From 147c9583fc7d701112e21279fd9746bf8ea0efda Mon Sep 17 00:00:00 2001 From: nfrerebeau Date: Thu, 8 Sep 2022 11:56:31 +0200 Subject: [PATCH] Prepare for next release --- CITATION.cff | 7 +-- DESCRIPTION | 2 +- NEWS.md | 2 +- R/AllGenerics.R | 86 +++++++++---------------- R/tabula-package.R | 2 +- codemeta.json | 4 +- cran-comments.md | 6 +- man/tabula-package.Rd | 2 +- revdep/README.md | 143 +++++++++++++++++++++--------------------- 9 files changed, 111 insertions(+), 143 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index cfaf9726..b7e1388d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.2.2 +# CITATION file created with {cffr} R package, v0.2.3 # See also: https://docs.ropensci.org/cffr/ # ----------------------------------------------------------- @@ -8,7 +8,7 @@ message: 'To cite package "tabula" in publications use:' type: software license: GPL-3.0-or-later title: 'tabula: Analysis and Visualization of Archaeological Count Data' -version: 1.7.0.9000 +version: 1.8.0 abstract: 'An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), @@ -30,7 +30,7 @@ preferred-citation: email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - version: 1.7.0.9000 + version: 1.8.0 abstract: 'An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), @@ -50,7 +50,6 @@ preferred-citation: - archaeological-science - archaeology - data-visualization - - matrix-seriation - r-package license: GPL-3.0-or-later year: '2022' diff --git a/DESCRIPTION b/DESCRIPTION index 8b468f13..4c0eab5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: tabula Title: Analysis and Visualization of Archaeological Count Data -Version: 1.7.0.9000 +Version: 1.8.0 Authors@R: c(person(given = "Nicolas", family = "Frerebeau", diff --git a/NEWS.md b/NEWS.md index 49dbc015..23992a15 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# tabula 1.7.0.9000 +# tabula 1.8.0 **Seriation methods are now reexported from kairos and will be removed in a future release.** ## New classes and methods diff --git a/R/AllGenerics.R b/R/AllGenerics.R index 26cf3698..20241126 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -288,11 +288,6 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name heterogeneity -#' @rdname heterogeneity -NULL - -#' @rdname heterogeneity #' @aliases heterogeneity-method setGeneric( name = "heterogeneity", @@ -459,11 +454,6 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name richness -#' @rdname richness -NULL - -#' @rdname richness #' @aliases richness-method setGeneric( name = "richness", @@ -521,6 +511,7 @@ setGeneric( def = function(x, ...) standardGeneric("index_menhinick") ) +## Rarefaction ----------------------------------------------------------------- #' Rarefaction #' #' @param object A \eqn{m \times p}{m x p} `numeric` [`matrix`] or @@ -556,11 +547,6 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name rarefaction -#' @rdname rarefaction -NULL - -#' @rdname rarefaction #' @aliases rarefaction-method setGeneric( name = "rarefaction", @@ -639,11 +625,6 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name similarity -#' @rdname similarity -NULL - -#' @rdname similarity #' @aliases similarity-method setGeneric( name = "similarity", @@ -707,11 +688,6 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name occurrence -#' @rdname occurrence -NULL - -#' @rdname occurrence #' @aliases occurrence-method setGeneric( name = "occurrence", @@ -766,14 +742,10 @@ setGeneric( #' @author N. Frerebeau #' @family diversity measures #' @docType methods -#' @name turnover -#' @rdname turnover -NULL - -#' @rdname turnover #' @aliases turnover-method setGeneric( name = "turnover", + def = function(object, ...) standardGeneric("turnover") ) @@ -869,6 +841,32 @@ NULL #' @rdname plot_diversity NULL +## Diversity Test -------------------------------------------------------------- +#' Diversity Test +#' +#' Compares Shannon diversity between samples. +#' @param object A \eqn{m \times p}{m x p} matrix of count data. +#' @param adjust A [`character`] string specifying the method for +#' adjusting \eqn{p} values (see [stats::p.adjust()]). +#' @param ... Further arguments to be passed to internal methods. +#' @details +#' This test produces two sided pairwise comparisons: it returns a matrix of +#' adjusted \eqn{p} values. +#' @return +#' A [`numeric`] [`matrix`]. +#' @example inst/examples/ex-test.R +#' @author N. Frerebeau +#' @references +#' Magurran, A. E. (1988). *Ecological Diversity and its Measurement*. +#' Princeton, NJ: Princeton University Press. \doi{10.1007/978-94-015-7358-0}. +#' @family statistics +#' @docType methods +#' @aliases test_diversity-method +setGeneric( + name = "test_diversity", + def = function(object, ...) standardGeneric("test_diversity") +) + # Plot ========================================================================= ## Heatmap --------------------------------------------------------------------- #' Heatmap @@ -1056,34 +1054,6 @@ setGeneric( def = function(object, ...) standardGeneric("plot_spot") ) -# Test ========================================================================= -## Diversity Test -------------------------------------------------------------- -#' Diversity Test -#' -#' Compares Shannon diversity between samples. -#' @param object A \eqn{m \times p}{m x p} matrix of count data. -#' @param adjust A [`character`] string specifying the method for -#' adjusting \eqn{p} values (see [stats::p.adjust()]). -#' @param ... Further arguments to be passed to internal methods. -#' @details -#' This test produces two sided pairwise comparisons: it returns a matrix of -#' adjusted \eqn{p} values. -#' @return -#' A [`numeric`] [`matrix`]. -#' @example inst/examples/ex-test.R -#' @author N. Frerebeau -#' @references -#' Magurran, A. E. (1988). *Ecological Diversity and its Measurement*. -#' Princeton, NJ: Princeton University Press. \doi{10.1007/978-94-015-7358-0}. -#' @family statistics -#' @docType methods -#' @rdname test_diversity -#' @aliases test_diversity-method -setGeneric( - name = "test_diversity", - def = function(object, ...) standardGeneric("test_diversity") -) - # Deprecated =================================================================== #' Deprecated Methods #' diff --git a/R/tabula-package.R b/R/tabula-package.R index