700 Subject: [PATCH 37/41] more notes on reverse dependency checks --- cran-comments.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 14cc8f24b..fe7c71330 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,10 +4,12 @@ This is a resubmission following a request to first deprecate breaking changes and send another reminder to maintainers. We have made the requested changes and carried out another round of reverse dependency checks, notifying maintainers with unfixed breakages. We note that several remaining breakages -are due to removal of mixed-model tidiers that were deprecated in previous -releases--we have not reverted these methods back to soft-deprecations as -their namespace conflicts with the broom.mixed package, which provides a -consistent interface to mixed model tidiers, have caused user confusion. +are due to removal of mixed-model tidiers that have been deprecated since broom +0.5.0's release two years ago--we have not reverted these methods back to +soft-deprecations as their namespace conflicts with the `broom.mixed` package, +which provides a consistent interface to mixed model tidiers, have caused user +confusion. More notes on our most recent round of reverse dependency checks +can be found at the bottom of this document. The previous submission was also a resubmission following an automated pretest failure due to breaking changes in the `epi.2by2` function from From dc5cf0e87bd9ef274e7d006bcb4c31e01e900a5b Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Wed, 24 Jun 2020 09:57:50 -0700 Subject: [PATCH 38/41] submit to cran --- CRAN-RELEASE | 4 ++-- NEWS.md | 4 ++-- cran-comments.md | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 6075bea3b..9cf46d2d4 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-18. -Once it is accepted, delete this file and tag the release (commit 7f8f9591c2). +This package was submitted to CRAN on 2020-06-24. +Once it is accepted, delete this file and tag the release (commit 2946998f3b). diff --git a/NEWS.md b/NEWS.md index 900073b78..90bb65a38 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,7 @@ # broom 0.7.0 `broom 0.7.0` is a major release with a large number of new tidiers, -soft-deprecations, and carrying out of planned breaking changes. +soft-deprecations, and planned hard-deprecations of functions and arguments. ### Big picture changes @@ -57,7 +57,7 @@ methods: - `tidy.summaryDefault()` and `glance.summaryDefault()` have been deprecated in favor of `skimr::skim()` -We have also gone forward with our planned mixed model deprecations, and have +We have also gone forward with our planned mixed model deprecations, and have removed the following methods, which now live in `broom.mixed`: - `tidy.brmsfit()` diff --git a/cran-comments.md b/cran-comments.md index fe7c71330..bf1d70f81 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,7 @@ # Release summary -This is a resubmission following a request to first deprecate breaking -changes and send another reminder to maintainers. We have made the requested +This is a resubmission following a request to first deprecate removed methods +and send another reminder to maintainers. We have made the requested changes and carried out another round of reverse dependency checks, notifying maintainers with unfixed breakages. We note that several remaining breakages are due to removal of mixed-model tidiers that have been deprecated since broom @@ -53,7 +53,7 @@ the following message: In the initial round of revdepchecks, we checked 149 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. -We saw 37 new problems and failed to check one package. +We saw 37 new problems and failed to check one package. We first notified affected maintainers three weeks prior to our initial submission, and checked in with maintainers again a week and a half prior. @@ -62,8 +62,8 @@ Records of our initial outreach attempts can be found on this issue: https://github.com/tidymodels/broom/issues/862 Since being asked to revert removals to soft-deprecations by the CRAN team on -23 June 2020, we -have ran revdepchecks again. 