Merge branch 'main' into devel

.Rbuildignore

@@ -8,7 +8,7 @@
 ^cran-comments\.md$
 ^\.travis\.yml
 ^.github$
-^example$
+^inst/example$
 ^_config.yml$
 ^inst/papaja_manuscripts.bib
 ^inst/apa_source_files.csl
@@ -20,3 +20,4 @@
 ^vignettes/papaja.Rmd$
 ^vignettes/papaja.tex$
 ^CRAN-SUBMISSION$
+^revdep$

.github/ISSUE_TEMPLATE/bug-report.md

@@ -13,7 +13,7 @@ If you think you have found a bug, please ensure your bug report includes all of
 A clear and concise description of what the bug is.
 
 **To Reproduce**
-A [minimal complete verifiable example](https://stackoverflow.com/help/mcve) and the error message if applicable.
+A [minimal complete verifiable example](https://stackoverflow.com/help/minimal-reproducible-example) and the error message if applicable.
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.

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

@@ -8,12 +8,10 @@ on:
   push:
     branches:
       - main
-      - master
       - devel
   pull_request:
     branches:
       - main
-      - master
       - devel
 
 name: R-CMD-check

.github/workflows/no-response.yml

@@ -0,0 +1,17 @@
+name: No Response
+
+on:
+  issue_comment:
+    types: [created]
+  schedule:
+    # Schedule 18:00 once every day
+    - cron: '0 18 * * *'
+
+jobs:
+  noResponse:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: lee-dohm/no-response@v0.5.0
+        with:
+          token: ${{ github.token }}
+          daysUntilClose: 28

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: papaja
 Title: Prepare American Psychological Association Journal Articles with
   R Markdown
-Version: 0.1.1.9001
+Version: 0.1.2.9000
 Description: Tools to create dynamic, submission-ready manuscripts, which
   conform to American Psychological Association manuscript guidelines. We
   provide R Markdown document formats for manuscripts (PDF and Word) and
@@ -15,7 +15,7 @@ Authors@R: c(
     , person("Joseph V.", "Casillas", email = "joseph.casillas@rutgers.edu", role = c("ctb"))
     , person("Rudolf", "Siegel", email = "rudolf.siegel@uni-saarland.de", role = c("ctb"))
   )
-Date: 2022-07-04
+Date: 2023-09-28
 URL: https://github.com/crsh/papaja
 BugReports: https://github.com/crsh/papaja/issues
 Depends:
@@ -38,7 +38,7 @@ Suggests:
   beeswarm,
   boot,
   car,
-  dplyr,
+  dplyr (>= 1.1.0),
   effectsize (>= 0.4.4),
   emmeans,
   ggforce,
@@ -58,7 +58,7 @@ SystemRequirements: Rendering the document template requires
   such as TinyTeX (>= 0.12; https://yihui.org/tinytex/)
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr, R.rsp
 Language: en-US
 Roxygen: list(markdown = TRUE)

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2020
+YEAR: 2023
 COPYRIGHT HOLDER: Frederik Aust

NAMESPACE

@@ -56,6 +56,7 @@ S3method(apa_print,summary_emm)
 S3method(apa_table,apa_results)
 S3method(apa_table,apa_results_table)
 S3method(apa_table,data.frame)
+S3method(apa_table,default)
 S3method(apa_table,list)
 S3method(apa_table,matrix)
 S3method(beautify_terms,character)

R/add_custom_effect_sizes.R

@@ -33,23 +33,39 @@ add_custom_effect_sizes.data.frame <- function(estimate, canonical_table, interc
 }
 
 
-add_custom_effect_sizes.function <- function(estimate, .x = NULL, observed = NULL, ...) {
+add_custom_effect_sizes.function <- function(estimate, canonical_table, intercept = FALSE, .x = NULL, observed = NULL, ...) {
 
   if(is.null(.x)) stop("Cannot apply custom effect-size function to this class of object.", call. = FALSE)
 
