Prepare CRAN release (#977)

* Prepare CRAN release * fix, lintr * Trigger CI * Fix #978 * news * typo, lintr * lintr * eval conditional on gt * Update model_parameters_print.Rmd * fix * Update DESCRIPTION * Update NEWS.md * Update DESCRIPTION * Update NEWS.md * lintr * lintr * doc cleanup * lintr * update orcid * newline * update news * docs * typo * support glmgee * newline * cran comm * news * wordlist * submitted * fix notes * lintr * re-submitted --------- Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
easystats · Jun 20, 2024 · d4a3b3c · d4a3b3c
1 parent 266c947
commit d4a3b3c
Show file tree

Hide file tree

Showing 38 changed files with 381 additions and 239 deletions.
diff --git a/.lintr b/.lintr
@@ -1,14 +1,15 @@
 linters: linters_with_defaults(
     absolute_path_linter = NULL,
     commented_code_linter = NULL,
-    cyclocomp_linter = cyclocomp_linter(25),
+    cyclocomp_linter = cyclocomp_linter(125),
     extraction_operator_linter = NULL,
     implicit_integer_linter = NULL,
     line_length_linter(120),
     namespace_linter = NULL,
     nonportable_path_linter = NULL,
     object_name_linter = NULL,
     object_length_linter(50),
+    library_call_linter = NULL,
     object_usage_linter = NULL,
     todo_comment_linter = NULL,
     undesirable_function_linter(c("mapply" = NA, "sapply" = NA, "setwd" = NA)),

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.21.7
-Date: 2024-05-13 17:50:43 UTC
-SHA: 5c707ee00026cae0f4439eb8514e2537275344cc
+Version: 0.22.0
+Date: 2024-06-19 20:40:00 UTC
+SHA: 3861512ee3c11ecca44c2edd412c2a5cb65e1f59
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.21.7.4
+Version: 0.22.0
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -40,7 +40,7 @@ Authors@R:
              family = "Arel-Bundock",
              role = "ctb",
              email = "vincent.arel-bundock@umontreal.ca",
-             comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@vincentab")),
+             comment = c(ORCID = "0000-0003-2042-7063", Twitter = "@vincentab")),
       person(given = "Jeffrey",
              family = "Girard",
              role = "ctb",
@@ -177,7 +177,7 @@ Suggests:
     panelr,
     pbkrtest,
     PCDimension,
-    performance (>= 0.10.8),
+    performance (>= 0.12.0),
     plm,
     PMCMRplus,
     poorman,
@@ -213,8 +213,5 @@ RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
 Config/testthat/parallel: true
-Config/Needs/website:
-    rstudio/bslib,
-    r-lib/pkgdown,
-    easystats/easystatstemplate
+Config/Needs/website: easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
diff --git a/NAMESPACE b/NAMESPACE
@@ -42,6 +42,7 @@ S3method(ci,gamm4)
 S3method(ci,geeglm)
 S3method(ci,glht)
 S3method(ci,glm)
+S3method(ci,glmgee)
 S3method(ci,glmm)
 S3method(ci,glmmTMB)
 S3method(ci,hglm)
@@ -462,6 +463,7 @@ S3method(p_value,gee)
 S3method(p_value,geeglm)
 S3method(p_value,glht)
 S3method(p_value,glimML)
+S3method(p_value,glmgee)
 S3method(p_value,glmm)
 S3method(p_value,glmx)
 S3method(p_value,gls)
@@ -792,6 +794,7 @@ S3method(standard_error,gee)
 S3method(standard_error,geeglm)
 S3method(standard_error,glht)
 S3method(standard_error,glimML)
+S3method(standard_error,glmgee)
 S3method(standard_error,glmm)
 S3method(standard_error,glmmTMB)
 S3method(standard_error,glmx)

diff --git a/NEWS.md b/NEWS.md
@@ -1,18 +1,25 @@
-# parameters 0.21.8
+# parameters 0.22.0
 
 ## Breaking changes
 
 * Deprecated arguments in `model_parameters()` for `htest`, `aov` and
   `BFBayesFactor` objects were removed.
 
+* Argument `effectsize_type` is deprecated. Please use `es_type` now. This change
+  was necessary to avoid conflicts with partial matching of argument names (here:
+  `effects`).
+
 ## New supported models
 
 * Support for objects from `stats::Box.test()`.
 
-## Bug fixes
+* Support for `glmgee` models from package *glmtoolbox*.
+
+## Bug fix
+
+* Fixed edge case in `predict()` for `factor_analysis()`.
 
-* Fixed issues with partial matching of argument `effects` and `effectsize_type`
-  in `model_parameters()` for objects of class `htest`.
+* Fixed wrong ORCID in `DESCRIPTION`.
 