20 issues remained, and after fixing 3 of them by +23 June 2020, we have ran revdepchecks again. +20 issues remained, and after fixing 3 of them by reverting removals to soft-deprecations, 17 remain. Of the 17 remaining issues, 9 of them have been fixed in development versions and are waiting on the release of `broom` 0.7.0 to submit. I've reached out to maintainers for all remaining issues, From 98f70c0323d00fb231af2ef609b231c0cf788301 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 25 Jun 2020 08:34:02 -0700 Subject: [PATCH 39/41] skip most unit tests on CRAN Per CRAN's request, cut down on check time. We'll now skip all tests besides core tidiers and some helper functions. --- cran-comments.md | 7 ++++++- tests/testthat/test-aer.R | 2 ++ tests/testthat/test-auc.R | 2 ++ tests/testthat/test-bbmle.R | 2 ++ tests/testthat/test-betareg.R | 2 ++ tests/testthat/test-biglm.R | 2 ++ tests/testthat/test-bingroup.R | 2 ++ tests/testthat/test-boot.R | 2 ++ tests/testthat/test-btergm.R | 2 ++ tests/testthat/test-car.R | 2 ++ tests/testthat/test-caret.R | 2 ++ tests/testthat/test-cluster.R | 2 ++ tests/testthat/test-drc.R | 2 ++ tests/testthat/test-emmeans.R | 2 ++ tests/testthat/test-epiR.R | 2 ++ tests/testthat/test-ergm.R | 2 ++ tests/testthat/test-fixest.R | 2 ++ tests/testthat/test-gam.R | 2 ++ tests/testthat/test-gamlss.R | 2 ++ tests/testthat/test-gee.R | 4 ++++ tests/testthat/test-geepack.R | 2 ++ tests/testthat/test-glmnetUtils.R | 2 ++ tests/testthat/test-gmm.R | 2 ++ tests/testthat/test-hmisc.R | 2 ++ tests/testthat/test-joineRML.R | 2 ++ tests/testthat/test-kendall.R | 2 ++ tests/testthat/test-ks.R | 2 ++ tests/testthat/test-lavaan.R | 2 ++ tests/testthat/test-leaps.R | 2 ++ tests/testthat/test-lfe.R | 2 ++ tests/testthat/test-list-irlba.R | 2 ++ tests/testthat/test-list-optim.R | 2 ++ tests/testthat/test-list-svd.R | 2 ++ tests/testthat/test-list-xyz.R | 2 ++ tests/testthat/test-list.R | 2 ++ tests/testthat/test-lmbeta-lm-beta.R | 2 ++ tests/testthat/test-lmodel2.R | 2 ++ tests/testthat/test-lmtest.R | 2 ++ tests/testthat/test-maps.R | 2 ++ tests/testthat/test-mass-fitdistr.R | 2 ++ tests/testthat/test-mass-polr.R | 2 ++ tests/testthat/test-mass-ridgelm.R | 2 ++ tests/testthat/test-mass-rlm.R | 2 ++ tests/testthat/test-mclogit.R | 4 ++++ tests/testthat/test-mclust.R | 4 ++++ tests/testthat/test-mediate.R | 1 + tests/testthat/test-mfx.R | 2 ++ tests/testthat/test-mgcv.R | 2 ++ tests/testthat/test-muhaz.R | 2 ++ tests/testthat/test-multcomp.R | 2 ++ tests/testthat/test-nnet.R | 2 ++ tests/testthat/test-orcutt.R | 2 ++ tests/testthat/test-ordinal.R | 2 ++ tests/testthat/test-pam.R | 2 ++ tests/testthat/test-plm.R | 2 ++ tests/testthat/test-polca.R | 2 ++ tests/testthat/test-psych.R | 2 ++ tests/testthat/test-quantreg-nlrq.R | 2 ++ tests/testthat/test-quantreg-rq.R | 2 ++ tests/testthat/test-quantreg-rqs.R | 2 ++ tests/testthat/test-rma.R | 2 ++ tests/testthat/test-robust.R | 2 ++ tests/testthat/test-robustbase.R | 2 ++ tests/testthat/test-sp.R | 2 ++ tests/testthat/test-spdep.R | 2 ++ tests/testthat/test-speedglm-speedglm.R | 2 ++ tests/testthat/test-speedglm-speedlm.R | 2 ++ tests/testthat/test-stats-arima.R | 2 ++ tests/testthat/test-stats-decompose.R | 2 ++ tests/testthat/test-stats-factanal.R | 2 ++ tests/testthat/test-stats-mlm.R | 2 ++ tests/testthat/test-stats-nls.R | 2 ++ tests/testthat/test-survey.R | 2 ++ tests/testthat/test-survival-aareg.R | 2 ++ tests/testthat/test-survival-cch.R | 2 ++ tests/testthat/test-survival-pyears.R | 2 ++ tests/testthat/test-survival-survdiff.R | 2 ++ tests/testthat/test-survival-survexp.R | 2 ++ tests/testthat/test-survival-survfit.R | 2 ++ tests/testthat/test-survival-survreg.R | 2 ++ tests/testthat/test-systemfit.R | 2 ++ tests/testthat/test-zoo.R | 2 ++ 82 files changed, 173 insertions(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index bf1d70f81..677761634 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,10 @@ # Release summary -This is a resubmission following a request to first deprecate removed methods +This submission is a resubmission following a request to further cut down on +check time. We've now skipped most all unit tests except for core functionality. + +The previous submission was also a resubmission +following a request to first deprecate removed methods and send another reminder to maintainers. We have made the