update after long pause

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
 # NOTE: This workflow is overkill for most R packages and
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,31 +24,40 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -16,15 +16,17 @@ License: GPL (>= 3)
 Encoding: UTF-8
 ByteCompile: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Depends: 
   R (>= 3.5.0)
 Imports:
     data.table (>= 1.14.0),
     glue (>= 1.4.2),
-    nortest (>= 1.0-4),
     effectsize (>= 0.4.5),
     afex (>= 0.28-1),
     PMCMRplus (>= 1.9.0),
     WRS2 (>= 1.1-1),
     lifecycle
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -3,7 +3,6 @@
 S3method(as.data.frame,writR)
 S3method(print,writR)
 export(aov_r)
-export(autest)
 export(cent_disp)
 export(clean_data)
 export(contingency)
@@ -14,24 +13,18 @@ export(lablr)
 export(one_sample)
 export(pairs_two_sample)
 export(pairwise_test)
+export(rm_anova)
+export(sphericity)
 export(sphericity_check)
 export(style.p)
 export(two_sample)
 importFrom(PMCMRplus,durbinAllPairsTest)
 importFrom(PMCMRplus,gamesHowellTest)
 importFrom(PMCMRplus,kwAllPairsDunnTest)
-importFrom(WRS2,dep.effect)
 importFrom(WRS2,lincon)
-importFrom(WRS2,rmanova)
 importFrom(WRS2,rmmcp)
-importFrom(WRS2,t1way)
-importFrom(WRS2,trimse)
-importFrom(WRS2,wmcpAKP)
-importFrom(WRS2,yuen)
-importFrom(WRS2,yuen.effect.ci)
-importFrom(WRS2,yuend)
-importFrom(afex,aov_ez)
 importFrom(data.table,"%chin%")
+importFrom(data.table,"%like%")
 importFrom(data.table,":=")
 importFrom(data.table,.N)
 importFrom(data.table,.SD)
@@ -42,40 +35,8 @@ importFrom(data.table,fcase)
 importFrom(data.table,fifelse)
 importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
-importFrom(data.table,rowidv)
-importFrom(data.table,setnames)
-importFrom(effectsize,cohens_d)
-importFrom(effectsize,cohens_g)
-importFrom(effectsize,cramers_v)
-importFrom(effectsize,eta_squared)
-importFrom(effectsize,hedges_g)
-importFrom(effectsize,kendalls_w)
-importFrom(effectsize,oddsratio)
-importFrom(effectsize,omega_squared)
-importFrom(effectsize,pearsons_c)
-importFrom(effectsize,rank_biserial)
-importFrom(effectsize,rank_epsilon_squared)
-importFrom(glue,glue)
 importFrom(lifecycle,deprecated)
-importFrom(nortest,lillie.test)
-importFrom(stats,IQR)
-importFrom(stats,anova)
-importFrom(stats,as.formula)
-importFrom(stats,chisq.test)
-importFrom(stats,complete.cases)
-importFrom(stats,fisher.test)
-importFrom(stats,friedman.test)
-importFrom(stats,kruskal.test)
-importFrom(stats,lm)
-importFrom(stats,mcnemar.test)
-importFrom(stats,median)
 importFrom(stats,na.omit)
-importFrom(stats,oneway.test)
 importFrom(stats,p.adjust)
 importFrom(stats,pairwise.t.test)
-importFrom(stats,pchisq)
-importFrom(stats,sd)
-importFrom(stats,shapiro.test)
-importFrom(stats,t.test)
-importFrom(stats,wilcox.test)
 importFrom(utils,combn)

R/aov_r.R

@@ -11,48 +11,47 @@
 #' @param effsize.type The effect size used to estimate the effects of the factors on the response variable. Possible values are "eta" ("biased") or "omega" ("unbiased", the default).
 #' @param sphericity If "none", then sphericity assumption is assumed to be met for within-subject(s) factor(s). "GG": applies Greenhouse-Geisser correction. "HF": applies Hyunh-Feldt correction. 'auto' (Default) choose the appropiate correction based on Mauchly test of sphericity (p-value > 0.05)
 #' @param conf.level Confidence/Credible Interval (CI) level. Default to 0.95 (95%).
-#' @param lbl Logical (default FALSE) indicating if a report ready output is desired. This will change the output to a list with characters rather than numeric vectors.
 #' @param markdown Logical (default FALSE). If `lbl` is TRUE, then this argument specify if the report-ready labels should be formated for inline code for R markdown (using mathjax and markdown syntax), or if the output should be in plain text (the default).
-#' @importFrom data.table %chin% as.data.table .SD fcase .N
-#' @importFrom utils combn
-#' @importFrom stats anova
-#' @importFrom effectsize eta_squared omega_squared
+#' @param character.only Logical. checks whether to use the unevaluated expression or its
+#' content (when TRUE), asumming is a character vector. Defaults to `FALSE`.
 #' @return A list with statistical results.
+#'
 #' @export
 