eb31ec41..7b5ee3c9 100644 --- a/R/tabula-package.R +++ b/R/tabula-package.R @@ -2,7 +2,7 @@ #' \tabular{ll}{ #' **Package:** \tab tabula \cr #' **Type:** \tab Package \cr -#' **Version:** \tab 1.7.0 \cr +#' **Version:** \tab 1.8.0 \cr #' **License:** \tab GPL-3 \cr #' **Zenodo:** \tab \doi{10.5281/zenodo.1489944} \cr #' **JOSS:** \tab \doi{10.21105/joss.01821} \cr diff --git a/codemeta.json b/codemeta.json index cddb3b88..1bb811fa 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,7 +8,7 @@ "codeRepository": "https://github.com/tesselle/tabula", "issueTracker": "https://github.com/tesselle/tabula/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.7.0.9000", + "version": "1.8.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -250,7 +250,7 @@ }, "SystemRequirements": null }, - "fileSize": "1888.796KB", + "fileSize": "1888.341KB", "citation": [ { "@type": "ScholarlyArticle", diff --git a/cran-comments.md b/cran-comments.md index 35bef712..b482f38f 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,16 +1,14 @@ ## Test environments -* Local R installation: R 4.2.0 +* Local R installation: R 4.2.1 * Ubuntu 20.04 (on GitHub Actions): R devel, release, oldrel * Windows (on GitHub Actions and win-builder): R devel, release, oldrel * MacOS (on GitHub Actions): R release ## R CMD check results -0 errors | 1 warnings | 1 note +0 errors | 0 warnings | 1 note -* CRAN package check warning ("replacing previous import") has been fixed. * Some links in the documentation point to articles behind paywalls that may return a 403 error. -* This is a resubmission. ## revdepcheck results diff --git a/man/tabula-package.Rd b/man/tabula-package.Rd index 91f209b7..1f022b54 100644 --- a/man/tabula-package.Rd +++ b/man/tabula-package.Rd @@ -15,7 +15,7 @@ An easy way to examine archaeological count data. This package provides several \tabular{ll}{ \strong{Package:} \tab tabula \cr \strong{Type:} \tab Package \cr -\strong{Version:} \tab 1.7.0 \cr +\strong{Version:} \tab 1.8.0 \cr \strong{License:} \tab GPL-3 \cr \strong{Zenodo:} \tab \doi{10.5281/zenodo.1489944} \cr \strong{JOSS:} \tab \doi{10.21105/joss.01821} \cr diff --git a/revdep/README.md b/revdep/README.md index de076eff..2598333b 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,79 +1,80 @@ # Platform -|field |value | -|:--------|:----------------------------------------| -|version |R version 4.2.0 (2022-04-22) | -|os |Ubuntu 20.04.4 LTS | -|system |x86_64, linux-gnu | -|ui |RStudio | -|language |(EN) | -|collate |fr_FR.UTF-8 | -|ctype |fr_FR.UTF-8 | -|tz |Europe/Paris | -|date |2022-06-19 | -|rstudio |2022.02.3+492 Prairie Trillium (desktop) | -|pandoc |NA | +|field |value | +|:--------|:-----------------------------------------| +|version |R version 4.2.1 (2022-06-23) | +|os |Ubuntu 20.04.4 LTS | +|system |x86_64, linux-gnu | +|ui |RStudio | +|language |(EN) | +|collate |fr_FR.UTF-8 | +|ctype |fr_FR.UTF-8 | +|tz |Europe/Paris | +|date |2022-09-08 | +|rstudio |2022.07.1+554 Spotted Wakerobin (desktop) | +|pandoc |NA | # Dependencies -|package |old |new |Δ | -|:------------|:------|:-------|:--| -|tabula |1.6.1 |1.7.0 |* | -|arkhe |0.5.0 |0.5.0 | | -|backports |NA |1.4.1 |* | -|base64enc |NA |0.1-3 |* | -|checkmate |NA |2.1.0 |* | -|cli |3.3.0 |3.3.0 | | -|colorspace |2.0-3 |2.0-3 | | -|crayon |1.5.1 |1.5.1 | | -|data.table |NA |1.14.2 |* | -|digest |0.6.29 |0.6.29 | | -|dimensio |0.2.2 |0.2.2 | | -|ellipsis |0.3.2 |0.3.2 | | -|evaluate |NA |0.15 |* | -|extraDistr |NA |1.9.1 |* | -|fansi |1.0.3 |1.0.3 | | -|farver |2.1.0 |2.1.0 | | -|fastmap |NA |1.1.0 |* | -|Formula |NA |1.2-4 |* | -|ggplot2 |3.3.6 |3.3.6 | | -|glue |1.6.2 |1.6.2 | | -|gridExtra |NA |2.3 |* | -|gtable |0.3.0 |0.3.0 | | -|highr |NA |0.9 |* | -|Hmisc |NA |4.7-0 |* | -|htmlTable |NA |2.4.0 |* | -|htmltools |NA |0.5.2 |* | -|htmlwidgets |NA |1.5.4 |* | -|isoband |0.2.5 |0.2.5 | | -|jpeg |NA |0.1-9 |* | -|jsonlite |NA |1.8.0 |* | -|kairos |NA |1.1.0 |* | -|knitr |NA |1.39 |* | -|labeling |0.4.2 |0.4.2 | | -|latticeExtra |NA |0.6-29 |* | -|lifecycle |1.0.1 |1.0.1 | | -|magrittr |2.0.3 |2.0.3 | | -|munsell |0.5.0 |0.5.0 | | -|pillar |1.7.0 |1.7.0 | | -|pkgconfig |2.0.3 |2.0.3 | | -|png |NA |0.1-7 |* | -|R6 |2.5.1 |2.5.1 | | -|RColorBrewer |1.1-3 |1.1-3 | | -|Rcpp |NA |1.0.8.3 |* | -|rlang |1.0.2 |1.0.2 | | -|rstudioapi |NA |0.13 |* | -|scales |1.2.0 |1.2.0 | | -|stringi |NA |1.7.6 |* | -|stringr |NA |1.4.0 |* | -|tibble |3.1.7 |3.1.7 | | -|utf8 |1.2.2 |1.2.2 | | -|vctrs |0.4.1 |0.4.1 | | -|viridis |NA |0.6.2 |* | -|viridisLite |0.4.0 |0.4.0 | | -|withr |2.5.0 |2.5.0 | | -|xfun |NA |0.31 |* | -|yaml |NA |2.3.5 |* | +|package |old |new |Δ | +|:------------|:---------|:----------|:--| +|tabula |1.7.0 |1.7.0.9000 |* | +|arkhe |0.5.0 |0.5.0 | | +|backports |1.4.1 |1.4.1 | | +|base64enc |0.1-3 |0.1-3 | | +|checkmate |2.1.0 |2.1.0 | | +|cli |3.4.0 |3.4.0 | | +|colorspace |2.0-3 |2.0-3 | | +|data.table |1.14.2 |1.14.2 | | +|deldir |1.0-6 |1.0-6 | | +|digest |0.6.29 |0.6.29 | | +|dimensio |0.3.0 |0.3.0 | | +|evaluate |0.16 |0.16 | | +|extraDistr |1.9.1 |1.9.1 | | +|fansi |1.0.3 |1.0.3 | | +|farver |2.1.1 |2.1.1 | | +|fastmap |1.1.0 |1.1.0 | | +|Formula |1.2-4 |1.2-4 | | +|ggplot2 |3.3.6 |3.3.6 | | +|glue |1.6.2 |1.6.2 | | +|gridExtra |2.3 |2.3 | | +|gtable |0.3.1 |0.3.1 | | +|highr |0.9 |0.9 | | +|Hmisc |4.7-1 |4.7-1 | | +|htmlTable |2.4.1 |2.4.1 | | +|htmltools |0.5.3 |0.5.3 | | +|htmlwidgets |1.5.4 |1.5.4 | | +|interp |1.1-3 |1.1-3 | | +|isoband |0.2.5 |0.2.5 | | +|jpeg |0.1-9 |0.1-9 | | +|jsonlite |1.8.0 |1.8.0 | | +|kairos |1.1.0 |1.1.0 | | +|knitr |1.40 |1.40 | | +|labeling |0.4.2 |0.4.2 | | +|latticeExtra |0.6-30 |0.6-30 | | +|lifecycle |1.0.1 |1.0.1 | | +|magrittr |2.0.3 |2.0.3 | | +|munsell |0.5.0 |0.5.0 | | +|pillar |1.8.1 |1.8.1 | | +|pkgconfig |2.0.3 |2.0.3 | | +|png |0.1-7 |0.1-7 | | +|R6 |2.5.1 |2.5.1 | | +|RColorBrewer |1.1-3 |1.1-3 | | +|Rcpp |1.0.9 |1.0.9 | | +|RcppEigen |0.3.3.9.2 |0.3.3.9.2 | | +|rlang |1.0.5 |1.0.5 | | +|rstudioapi |0.14 |0.14 | | +|scales |1.2.1 |1.2.1 | | +|stringi |1.7.8 |1.7.8 | | +|stringr |1.4.1 |1.4.1 | | +|tibble |3.1.8 |3.1.8 | | +|utf8 |1.2.2 |1.2.2 | | +|vctrs |0.4.1 |0.4.1 | | +|viridis |0.6.2 |0.6.2 | | +|viridisLite |0.4.1 |0.4.1 | | +|withr |2.5.0 |2.5.0 | | +|xfun |0.32 |0.32 | | +|yaml |2.3.5 |2.3.5 | | # Revdeps