requested changes and carried out another round of reverse dependency checks, notifying maintainers with unfixed breakages. We note that several remaining breakages @@ -23,6 +27,7 @@ The previous submission was also a resubmission following an automated pretest failure due to "[n]on-file package-anchored link(s) in documentation object[s]." This seemed to be a new test as of our previous submission, and has been addressed by linking to documentation files rather than topics. +Check times were also too long for this submission. The previous submission was also a resubmission following an automated pretest failure. The failure was due to breaking changes in the `residuals.fixest()` diff --git a/tests/testthat/test-aer.R b/tests/testthat/test-aer.R index 34728d958..13783e703 100644 --- a/tests/testthat/test-aer.R +++ b/tests/testthat/test-aer.R @@ -1,5 +1,7 @@ context("aer") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-auc.R b/tests/testthat/test-auc.R index 63deb804a..8eadb58d0 100644 --- a/tests/testthat/test-auc.R +++ b/tests/testthat/test-auc.R @@ -1,5 +1,7 @@ context("auc") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-bbmle.R b/tests/testthat/test-bbmle.R index 0dad5667c..409b9fd92 100644 --- a/tests/testthat/test-bbmle.R +++ b/tests/testthat/test-bbmle.R @@ -1,5 +1,7 @@ context("bbmle") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-betareg.R b/tests/testthat/test-betareg.R index 7742b753a..f7de905c9 100644 --- a/tests/testthat/test-betareg.R +++ b/tests/testthat/test-betareg.R @@ -1,5 +1,7 @@ context("betareg") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-biglm.R b/tests/testthat/test-biglm.R index d4dc0f536..f3b25f089 100644 --- a/tests/testthat/test-biglm.R +++ b/tests/testthat/test-biglm.R @@ -1,5 +1,7 @@ context("biglm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-bingroup.R b/tests/testthat/test-bingroup.R index 06f89cf8e..681587e80 100644 --- a/tests/testthat/test-bingroup.R +++ b/tests/testthat/test-bingroup.R @@ -1,5 +1,7 @@ context("bingroup") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-boot.R b/tests/testthat/test-boot.R index d10336bac..c90e3a114 100644 --- a/tests/testthat/test-boot.R +++ b/tests/testthat/test-boot.R @@ -1,5 +1,7 @@ context("boot") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-btergm.R b/tests/testthat/test-btergm.R index a15fe9d41..78765b8f6 100644 --- a/tests/testthat/test-btergm.R +++ b/tests/testthat/test-btergm.R @@ -1,5 +1,7 @@ context("btergm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-car.R b/tests/testthat/test-car.R index 34bb640c3..7144748c0 100644 --- a/tests/testthat/test-car.R +++ b/tests/testthat/test-car.R @@ -1,5 +1,7 @@ context("car") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) library(survival) diff --git a/tests/testthat/test-caret.R b/tests/testthat/test-caret.R index 17bd5f4e0..dd47979b0 100644 --- a/tests/testthat/test-caret.R +++ b/tests/testthat/test-caret.R @@ -1,5 +1,7 @@ context("caret") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-cluster.R b/tests/testthat/test-cluster.R index 1547608c8..5e3e07741 100644 --- a/tests/testthat/test-cluster.R +++ b/tests/testthat/test-cluster.R @@ -1,5 +1,7 @@ context("cluster") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-drc.R b/tests/testthat/test-drc.R index 408eed580..61e1ea050 100644 --- a/tests/testthat/test-drc.R +++ b/tests/testthat/test-drc.R @@ -1,5 +1,7 @@ context("drc") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-emmeans.R b/tests/testthat/test-emmeans.R index 5a28b19d5..65f955d4b 100644 --- a/tests/testthat/test-emmeans.R +++ b/tests/testthat/test-emmeans.R @@ -1,5 +1,7 @@ context("emmeans") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-epiR.R b/tests/testthat/test-epiR.R index 5db3a4cfc..7649abe02 100644 --- a/tests/testthat/test-epiR.R +++ b/tests/testthat/test-epiR.R @@ -1,5 +1,7 @@ context("epiR") +skip_on_cran() + skip_if_not_installed("epiR") dat <- matrix(c(13, 2163, 5, 3349), nrow = 2, byrow = TRUE) diff --git a/tests/testthat/test-ergm.R b/tests/testthat/test-ergm.R index 7c457db0c..1db19c77f 100644 --- a/tests/testthat/test-ergm.R +++ b/tests/testthat/test-ergm.R @@ -1,5 +1,7 @@ context("ergm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-fixest.R