 # parameters 0.21.7
 

diff --git a/R/1_model_parameters.R b/R/1_model_parameters.R
@@ -87,7 +87,7 @@
 #' include interactions or transformations (e.g., polynomial or spline terms).
 #' The `robust` (default to `FALSE`) argument enables a robust standardization
 #' of data, i.e., based on the `median` and `MAD` instead of the `mean` and
-#' `SD`. **See [standardize()] for more details.**
+#' `SD`. **See [`datawizard::standardize()`] for more details.**
 #' **Note** that `standardize_parameters(method = "refit")` may not return
 #' the same results as fitting a model on data that has been standardized with
 #' `standardize()`; `standardize_parameters()` used the data used by the model

diff --git a/R/bootstrap_model.R b/R/bootstrap_model.R
@@ -178,7 +178,7 @@ bootstrap_model.merMod <- function(model,
     } else {
       params <- stats::setNames(params$Estimate, params$Parameter) # Transform to named vector
     }
-    return(params)
+    params
   }
 
   if (verbose) {
@@ -244,9 +244,7 @@ bootstrap_model.nestedLogit <- function(model,
     }
 
     params <- insight::get_parameters(fit, verbose = FALSE)
-    params <- stats::setNames(params$Estimate, params$Parameter) # Transform to named vector
-
-    return(params)
+    stats::setNames(params$Estimate, params$Parameter) # Transform to named vector
   }
 
   results <- boot::boot(

diff --git a/R/extract_parameters.R b/R/extract_parameters.R
@@ -355,7 +355,7 @@
                                       verbose = TRUE) {
   # check pattern
   if (!is.null(keep) && length(keep) > 1) {
-    keep <- paste0("(", paste0(keep, collapse = "|"), ")")
+    keep <- paste0("(", paste(keep, collapse = "|"), ")")
     if (verbose) {
       insight::format_alert(
         sprintf("The `keep` argument has more than 1 element. Merging into following regular expression: `%s`.", keep)
@@ -365,7 +365,7 @@
 
   # check pattern
   if (!is.null(drop) && length(drop) > 1) {
-    drop <- paste0("(", paste0(drop, collapse = "|"), ")")
+    drop <- paste0("(", paste(drop, collapse = "|"), ")")
     if (verbose) {
       insight::format_alert(
         sprintf("The `drop` argument has more than 1 element. Merging into following regular expression: `%s`.", drop)
@@ -486,7 +486,9 @@
     } else {
       ci_df <- ci(model, ci = ci, method = ci_method, effects = "fixed")
     }
-    if (length(ci) > 1) ci_df <- datawizard::reshape_ci(ci_df)
+    if (length(ci) > 1) {
+      ci_df <- datawizard::reshape_ci(ci_df)
+    }
     ci_cols <- names(ci_df)[!names(ci_df) %in% c("CI", "Parameter")]
     parameters <- merge(parameters, ci_df, by = "Parameter", sort = FALSE)
   }

diff --git a/R/methods_BayesFactor.R b/R/methods_BayesFactor.R
@@ -33,7 +33,7 @@
 #' # Bayesian t-test
 #' model <- BayesFactor::ttestBF(x = rnorm(100, 1, 1))
 #' model_parameters(model)
-#' model_parameters(model, effectsize_type = "cohens_d", ci = 0.9)
+#' model_parameters(model, es_type = "cohens_d", ci = 0.9)
 #'
 #' # Bayesian contingency table analysis
 #' data(raceDolls)
@@ -46,7 +46,7 @@
 #'   centrality = "mean",
 #'   dispersion = TRUE,
 #'   verbose = FALSE,
-#'   effectsize_type = "cramers_v"
+#'   es_type = "cramers_v"
 #' )
 #' }
 #' @return A data frame of indices related to the model's parameters.
@@ -60,9 +60,10 @@ model_parameters.BFBayesFactor <- function(model,
                                            rope_range = "default",
                                            rope_ci = 0.95,
                                            priors = TRUE,
-                                           effectsize_type = NULL,
+                                           es_type = NULL,
                                            include_proportions = FALSE,
                                            verbose = TRUE,
+                                           effectsize_type = NULL,
                                            ...) {
   insight::check_if_installed("BayesFactor")
 
@@ -83,6 +84,12 @@ model_parameters.BFBayesFactor <- function(model,
     return(NULL)
   }
 
+  ## TODO: remove deprecation warning later
+  if (!is.null(effectsize_type)) {
+    insight::format_warning("Argument `effectsize_type` is deprecated. Use `es_type` instead.")
+    es_type <- effectsize_type
+  }
+
   out <- bayestestR::describe_posterior(
     model,
     centrality = centrality,
@@ -115,10 +122,10 @@ model_parameters.BFBayesFactor <- function(model,
   tryCatch(
     {
       bfm <- as.data.frame(bayestestR::bayesfactor_models(model)[-1, ])
-      if (!is.null(bfm$log_BF)) {
-        out$BF <- exp(bfm$log_BF)
-      } else {
+      if (is.null(bfm$log_BF)) {
         out$BF <- bfm$BF
+      } else {
+        out$BF <- exp(bfm$log_BF)
       }
     },
     error = function(e) {
@@ -132,7 +139,7 @@ model_parameters.BFBayesFactor <- function(model,
   }
 
   # Effect size?
-  if (!is.null(effectsize_type)) {
+  if (!is.null(es_type)) {
     # needs {effectsize} to be installed
     insight::check_if_installed("effectsize")
 
@@ -144,7 +151,7 @@ model_parameters.BFBayesFactor <- function(model,
           dispersion = dispersion,
           ci_method = ci_method,
           rope_ci = rope_ci,
-          type = effectsize_type,
+          type = es_type,
           ...
         )