Move afex and PMCMRplus to Imports (#241)

* Move afex and PMCMRplus to Imports IndrajeetPatil/ggstatsplot#837 * Apply automatic changes * minor * rstantools is needed * rstantools in suggests * fix lint --------- Co-authored-by: IndrajeetPatil <[email protected]>
IndrajeetPatil · Apr 16, 2023 · 214b9a5 · 214b9a5
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diff --git a/CITATION.cff b/CITATION.cff
@@ -74,6 +74,28 @@ references:
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 4.1.0'
+- type: software
+  title: afex
+  abstract: 'afex: Analysis of Factorial Experiments'
+  notes: Imports
+  url: https://afex.singmann.science/
+  repository: https://CRAN.R-project.org/package=afex
+  authors:
+  - family-names: Singmann
+    given-names: Henrik
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-4842-3657
+  - family-names: Bolker
+    given-names: Ben
+  - family-names: Westfall
+    given-names: Jake
+  - family-names: Aust
+    given-names: Frederik
+    orcid: https://orcid.org/0000-0003-4900-788X
+  - family-names: Ben-Shachar
+    given-names: Mattan S.
+  year: '2023'
+  version: '>= 1.2-0'
 - type: software
   title: BayesFactor
   abstract: 'BayesFactor: Computation of Bayes Factors for Common Designs'
@@ -340,6 +362,18 @@ references:
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2023'
   version: '>= 0.10.2'
+- type: software
+  title: PMCMRplus
+  abstract: 'PMCMRplus: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
+    Extended'
+  notes: Imports
+  repository: https://CRAN.R-project.org/package=PMCMRplus
+  authors:
+  - family-names: Pohlert
+    given-names: Thorsten
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-3855-3025
+  year: '2023'
 - type: software
   title: purrr
   abstract: 'purrr: Functional Programming Tools'
@@ -463,28 +497,6 @@ references:
     given-names: Nathan
     email: [email protected]
   year: '2023'
-- type: software
-  title: afex
-  abstract: 'afex: Analysis of Factorial Experiments'
-  notes: Suggests
-  url: https://afex.singmann.science/
-  repository: https://CRAN.R-project.org/package=afex
-  authors:
-  - family-names: Singmann
-    given-names: Henrik
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-4842-3657
-  - family-names: Bolker
-    given-names: Ben
-  - family-names: Westfall
-    given-names: Jake
-  - family-names: Aust
-    given-names: Frederik
-    orcid: https://orcid.org/0000-0003-4900-788X
-  - family-names: Ben-Shachar
-    given-names: Mattan S.
-  year: '2023'
-  version: '>= 1.2-0'
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -570,18 +582,6 @@ references:
     email: [email protected]
   - name: R Development Core Team
   year: '2023'
-- type: software
-  title: PMCMRplus
-  abstract: 'PMCMRplus: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
-    Extended'
-  notes: Suggests
-  repository: https://CRAN.R-project.org/package=PMCMRplus
-  authors:
-  - family-names: Pohlert
-    given-names: Thorsten
-    email: [email protected]
-    orcid: https://orcid.org/0000-0003-3855-3025
-  year: '2023'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -625,6 +625,25 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2023'
+- type: software
+  title: rstantools
+  abstract: 'rstantools: Tools for Developing R Packages Interfacing with ''Stan'''
+  notes: Suggests
+  url: https://mc-stan.org/rstantools/
+  repository: https://CRAN.R-project.org/package=rstantools
+  authors:
+  - family-names: Gabry
+    given-names: Jonah
+    email: [email protected]
+  - family-names: Goodrich
+    given-names: Ben
+    email: [email protected]
+  - family-names: Lysy
+    given-names: Martin
+    email: [email protected]
+  - family-names: Johnson
+    given-names: Andrew
+  year: '2023'
 - type: software
   title: survival
   abstract: 'survival: Survival Analysis'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,6 +25,7 @@ BugReports: https://github.com/IndrajeetPatil/statsExpressions/issues
 Depends: 
     R (>= 4.1.0)
 Imports:
+    afex (>= 1.2-0),
     BayesFactor (>= 0.9.12-4.4),
     correlation (>= 0.8.4),
     datawizard (>= 0.7.1),
@@ -35,6 +36,7 @@ Imports:
     magrittr,
     parameters (>= 0.20.3),
     performance (>= 0.10.2),
+    PMCMRplus,
     purrr (>= 1.0.1),
     rlang,
     stats,
@@ -44,14 +46,13 @@ Imports:
     WRS2 (>= 1.1-4),
     zeallot
 Suggests:
-    afex (>= 1.2-0),
     ggplot2,
     knitr,
     metaBMA,
     metafor,
     metaplus,
-    PMCMRplus,
     rmarkdown,
+    rstantools,
     survival,
     testthat (>= 3.1.7),
     utils