b/tests/testthat/test-fixest.R index 5d2eeb8d8..2be89af40 100644 --- a/tests/testthat/test-fixest.R +++ b/tests/testthat/test-fixest.R @@ -1,5 +1,7 @@ context("fixest") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-gam.R b/tests/testthat/test-gam.R index 183c26a98..5b3af73c4 100644 --- a/tests/testthat/test-gam.R +++ b/tests/testthat/test-gam.R @@ -1,5 +1,7 @@ context("gam") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-gamlss.R b/tests/testthat/test-gamlss.R index 1e3eaae54..70384a7c3 100644 --- a/tests/testthat/test-gamlss.R +++ b/tests/testthat/test-gamlss.R @@ -1,5 +1,7 @@ context("gamlss") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-gee.R b/tests/testthat/test-gee.R index ff12e44c6..592a73aad 100644 --- a/tests/testthat/test-gee.R +++ b/tests/testthat/test-gee.R @@ -1,3 +1,7 @@ +context("gee") + +skip_on_cran() + skip_if_not_installed("gee") library(gee) diff --git a/tests/testthat/test-geepack.R b/tests/testthat/test-geepack.R index a7dfb0006..94d68a434 100644 --- a/tests/testthat/test-geepack.R +++ b/tests/testthat/test-geepack.R @@ -1,5 +1,7 @@ context("geepack") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-glmnetUtils.R b/tests/testthat/test-glmnetUtils.R index fc9f61462..3269b6a58 100644 --- a/tests/testthat/test-glmnetUtils.R +++ b/tests/testthat/test-glmnetUtils.R @@ -1,5 +1,7 @@ context("glmnetUtils") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-gmm.R b/tests/testthat/test-gmm.R index 1ad4a0c8a..bd86aa5d6 100644 --- a/tests/testthat/test-gmm.R +++ b/tests/testthat/test-gmm.R @@ -1,5 +1,7 @@ context("gmm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-hmisc.R b/tests/testthat/test-hmisc.R index 61326a951..193519da9 100644 --- a/tests/testthat/test-hmisc.R +++ b/tests/testthat/test-hmisc.R @@ -1,5 +1,7 @@ context("hmisc") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-joineRML.R b/tests/testthat/test-joineRML.R index bfd9c148b..e93ddb032 100644 --- a/tests/testthat/test-joineRML.R +++ b/tests/testthat/test-joineRML.R @@ -1,5 +1,7 @@ context("joinerml") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-kendall.R b/tests/testthat/test-kendall.R index eb31f497e..98a5d5e43 100644 --- a/tests/testthat/test-kendall.R +++ b/tests/testthat/test-kendall.R @@ -1,5 +1,7 @@ context("kendall") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-ks.R b/tests/testthat/test-ks.R index a397d3363..17b72cebb 100644 --- a/tests/testthat/test-ks.R +++ b/tests/testthat/test-ks.R @@ -1,5 +1,7 @@ context("ks") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-lavaan.R b/tests/testthat/test-lavaan.R index d8d98fb43..c30e64fea 100644 --- a/tests/testthat/test-lavaan.R +++ b/tests/testthat/test-lavaan.R @@ -1,5 +1,7 @@ context("lavaan") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-leaps.R b/tests/testthat/test-leaps.R index acb8e380f..98ea18c06 100644 --- a/tests/testthat/test-leaps.R +++ b/tests/testthat/test-leaps.R @@ -1,5 +1,7 @@ context("lmtest") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-lfe.R b/tests/testthat/test-lfe.R index a92032f4b..790aad7b5 100644 --- a/tests/testthat/test-lfe.R +++ b/tests/testthat/test-lfe.R @@ -1,5 +1,7 @@ context("lfe") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-list-irlba.R b/tests/testthat/test-list-irlba.R index 2b8df2fd6..5f74e1673 100644 --- a/tests/testthat/test-list-irlba.R +++ b/tests/testthat/test-list-irlba.R @@ -1,5 +1,7 @@ context("list-irlba") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-list-optim.R b/tests/testthat/test-list-optim.R index a74e68fbb..c380a937f 100644 --- a/tests/testthat/test-list-optim.R +++ b/tests/testthat/test-list-optim.R @@ -1,5 +1,7 @@ context("list-optim") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-list-svd.R b/tests/testthat/test-list-svd.R index f3857218b..a517f8a07 100644 --- a/tests/testthat/test-list-svd.R +++ b/tests/testthat/test-list-svd.R @@ -1,5 +1,7 @@ context("list-svd") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-list-xyz.R b/tests/testthat/test-list-xyz.R index c608f9359..7d65d2acb 100644 --- a/tests/testthat/test-list-xyz.R +++ b/tests/testthat/test-list-xyz.R @@ -1,5 +1,7 @@ context("list-xyz") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-list.R