   estimate_formals <- names(formals(estimate))
-  # print(estimate_formals)
-  if(any(estimate_formals == "observed")) {
-    add_custom_effect_sizes(estimate = estimate(.x, observed = observed), .x = .x, ...)
-  } else if(any(estimate_formals == "generalized")) {
-    add_custom_effect_sizes(estimate = estimate(.x, generalized = observed), .x = .x, ...)
-  } else if (!is.null(observed)) {
-    warning(
-      "Some terms have been specified as being observed, but the provided effect-size function does not seem to support observed terms."
-      , call. = FALSE
-    )
-    add_custom_effect_sizes(estimate = estimate(.x), .x = .x, ...)
-  } else {
-    add_custom_effect_sizes(estimate = estimate(.x), .x = .x, ...)
+
+  estimate_args <- list(
+    .x
+  )
+
+  if(length(observed)) {
+    if(any(estimate_formals == "observed"))    estimate_args$observed    <- observed
+    if(any(estimate_formals == "generalized")) estimate_args$generalized <- observed
+
+    # warnings
+    if(!any(estimate_formals == "observed") & !any(estimate_formals == "generalized")) {
+      warning(
+        "Some terms have been specified as being observed, but the provided effect-size function does not seem to support observed terms."
+        , call. = FALSE
+      )
+    }
   }
+
+  if(isTRUE(intercept) & any(estimate_formals == "include_intercept")) {
+    estimate_args$include_intercept <- TRUE
+    message("Turning on intercept")
+  }
+
+
+  add_custom_effect_sizes(
+    estimate = do.call(what = estimate, args = estimate_args)
+    , canonical_table = canonical_table
+    , .x = .x
+    , ...
+  )
 }

R/apa6_formats.R

@@ -17,15 +17,15 @@
 #'   \href{ftp://ftp.fu-berlin.de/tex/CTAN/macros/latex/contrib/apa6/apa6.pdf}{documentation}
 #'   to find out about class options such as paper size or draft watermarks.
 #'
-#'   Please refer to the \href{http://frederikaust.com/papaja_man/r-markdown-components.html#yaml-front-matter}{\pkg{papaja} online-manual}
+#'   Please refer to the \href{https://frederikaust.com/papaja_man/r-markdown-components.html#yaml-front-matter}{\pkg{papaja} online-manual}
 #'   for additional information on available YAML front matter settings.
 #'   Note that the available settings for DOCX documents are more limited
 #'   than for PDF documents.
 #'
 #'   When creating PDF documents the output device for figures defaults to
 #'   \code{c("pdf", "png")}, so that each figure is saved in all four formats
 #'   at a resolution of 300 dpi.
-#' @return R Markdown output format to pass to [rmarkdown::render()]
+#' @return R Markdown output format to pass to [rmarkdown::render()].
 #' @seealso [bookdown::pdf_document2()], [bookdown::word_document2()]
 #' @export
 
@@ -437,6 +437,7 @@ pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, files_di
       metadata$lang
       , english = "en-EN"
       , american = "en-US"
+      , german = "de-DE"
       , metadata$lang
     )
   }

R/apa_num.R

@@ -430,12 +430,13 @@ print_p <- apa_p
 #'   should be determined for each element of `x` separately (the default),
 #'   or for the complete vector `x`.
 #' @inherit apa_num return
+#' @inheritParams base::formatC
 #' @seealso [apa_num()], [apa_p()]
 #' @examples
 #' apa_df(c(1, 1.23151))
 #' @export
 
-apa_df <- function(x, digits = 2L, elementwise = TRUE) {
+apa_df <- function(x, digits = 2L, big.mark = "", elementwise = TRUE) {
 
   if(is.null(x))    return(NULL)
   if(is.integer(x)) return(apa_num(x))
@@ -455,7 +456,7 @@ apa_df <- function(x, digits = 2L, elementwise = TRUE) {
     digits <- 0L
   }
 
-  apa_num(x, digits = digits)
+  apa_num(x, digits = digits, big.mark = big.mark)
 }
 