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # statsExpressions 1.5.0.9000
 
+## MAJOR CHANGES
+
+- Following dependencies move from being weak to strong dependencies given their
+  importance in key functions: `{afex}` and `{PMCMRplus}`.
+
 # statsExpressions 1.5.0
 
 ## BREAKING CHANGES

diff --git a/R/one_sample_test.R b/R/one_sample_test.R
@@ -43,8 +43,6 @@ one_sample_test <- function(data,
                             effsize.type = "g",
                             ...) {
   type <- stats_type_switch(type)
-
-  # preparing the vector
   x_vec <- stats::na.omit(data %>% pull({{ x }}))
 
   # parametric ---------------------------------------

diff --git a/R/oneway_anova.R b/R/oneway_anova.R
@@ -41,11 +41,10 @@
 #' @param ... Additional arguments (currently ignored).
 #' @inheritParams stats::oneway.test
 #'
-#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") && requireNamespace("afex", quietly = TRUE)
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # for reproducibility
 #' set.seed(123)
 #' library(statsExpressions)
-#' suppressPackageStartupMessages(library(afex)) # for within-subjects parametric ANOVA
 #'
 #' # ----------------------- parametric -------------------------------------
 #'
@@ -105,6 +104,8 @@
 #'   type       = "r"
 #' )
 #'
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") && requireNamespace("rstantools", quietly = TRUE)
+#'
 #' # ----------------------- Bayesian -------------------------------------
 #'
 #' # between-subjects
@@ -140,7 +141,6 @@ oneway_anova <- function(data,
                          nboot = 100L,
                          ...) {
   type <- stats_type_switch(type)
-
   c(x, y) %<-% c(ensym(x), ensym(y))
 
   data %<>% long_to_wide_converter(
@@ -163,8 +163,6 @@ oneway_anova <- function(data,
     # styler: on
 
     if (paired) {
-      check_if_installed("afex", minimum_version = "1.0-0")
-
       mod <- afex::aov_ez(
         id          = ".rowid",
         dv          = as_string(y),

diff --git a/R/pairwise_comparisons.R b/R/pairwise_comparisons.R
@@ -32,11 +32,10 @@
 #' @references For more, see:
 #' <https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/pairwise.html>
 #'
-#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") && requireNamespace("PMCMRplus", quietly = TRUE)
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # for reproducibility
 #' set.seed(123)
 #' library(statsExpressions)
-#' library(PMCMRplus)
 #'
 #' #------------------- between-subjects design ----------------------------
 #'
@@ -149,7 +148,6 @@ pairwise_comparisons <- function(data,
                                  p.adjust.method = "holm",
                                  k = 2L,
                                  ...) {
-  if (type != "robust") check_if_installed("PMCMRplus", reason = "for pairwise comparisons")
   type <- stats_type_switch(type)
   c(x, y) %<-% c(ensym(x), ensym(y))
 

diff --git a/R/two_sample_test.R b/R/two_sample_test.R
@@ -125,7 +125,6 @@ two_sample_test <- function(data,
                             nboot = 100L,
                             ...) {
   type <- stats_type_switch(type)
-
   c(x, y) %<-% c(ensym(x), ensym(y))
 
   data %<>% long_to_wide_converter(