b/tests/testthat/test-list.R index 7425236e2..fa2e6e23d 100644 --- a/tests/testthat/test-list.R +++ b/tests/testthat/test-list.R @@ -1,5 +1,7 @@ context("list") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-lmbeta-lm-beta.R b/tests/testthat/test-lmbeta-lm-beta.R index eceab90f0..61d46eef8 100644 --- a/tests/testthat/test-lmbeta-lm-beta.R +++ b/tests/testthat/test-lmbeta-lm-beta.R @@ -1,5 +1,7 @@ context("lmbeta-lm-beta") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-lmodel2.R b/tests/testthat/test-lmodel2.R index 96dc916a9..7fe9f3a78 100644 --- a/tests/testthat/test-lmodel2.R +++ b/tests/testthat/test-lmodel2.R @@ -1,5 +1,7 @@ context("lmodel2") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-lmtest.R b/tests/testthat/test-lmtest.R index acfd60c1b..b3eb7603a 100644 --- a/tests/testthat/test-lmtest.R +++ b/tests/testthat/test-lmtest.R @@ -1,5 +1,7 @@ context("lmtest") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-maps.R b/tests/testthat/test-maps.R index cd538832f..9a752b481 100644 --- a/tests/testthat/test-maps.R +++ b/tests/testthat/test-maps.R @@ -1,5 +1,7 @@ context("maps tidiers") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mass-fitdistr.R b/tests/testthat/test-mass-fitdistr.R index 58d874772..bffd5ead4 100644 --- a/tests/testthat/test-mass-fitdistr.R +++ b/tests/testthat/test-mass-fitdistr.R @@ -1,5 +1,7 @@ context("mass-fitdistr") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mass-polr.R b/tests/testthat/test-mass-polr.R index 52e6e6df1..075709334 100644 --- a/tests/testthat/test-mass-polr.R +++ b/tests/testthat/test-mass-polr.R @@ -1,5 +1,7 @@ context("mass-polr") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mass-ridgelm.R b/tests/testthat/test-mass-ridgelm.R index 13753840d..3d5be3304 100644 --- a/tests/testthat/test-mass-ridgelm.R +++ b/tests/testthat/test-mass-ridgelm.R @@ -1,5 +1,7 @@ context("mass-ridgelm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mass-rlm.R b/tests/testthat/test-mass-rlm.R index 17d413f5d..34ead81ea 100644 --- a/tests/testthat/test-mass-rlm.R +++ b/tests/testthat/test-mass-rlm.R @@ -1,5 +1,7 @@ context("mass-rlm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mclogit.R b/tests/testthat/test-mclogit.R index dc27103f7..b92c0b616 100644 --- a/tests/testthat/test-mclogit.R +++ b/tests/testthat/test-mclogit.R @@ -1,3 +1,7 @@ +context("mclogit") + +skip_on_cran() + skip_if_not_installed("mclogit") library(mclogit) diff --git a/tests/testthat/test-mclust.R b/tests/testthat/test-mclust.R index 10b2a30fc..79047d722 100644 --- a/tests/testthat/test-mclust.R +++ b/tests/testthat/test-mclust.R @@ -1,3 +1,7 @@ +context("mclust") + +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mediate.R b/tests/testthat/test-mediate.R index 9bd922cb7..7edf96aff 100644 --- a/tests/testthat/test-mediate.R +++ b/tests/testthat/test-mediate.R @@ -1,5 +1,6 @@ context("mediate") +skip_on_cran() skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mfx.R b/tests/testthat/test-mfx.R index a3145878d..ef1bae0c8 100644 --- a/tests/testthat/test-mfx.R +++ b/tests/testthat/test-mfx.R @@ -1,5 +1,7 @@ context("mfx") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-mgcv.R b/tests/testthat/test-mgcv.R index 9ba963c65..a8b09a008 100644 --- a/tests/testthat/test-mgcv.R +++ b/tests/testthat/test-mgcv.R @@ -1,5 +1,7 @@ context("mgcv") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-muhaz.R b/tests/testthat/test-muhaz.R index 584ac8590..b541bdf06 100644 --- a/tests/testthat/test-muhaz.R +++ b/tests/testthat/test-muhaz.R @@ -1,5 +1,7 @@ context("muhaz") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-multcomp.R b/tests/testthat/test-multcomp.R index b551cf1f6..a8e2f4fee 100644 --- a/tests/testthat/test-multcomp.R +++ b/tests/testthat/test-multcomp.R @@ -1,5 +1,7 @@ context("multcomp") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-nnet.R b/tests/testthat/test-nnet.R index ce84d55da..0a47ac356 100644 --- a/tests/testthat/test-nnet.R +++ b/tests/testthat/test-nnet.R @@ -1,5 +1,7 @@ context("nnet") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-orcutt.R b/tests/testthat/test-orcutt.R index d2e70ef85..d78d8fc73 100644 --- a/tests/testthat/test-orcutt.R +++ b/tests/testthat/test-orcutt.R @@ -1,5 +1,7 @@ context("orcutt") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-ordinal.R b/tests/testthat/test-ordinal.R index c9ee01541..2da988dc8 100644 --- a/tests/testthat/test-ordinal.R +++ b/tests/testthat/test-ordinal.R @@ -1,5 +1,7 @@ context("ordinal") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-pam.R b/tests/testthat/test-pam.R index 370574c3f..9475c5cf0 100644 --- a/tests/testthat/test-pam.R +++ b/tests/testthat/test-pam.R @@ -1,5 +1,7 @@ context("pam") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-plm.R b/tests/testthat/test-plm.R index 077428ca9..5d9635ac9 100644 --- a/tests/testthat/test-plm.R +++ b/tests/testthat/test-plm.R @@ -1,5 +1,7 @@ context("plm tidiers") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-polca.R b/tests/testthat/test-polca.R index f5c09de3f..30abefbfe 100644 --- a/tests/testthat/test-polca.R +++ b/tests/testthat/test-polca.R @@ -1,5 +1,7 @@ context("polca") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-psych.R b/tests/testthat/test-psych.R index 7afd4ab4c..94261f4a6 100644 --- a/tests/testthat/test-psych.R +++ b/tests/testthat/test-psych.R @@ -1,5 +1,7 @@ context("psych") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-quantreg-nlrq.R b/tests/testthat/test-quantreg-nlrq.R index e1e938f00..0ac21f381 100644 --- a/tests/testthat/test-quantreg-nlrq.R +++ b/tests/testthat/test-quantreg-nlrq.R @@ -1,5 +1,7 @@ context("quantreg-nlrq") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-quantreg-rq.R b/tests/testthat/test-quantreg-rq.R index beb1e0cd2..919e133a5 100644 --- a/tests/testthat/test-quantreg-rq.R +++ b/tests/testthat/test-quantreg-rq.R @@ -1,5 +1,7 @@ context("quantreg-rq") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-quantreg-rqs.R b/tests/testthat/test-quantreg-rqs.R index 1c3908758..a8232e296 100644 --- a/tests/testthat/test-quantreg-rqs.R +++ b/tests/testthat/test-quantreg-rqs.R @@ -1,5 +1,7 @@ context("quantreg-rqs") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-rma.R b/tests/testthat/test-rma.R index 84f5aff9b..2681fd5e3 100644 --- a/tests/testthat/test-rma.R +++ b/tests/testthat/test-rma.R @@ -1,5 +1,7 @@ context("rma") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-robust.R b/tests/testthat/test-robust.R index 2678d2e93..72a23af3a 100644 --- a/tests/testthat/test-robust.R +++ b/tests/testthat/test-robust.R @@ -1,5 +1,7 @@ context("robust") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-robustbase.R b/tests/testthat/test-robustbase.R index c0b5f60ff..093eeec20 100644 --- a/tests/testthat/test-robustbase.R +++ b/tests/testthat/test-robustbase.R @@ -1,5 +1,7 @@ context("robustbase") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-sp.R b/tests/testthat/test-sp.R index 3d4823a7d..f0d1332bd 100644 --- a/tests/testthat/test-sp.R +++ b/tests/testthat/test-sp.R @@ -1,5 +1,7 @@ context("sp") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-spdep.R b/tests/testthat/test-spdep.R index 0fd8dc388..b0383799f 100644 --- a/tests/testthat/test-spdep.R +++ b/tests/testthat/test-spdep.R @@ -1,5 +1,7 @@ context("spdep") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-speedglm-speedglm.R b/tests/testthat/test-speedglm-speedglm.R index 7838bd1fc..4f677b861 100644 --- a/tests/testthat/test-speedglm-speedglm.R +++ b/tests/testthat/test-speedglm-speedglm.R @@ -1,5 +1,7 @@ context("test-speedglm-speedglm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-speedglm-speedlm.R b/tests/testthat/test-speedglm-speedlm.R index f4e1c56bf..64ced4116 100644 --- a/tests/testthat/test-speedglm-speedlm.R +++ b/tests/testthat/test-speedglm-speedlm.R @@ -1,5 +1,7 @@ context("speedglm") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-stats-arima.R b/tests/testthat/test-stats-arima.R index 8452d66cb..660e8d926 100644 --- a/tests/testthat/test-stats-arima.R +++ b/tests/testthat/test-stats-arima.R @@ -1,5 +1,7 @@ context("stats-arima") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-stats-decompose.R b/tests/testthat/test-stats-decompose.R index 8ad95db6e..ec21b6ef3 100644 --- a/tests/testthat/test-stats-decompose.R +++ b/tests/testthat/test-stats-decompose.R @@ -1,5 +1,7 @@ context("stats-decompose") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-stats-factanal.R