prepare CRAN hotfix (#876)

* prepare CRAN hotfix * requires insight dev * check on insight dev * update NAMESPACE * update wordlist * remove remotes * cran comments, release version * submitted * Revert "Remove re-exports (#873)" This reverts commit 9a654da. * news * cran comments * submitted
easystats · Apr 19, 2023 · e90b9d0 · e90b9d0
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.20.3
-Date: 2023-04-05 06:07:12 UTC
-SHA: ac64894ca63668acf04804f79a9f02490ade31ca
+Version: 0.21.0
+Date: 2023-04-19 11:52:51 UTC
+SHA: ad9c5390202be4b3132e30dd122cad323f0cbec7
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.20.3.1
+Version: 0.21.0
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -140,7 +140,6 @@ Suggests:
     ivreg,
     knitr,
     lavaan,
-    lavaSearch2,
     lfe,
     lm.beta,
     lme4,

diff --git a/NAMESPACE b/NAMESPACE
@@ -177,7 +177,6 @@ S3method(display,parameters_pca)
 S3method(display,parameters_pca_summary)
 S3method(display,parameters_sem)
 S3method(display,parameters_simulate)
-S3method(dof_satterthwaite,lme)
 S3method(dof_satterthwaite,lmerMod)
 S3method(equivalence_test,MixMod)
 S3method(equivalence_test,feis)
@@ -624,8 +623,6 @@ S3method(reduce_parameters,merMod)
 S3method(reshape_loadings,data.frame)
 S3method(reshape_loadings,parameters_efa)
 S3method(se_satterthwaite,default)
-S3method(se_satterthwaite,gls)
-S3method(se_satterthwaite,lme)
 S3method(select_parameters,lm)
 S3method(select_parameters,merMod)
 S3method(simulate_model,LORgee)
@@ -914,6 +911,8 @@ export(confidence_curve)
 export(consonance_function)
 export(convert_efa_to_cfa)
 export(degrees_of_freedom)
+export(demean)
+export(describe_distribution)
 export(display)
 export(dof)
 export(dof_betwithin)
@@ -929,6 +928,7 @@ export(format_order)
 export(format_p_adjust)
 export(format_parameters)
 export(get_scores)
+export(kurtosis)
 export(model_parameters)
 export(n_clusters)
 export(n_clusters_dbscan)
@@ -955,27 +955,38 @@ export(print_md)
 export(random_parameters)
 export(reduce_data)
 export(reduce_parameters)
+export(rescale_weights)
 export(reshape_loadings)
 export(rotated_data)
 export(se_kenward)
 export(se_satterthwaite)
 export(select_parameters)
 export(simulate_model)
 export(simulate_parameters)
+export(skewness)
 export(sort_parameters)
 export(standard_error)
 export(standardise_info)
 export(standardise_parameters)
 export(standardise_posteriors)
 export(standardize_info)
+export(standardize_names)
 export(standardize_parameters)
 export(standardize_posteriors)
+export(supported_models)
 export(visualisation_recipe)
 importFrom(bayestestR,ci)
 importFrom(bayestestR,equivalence_test)
+importFrom(datawizard,demean)
+importFrom(datawizard,describe_distribution)
+importFrom(datawizard,kurtosis)
+importFrom(datawizard,rescale_weights)
+importFrom(datawizard,skewness)
 importFrom(datawizard,visualisation_recipe)
 importFrom(graphics,plot)
 importFrom(insight,display)
 importFrom(insight,n_parameters)
 importFrom(insight,print_html)
 importFrom(insight,print_md)
+importFrom(insight,standardize_names)
+importFrom(insight,supported_models)
diff --git a/NEWS.md b/NEWS.md
@@ -2,11 +2,9 @@
 
 ## Breaking Changes
 
-* As noted in release notes for 0.15.0 version, all re-exported functions from
-  *datawizard* package have now been removed.
-
-* Following re-exported functions from *insight* have been removed:
-  `standardize_names()`, `supported_models()`
+* It is no longer possible to calculate Satterthwaite-approximated degrees of
+  freedom for mixed models from package *nlme*. This was based on the
+  *lavaSearch2* package, which no longer seems to support models of class `lme`.
 
 ## Changes to functions
 

diff --git a/R/dof_satterthwaite.R b/R/dof_satterthwaite.R
@@ -15,14 +15,3 @@ dof_satterthwaite.lmerMod <- function(model) {
 
   stats::setNames(as.vector(s$coefficients[, 3]), parameters)
 }
-
-
-#' @export
-dof_satterthwaite.lme <- function(model) {
-  insight::check_if_installed("lavaSearch2")
-
-  parameters <- insight::find_parameters(model, effects = "fixed", flatten = TRUE)
-  lavaSearch2::sCorrect(model) <- TRUE
-  s <- lavaSearch2::summary2(model)
-  stats::setNames(as.vector(s$tTable[, "df"]), parameters)
-}
diff --git a/R/methods_nlme.R b/R/methods_nlme.R
@@ -15,7 +15,7 @@ ci.lme <- function(x,
                    method = "wald",
                    ...) {
   method <- tolower(method)
-  method <- match.arg(method, choices = c("wald", "normal", "residual", "betwithin", "ml1", "satterthwaite"))
+  method <- match.arg(method, choices = c("wald", "normal", "residual", "betwithin", "ml1"))
 
   if (method %in% c("wald", "residual", "normal")) {
     # `vcov` argument must be computed using the `.ci_generic` function.
@@ -49,10 +49,6 @@ ci.lme <- function(x,
     # betwithin approx
   } else if (method == "betwithin") {
     ci_betwithin(x, ci)
-
-    # Satterthwaite
-  } else if (method == "satterthwaite") {
-    ci_satterthwaite(x, ci)
   }
 }
 

diff --git a/R/reexports.R b/R/reexports.R
@@ -1,7 +1,39 @@
+# ----------------------- insight -------------------------------------
+
+#' @importFrom insight standardize_names
+#' @export
+insight::standardize_names
+
+#' @importFrom insight supported_models
+#' @export
+insight::supported_models
+
 #' @importFrom insight print_html
 #' @export
 insight::print_html
 