 #' @rdname apa_df

R/apa_print_anova.R

@@ -15,9 +15,11 @@
 #' @param estimate Character, function, or data frame. Determines which
 #'   estimate of effect size is to be used. See details.
 #' @param mse Logical. Indicates if mean squared errors should be included in
-#'   output. The default is `TRUE`, but this can be changed either by supplying
-#'   a different value in the function call or by changing the global default
-#'   via `options(papaja.mse = FALSE)`.
+#'   output. The default is taken from the global option `getOption("papaja.mse")`.
+#'   It is `FALSE` if the \pkg{effectsize} package is installed and `TRUE` if it
+#'   is not installed. This can be changed either by supplying a different value
+#'   in the function call or by changing the global default via
+#'   `options(papaja.mse = ...)`.
 #' @param observed Character. The names of the factors that are observed,
 #'   i.e., not manipulated. Necessary only for calculating *generalized* eta
 #'   squared; otherwise ignored. If `x` is of class `afex_aov`, `observed` is
@@ -30,9 +32,9 @@
 #'
 #'   Argument `estimate` determines which measure of effect size is to be used:
 #'   It is currently possible to provide one of three characters to specify the
-#'   to-be-calculated effect size: \code{"ges"} for generalized \eqn{eta^2},
-#'   \code{"pes"} for partial \eqn{eta^2}, and \code{"es"} for \eqn{eta^2}.
-#'   Note that \eqn{eta^2} is calculated correctly if and only if the design is
+#'   to-be-calculated effect size: `"ges"` for generalized \eqn{\eta^2},
+#'   \code{"pes"} for partial \eqn{\eta^2}, and `"es"` for \eqn{\eta^2}.
+#'   Note that \eqn{\eta^2} is calculated correctly if and only if the design is
 #'   balanced.
 #'
 #'   It is also possible to provide a `data.frame` with columns `estimate`,
@@ -69,7 +71,7 @@ apa_print.aov <- function(
   , estimate = getOption("papaja.estimate_anova", "ges")
   , observed = NULL
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -95,7 +97,7 @@ apa_print.summary.aov <- function(
   , estimate = getOption("papaja.estimate_anova", "ges")
   , observed = NULL
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -120,7 +122,7 @@ apa_print.aovlist <- function(
   , estimate = getOption("papaja.estimate_anova", "ges")
   , observed = NULL
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -146,7 +148,7 @@ apa_print.summary.aovlist <- function(
   , estimate = getOption("papaja.estimate_anova", "ges")
   , observed = NULL
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -172,10 +174,10 @@ apa_print.summary.aovlist <- function(
     canonical_table = canonical_table
     , .x = .x
     , estimate = estimate
-    , mse = mse
     , observed = observed
     , intercept = intercept
   )
+  if(isTRUE(mse)) canonical_table <- add_mse(canonical_table)
 
   if(!intercept) canonical_table <- canonical_table[canonical_table$term != "(Intercept)", , drop = FALSE]
 
@@ -211,7 +213,7 @@ apa_print.Anova.mlm <- function(
   , observed = NULL
   , correction = getOption("papaja.sphericity_correction")
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -245,7 +247,7 @@ apa_print.summary.Anova.mlm <- function(
   , observed = NULL
   , correction = getOption("papaja.sphericity_correction")
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -263,11 +265,12 @@ apa_print.summary.Anova.mlm <- function(
   canonical_table <- add_custom_effect_sizes(
     canonical_table
     , estimate = estimate
-    , mse = mse
     , observed = observed
     , intercept = intercept
     , .x = .x
   )
+  if(isTRUE(mse)) canonical_table <- add_mse(canonical_table)
+
 
   # Remove intercept if the user doesn't want it:
   if(!intercept) canonical_table <- canonical_table[canonical_table$term != "(Intercept)", , drop = FALSE]
@@ -305,7 +308,7 @@ apa_print.afex_aov <- function(
   , observed = NULL
   , correction = getOption("papaja.sphericity_correction")
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   , ...
 ) {
@@ -374,7 +377,7 @@ apa_print.anova <- function(
   , estimate = getOption("papaja.estimate_anova", "ges")
   , observed = NULL
   , intercept = FALSE
-  , mse = TRUE
+  , mse = getOption("papaja.mse", TRUE)
   , in_paren = FALSE
   # , conf.int = 0.95
   , ...
@@ -489,11 +492,11 @@ apa_print.anova <- function(
   canonical_table <- add_custom_effect_sizes(
     estimate = estimate
     , canonical_table = canonical_table
-    , mse = mse
     , observed = observed
     , intercept = intercept
     , .x = .x
   )
+  if(isTRUE(mse)) canonical_table <- add_mse(canonical_table)
 
   if(!intercept) canonical_table <- canonical_table[canonical_table$term != "(Intercept)", , drop = FALSE]
 

R/apa_print_emm_lsm.R

@@ -151,7 +151,7 @@ apa_print.summary_emm <- function(
     if(is.null(adjust)) {
       conf_level <- paste0(conf_level, "\\% CI")
     } else {
-      conf_level <- paste0("$", conf_level, "\\%\\ \\mathrm{CI}_\\mathrm{\\scriptsize ", adjust["conf.int"], "}$")
+      conf_level <- paste0("$", conf_level, "\\%\\ \\mathrm{CI}_\\mathrm{\\scriptstyle ", adjust["conf.int"], "}$")
     }
   }
 
@@ -245,7 +245,7 @@ apa_print.summary_emm <- function(
     variable_labels(tidy_x[[p_value]]) <- switch(
       p_value
       , "p.value" = "$p$"
-      , "adj.p.value" = paste0("$p_\\mathrm{\\scriptsize ", adjust["p.value"], "}$")
+      , "adj.p.value" = paste0("$p_\\mathrm{\\scriptstyle ", adjust["p.value"], "}$")
     )
   }