b/tests/testthat/test-stats-factanal.R index 096a73e73..4dffa94eb 100644 --- a/tests/testthat/test-stats-factanal.R +++ b/tests/testthat/test-stats-factanal.R @@ -1,5 +1,7 @@ context("stats-factanal") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-stats-mlm.R b/tests/testthat/test-stats-mlm.R index af58c5150..ebec72d3a 100644 --- a/tests/testthat/test-stats-mlm.R +++ b/tests/testthat/test-stats-mlm.R @@ -1,5 +1,7 @@ context("stats-mlm") +skip_on_cran() + fit_mlm <- lm(cbind(mpg, disp) ~ wt, mtcars) df_tidy <- tidy(fit_mlm, conf.int = TRUE) diff --git a/tests/testthat/test-stats-nls.R b/tests/testthat/test-stats-nls.R index 970cf8c14..11b6da253 100644 --- a/tests/testthat/test-stats-nls.R +++ b/tests/testthat/test-stats-nls.R @@ -1,5 +1,7 @@ context("stats-nls") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survey.R b/tests/testthat/test-survey.R index 642f4dcf3..d7ef7cde4 100644 --- a/tests/testthat/test-survey.R +++ b/tests/testthat/test-survey.R @@ -1,5 +1,7 @@ context("survey") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-aareg.R b/tests/testthat/test-survival-aareg.R index f50fbc140..62496a9fc 100644 --- a/tests/testthat/test-survival-aareg.R +++ b/tests/testthat/test-survival-aareg.R @@ -1,5 +1,7 @@ context("survival-aareg") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-cch.R b/tests/testthat/test-survival-cch.R index 7e3fbccd1..d06e4b286 100644 --- a/tests/testthat/test-survival-cch.R +++ b/tests/testthat/test-survival-cch.R @@ -1,5 +1,7 @@ context("survival-cch") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-pyears.R b/tests/testthat/test-survival-pyears.R index caa197726..fb1014086 100644 --- a/tests/testthat/test-survival-pyears.R +++ b/tests/testthat/test-survival-pyears.R @@ -1,5 +1,7 @@ context("survival-pyears") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-survdiff.R b/tests/testthat/test-survival-survdiff.R index 9091cbb35..39f596ff0 100644 --- a/tests/testthat/test-survival-survdiff.R +++ b/tests/testthat/test-survival-survdiff.R @@ -1,5 +1,7 @@ context("survival-survdiff") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-survexp.R b/tests/testthat/test-survival-survexp.R index 8ddf991af..f44c0bd2f 100644 --- a/tests/testthat/test-survival-survexp.R +++ b/tests/testthat/test-survival-survexp.R @@ -1,5 +1,7 @@ context("survival-survexp") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-survfit.R b/tests/testthat/test-survival-survfit.R index eb03f3338..54a997551 100644 --- a/tests/testthat/test-survival-survfit.R +++ b/tests/testthat/test-survival-survfit.R @@ -1,5 +1,7 @@ context("survival-survfit") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-survival-survreg.R b/tests/testthat/test-survival-survreg.R index acc03d28e..e90798c05 100644 --- a/tests/testthat/test-survival-survreg.R +++ b/tests/testthat/test-survival-survreg.R @@ -1,5 +1,7 @@ context("survival-survreg") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-systemfit.R b/tests/testthat/test-systemfit.R index 1f28386bc..d77b008bb 100644 --- a/tests/testthat/test-systemfit.R +++ b/tests/testthat/test-systemfit.R @@ -1,5 +1,7 @@ context("systemfit") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) diff --git a/tests/testthat/test-zoo.R b/tests/testthat/test-zoo.R index 592f0d5cb..7ff6a11d0 100644 --- a/tests/testthat/test-zoo.R +++ b/tests/testthat/test-zoo.R @@ -1,5 +1,7 @@ context("zoo") +skip_on_cran() + skip_if_not_installed("modeltests") library(modeltests) From 284dbe5ed6385e48bc408764d46f12eea1f61cf0 Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 25 Jun 2020 12:51:46 -0700 Subject: [PATCH 40/41] submit to cran --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 9cf46d2d4..14ebd7c80 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-06-24. -Once it is accepted, delete this file and tag the release (commit 2946998f3b). +This package was submitted to CRAN on 2020-06-25. +Once it is accepted, delete this file and tag the release (commit 98f70c0323). From 8c58f0e4fb41b8637da21155f75e4f18017dd56a Mon Sep 17 00:00:00 2001 From: "Simon P. Couch" Date: Thu, 9 Jul 2020 07:22:09 -0700 Subject: [PATCH 41/41] =?UTF-8?q?accepted=20to=20CRAN=F0=9F=8E=89?