+# ----------------------- datawizard -------------------------------------
+
+#' @importFrom datawizard describe_distribution
+#' @export
+datawizard::describe_distribution
+
+#' @importFrom datawizard demean
+#' @export
+datawizard::demean
+
+#' @importFrom datawizard rescale_weights
+#' @export
+datawizard::rescale_weights
+
 #' @importFrom datawizard visualisation_recipe
 #' @export
 datawizard::visualisation_recipe
+
+#' @importFrom datawizard kurtosis
+#' @export
+datawizard::kurtosis
+
+#' @importFrom datawizard skewness
+#' @export
+datawizard::skewness
diff --git a/R/standard_error_satterthwaite.R b/R/standard_error_satterthwaite.R
@@ -10,19 +10,3 @@ se_satterthwaite.default <- function(model) {
   .is_model_valid(model)
   standard_error(model)
 }
-
-#' @export
-se_satterthwaite.lme <- function(model) {
-  insight::check_if_installed("lavaSearch2")
-  params <- insight::get_parameters(model, effects = "fixed")
-  lavaSearch2::sCorrect(model) <- TRUE
-  s <- lavaSearch2::summary2(model)
-
-  .data_frame(
-    Parameter = params$Parameter,
-    SE = as.vector(s$tTable[, "Std.Error"])
-  )
-}
-
-#' @export
-se_satterthwaite.gls <- se_satterthwaite.lme
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,8 @@
+This update fixes CRAN check issues due to breaking changes in the *lavaSearch2* package, as requested by the CRAN team.
+
+## revdepcheck results
+
 We checked 33 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 1 new problems
+ * We saw 0 new problems
  * We failed to check 0 packages
-
-This update breaks the *performance* package. Test failures are expected, because a bug fix in *parameters* affects test results of the *performance* package. Tests have been corrected and an update of *performance* is ready to be submitted once the *parameters* package is accepted on CRAN.
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -238,6 +238,7 @@ jstatsoft
 kmeans
 labelled
 lavaan
+lavaSearch
 lesslikely
 lm
 lme

diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/tests/testthat/test-lme.R b/tests/testthat/test-lme.R
@@ -1,6 +1,5 @@
 skip_if_not_installed("nlme")
 skip_if_not_installed("lme4")
-skip_if_not_installed("lavaSearch2")
 
 data("sleepstudy", package = "lme4")
 m1_lme <- nlme::lme(Reaction ~ Days, random = ~ 1 + Days | Subject, data = sleepstudy)
@@ -96,19 +95,3 @@ test_that("model_parameters", {
   # expect_equal(params$df, c(80, 80, 25), tolerance = 1e-4)
   expect_equal(params$CI_low, c(16.07503, 0.53834, -3.82999), tolerance = 1e-4)
 })
-
-test_that("model_parameters, satterthwaite", {
-  params <- model_parameters(m2_lme, ci_method = "satterthwaite", effects = "fixed")
-  expect_equal(params$Coefficient, c(17.70671, 0.66019, -2.32102), tolerance = 1e-4)
-  expect_equal(params$SE, c(0.83155, 0.06209, 0.74307), tolerance = 1e-4)
-  # expect_equal(params$df, c(104.1503, 82.87867, 26.25), tolerance = 1e-4)
-  expect_equal(params$CI_low, c(16.0391, 0.53609, -3.88541), tolerance = 1e-3)
-})
-
-test_that("model_parameters, satterthwaite", {
-  params <- model_parameters(m2_lme, ci_method = "satterthwaite", effects = "all")
-  expect_equal(params$Coefficient, c(17.70671, 0.66019, -2.32102, 1.73008, 1.42273), tolerance = 1e-4)
-  expect_equal(params$SE, c(0.83155, 0.06209, 0.74307, NA, NA), tolerance = 1e-4)
-  # expect_equal(params$df, c(104.1503, 82.87867, 26.25), tolerance = 1e-4)
-  expect_equal(params$CI_low, c(16.0391, 0.53609, -3.88541, NA, NA), tolerance = 1e-3)
-})
diff --git a/tests/testthat/test-mipo.R b/tests/testthat/test-mipo.R
@@ -1,5 +1,6 @@
 skip_if_not_installed("mice")
 skip_if_not_installed("nnet")
+skip_if_not(packageVersion("insight") > "0.19.1")
 
 test_that("param ordinal", {
   set.seed(1234)

diff --git a/tests/testthat/test-model_parameters.mixed.R b/tests/testthat/test-model_parameters.mixed.R
@@ -96,7 +96,7 @@ test_that("model_parameters.mixed-all_pars", {
 data("qol_cancer")
 qol_cancer <- cbind(
   qol_cancer,
-  datawizard::demean(qol_cancer, select = c("phq4", "QoL"), group = "ID")
+  demean(qol_cancer, select = c("phq4", "QoL"), group = "ID")
 )
 model <- lme4::lmer(
   QoL ~ time + phq4_within + phq4_between + (1 | ID),