 aov_r <- function(data,
-                  response = NULL,
+                  response,
                   between = NULL,
                   within = NULL,
                   rowid = NULL,
                   ss_type = 3,
                   effsize.type = "unbiased",
                   sphericity = "auto",
                   conf.level = 0.95,
-                  lbl = if (is.null(markdown)) FALSE else TRUE,
-                  markdown = NULL) {
+                  character.only = FALSE,
+                  markdown) {
 
   `Pr(>F)` <- rn <- `num Df` <- `den Df` <- NULL
 
-  # Auxiliary functions
-  is_empty <- function(i) length(i) == 0;
-  is_not_empty <- function(i) length(i) > 0;
-  is_not_null <- function(i) !is.null(i);
-
-  # Argument checking
-  if (is.null(between) && is.null(within)) stop("between and within can't both be NULL", call. = FALSE)
-  if (is.null(response)) stop("response can't be NULL", call. = FALSE)
-  if (is_not_empty(within) && is.null(rowid)) stop("If within is provided, rowid can't be NULL", call. = FALSE)
+  # Argument checking - Response
+  if (missing(response)) stop("response can't be NULL", call. = FALSE)
 
   # Transform data to data.table
-  if (!"data.table" %chin% class(data)) {
-    data <- data.table::as.data.table(data)
-  }
+  if (!"data.table" %chin% class(data)) data <- data.table::as.data.table(data)
+
+  # Transform arguments to character
+  response <- deparser(response, character.only)
+  between  <- deparser(between, character.only)
+  within   <- deparser(within, character.only)
+  rowid    <- deparser(rowid, character.only)
+
+  # Argument checking - arguments
+  if (is.null(between) && is.null(within)) stop("between and within can't both be NULL", call. = FALSE)
+  if (!is.null(within) && is.null(rowid)) stop("if within is provided, rowid can't be NULL", call. = FALSE)
 
   # Get only variables of interest
-  data <- droplevels(data[j = .SD, .SDcols = c(rowid, response, between, within)])
+  data <- droplevels(data[, .SD, .SDcols = c(rowid, response, between, within)])
 
-  if (is_empty(within) && is.null(rowid) && is_not_empty(between)) {
+  if (length(within) == 0 && is.null(rowid) && length(between) > 0) {
     rowid <- "rowid"
     data[, rowid := seq_len(.N)]
   }
@@ -75,7 +74,7 @@ aov_r <- function(data,
   n_obs <- nrow(model$data$wide)
 
   # Get sphericity correction
-  if (is_empty(within)) {
+  if (length(within) == 0) {
     sphericity <- NULL
   } else {
     sphericity <- sphericity_check(model)
@@ -100,11 +99,11 @@ aov_r <- function(data,
 
   # Set sphericity correction (if available)
   within_method <- NA_character_
-  if (is_not_null(within)) {
+  if (!is.null(within)) {
     within_method <- data.table::fcase(
-      sphericity == "none", "Fisher's repeated measures ANOVA",
-      sphericity == "GG", "Repeated measures ANOVA with GG correction",
-      sphericity == "HF", "Repeated measures ANOVA with HG correction"
+      sphericity == "none", "Fisher's rmANOVA",
+      sphericity == "GG", "Greenhouse-Geisser's rmANOVA",
+      sphericity == "HF", "Huynh-Feldt's rmANOVA"
     )
   }
 
@@ -116,8 +115,8 @@ aov_r <- function(data,
     df.error = `den Df`,
     p.value = `Pr(>F)`,
     method = data.table::fcase(rn %chin% between, "Fisher's ANOVA",
-                   rn %chin% within, within_method,
-                   utils::combn(within, 1, grepl, T, rn), within_method),
+                               rn %chin% within, within_method,
+                               utils::combn(within, 1, grepl, T, rn), within_method),
     estimate = efs[[2L]],
     conf.level = efs$CI,
     conf.low = efs$CI_low,
@@ -126,7 +125,7 @@ aov_r <- function(data,
     n_obs = n_obs
   )]
 
-  if (lbl) {
+  if (!missing(markdown) && isTRUE(markdown)) {
     model <- model[j = lablr(.SD, markdown = markdown), by = "x"]
   }