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CRAN-RELEASE | 2 -- cran-comments.md | 61 ------------------------------------------------ 2 files changed, 63 deletions(-) delete mode 100644 CRAN-RELEASE diff --git a/CRAN-RELEASE b/CRAN-RELEASE deleted file mode 100644 index 14ebd7c80..000000000 --- a/CRAN-RELEASE +++ /dev/null @@ -1,2 +0,0 @@ -This package was submitted to CRAN on 2020-06-25. -Once it is accepted, delete this file and tag the release (commit 98f70c0323). diff --git a/cran-comments.md b/cran-comments.md index 677761634..2b7347eb5 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,39 +1,5 @@ # Release summary -This submission is a resubmission following a request to further cut down on -check time. We've now skipped most all unit tests except for core functionality. - -The previous submission was also a resubmission -following a request to first deprecate removed methods -and send another reminder to maintainers. We have made the requested -changes and carried out another round of reverse dependency checks, notifying -maintainers with unfixed breakages. We note that several remaining breakages -are due to removal of mixed-model tidiers that have been deprecated since broom -0.5.0's release two years ago--we have not reverted these methods back to -soft-deprecations as their namespace conflicts with the `broom.mixed` package, -which provides a consistent interface to mixed model tidiers, have caused user -confusion. More notes on our most recent round of reverse dependency checks -can be found at the bottom of this document. - -The previous submission was also a resubmission following an automated -pretest failure due to breaking changes in the `epi.2by2` function from -the `epiR` package, a new version of which was released on CRAN since -our previous submission. - -The previous submission was also a resubmission following an erroniously -included Remotes section in the package DESCRIPTION. - -The previous submission was also a resubmission following an automated pretest -failure due to "[n]on-file package-anchored link(s) in documentation -object[s]." This seemed to be a new test as of our previous submission, -and has been addressed by linking to documentation files rather than topics. -Check times were also too long for this submission. - -The previous submission was also a resubmission following an automated pretest -failure. The failure was due to breaking changes in the `residuals.fixest()` -S3 method from the `fixest` package, a new version of which was -released on CRAN the same day as the original submission. - broom 0.7.0 is a major release featuring a number of new S3 methods, bug fixes, and improvements to internal consistency and performance. This release also carries out a planned deprecation of a number of @@ -53,30 +19,3 @@ methods to the `broom.mixed` package. the following message: > Maintainer: 'Alex Hayes ' - -## revdepcheck results - -In the initial round of revdepchecks, we checked 149 reverse dependencies, -comparing R CMD check results across CRAN and dev versions of this package. -We saw 37 new problems and failed to check one package. - -We first notified affected maintainers three weeks prior to our initial -submission, and checked in with maintainers again a week and a half prior. -Records of our initial outreach attempts can be found on this issue: - -https://github.com/tidymodels/broom/issues/862 - -Since being asked to revert removals to soft-deprecations by the CRAN team on -23 June 2020, we have ran revdepchecks again. -20 issues remained, and after fixing 3 of them by -reverting removals to soft-deprecations, 17 remain. Of the 17 remaining issues, -9 of them have been fixed in development versions and are waiting on the release -of `broom` 0.7.0 to submit. I've reached out to maintainers for all remaining issues, -besides `eyetrackingR`, which currently does not have a maintainer. The majority of -remaining issues are due to the planned deprecation of mixed model tidiers to -`broom.mixed`, initially announced with the release of broom 0.5.0 two years ago. -Records of our most recent revdepchecks, and attempts to reach out to maintainers, -can be found on this issue: - -https://github.com/tidymodels/broom/issues/885 -