Merge branch 'main' into fail-on-lints

.github/workflows/pre-commit.yaml

@@ -20,13 +20,11 @@ jobs:
           access_token: ${{ github.token }}
 
       - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.1.0
         with:
-          python-version: "3.9"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Run pre-commit

CITATION.cff

@@ -2,7 +2,7 @@
 # CITATION file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
 # --------------------------------------------
- 
+
 cff-version: 1.2.0
 message: 'To cite package "ggstatsplot" in publications use:'
 type: software
@@ -278,7 +278,7 @@ references:
   abstract: 'insight: Easy Access to Model Information for Various Model Objects'
   notes: Imports
   url: https://easystats.github.io/insight/
-  repository: https://easystats.r-universe.dev
+  repository: https://CRAN.R-project.org/package=insight
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -313,7 +313,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9271-5075
   year: '2024'
-  version: '>= 0.19.10'
+  version: '>= 0.19.11'
 - type: software
   title: paletteer
   abstract: 'paletteer: Comprehensive Collection of Color Palettes'
@@ -330,7 +330,7 @@ references:
   abstract: 'parameters: Processing of Model Parameters'
   notes: Imports
   url: https://easystats.github.io/parameters/
-  repository: https://easystats.r-universe.dev
+  repository: https://CRAN.R-project.org/package=parameters
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -356,7 +356,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2024'
-  version: '>= 0.21.6'
+  version: '>= 0.21.7'
 - type: software
   title: patchwork
   abstract: 'patchwork: The Composer of Plots'
@@ -581,6 +581,18 @@ references:
     given-names: Brian
     email: [email protected]
   year: '2024'
+- type: software
+  title: metaBMA
+  abstract: 'metaBMA: Bayesian Model Averaging for Random and Fixed Effects Meta-Analysis'
+  notes: Suggests
+  url: https://danheck.github.io/metaBMA/
+  repository: https://CRAN.R-project.org/package=metaBMA
+  authors:
+  - family-names: Heck
+    given-names: Daniel W.
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-6302-9252
+  year: '2024'
 - type: software
   title: metafor
   abstract: 'metafor: Meta-Analysis Package for R'
@@ -600,6 +612,20 @@ references:
     value: https://wviechtb.github.io/metafor/
   - type: url
     value: https://www.wvbauer.com
+- type: software
+  title: metaplus
+  abstract: 'metaplus: Robust Meta-Analysis and Meta-Regression'
+  notes: Suggests
+  repository: https://CRAN.R-project.org/package=metaplus
+  authors:
+  - family-names: Beath
+    given-names: Ken
+    email: [email protected]
+  - family-names: Bolker
+    given-names: Ben
+    email: [email protected]
+  - name: R Development Core Team
+  year: '2024'
 - type: software
   title: psych
   abstract: 'psych: Procedures for Psychological, Psychometric, and Personality Research'

DESCRIPTION

@@ -40,9 +40,9 @@ Imports:
     ggside (>= 0.3.1),
     ggsignif (>= 0.6.4),
     glue (>= 1.7.0),
-    insight (>= 0.19.10),
+    insight (>= 0.19.11),
     paletteer (>= 1.6.0),
-    parameters (>= 0.21.6),
+    parameters (>= 0.21.7),
     patchwork (>= 1.2.0),
     performance (>= 0.11.0),
     purrr (>= 1.0.2),

NEWS.md

@@ -5,6 +5,10 @@ N.B. All statistical analysis in `{ggstatsplot}` is carried out in
 read the `NEWS` for that package:
 <https://indrajeetpatil.github.io/statsExpressions/news/index.html>
 
+## BUG FIXES
+
+- Empty groups in factors are no longer dropped in `ggpiestats()` and `ggbarstats()` (#935).
+
 # ggstatsplot 0.12.3
 
 ## MAJOR CHANGES

R/ggbarstats.R

@@ -82,8 +82,8 @@ ggbarstats <- function(
   # untable the data frame based on the count for each observation
   if (".counts" %in% names(data)) data %<>% tidyr::uncount(weights = .counts)
 
-  # x and y need to be a factor; also drop the unused levels of the factors
-  data %<>% mutate(across(.cols = everything(), .fns = ~ droplevels(as.factor(.x))))
+  # x and y need to be a factor
+  data %<>% mutate(across(.cols = everything(), .fns = ~ as.factor(.x)))
 
   # TO DO: until one-way table is supported by `BayesFactor`
   if (nlevels(pull(data, {{ y }})) == 1L) c(bf.message, proportion.test) %<-% c(FALSE, FALSE)
@@ -126,7 +126,6 @@ ggbarstats <- function(
   # if no. of factor levels is greater than the default palette color count
   .is_palette_sufficient(package, palette, nlevels(pull(data, {{ x }})))
 
-  # plot
   plotBar <- ggplot(descriptive_df, aes({{ y }}, perc, fill = {{ x }})) +
     geom_bar(stat = "identity", position = "fill", color = "black") +
     scale_y_continuous(
@@ -145,9 +144,8 @@ ggbarstats <- function(
     guides(fill = guide_legend(title = legend.title %||% as_name(x))) +
     paletteer::scale_fill_paletteer_d(paste0(package, "::", palette), name = "")
 
-  # sample size + proportion test ------------------------------------------
+  # proportion test ------------------------------------------
 
-  # adding significance labels to bars for proportion tests
   if (isTRUE(proportion.test)) {
     plotBar <- plotBar +
       geom_text(
@@ -158,7 +156,8 @@ ggbarstats <- function(
       )
   }
 
-  # adding sample size info
+  # sample size -------------------------------------------------
+
   plotBar <- plotBar +
     exec(
       geom_text,
@@ -207,13 +206,12 @@ ggbarstats <- function(
 #' set.seed(123)
 #' library(dplyr, warn.conflicts = FALSE)
 #'
-#' # let's create a smaller data frame
+#' # let's create a smaller data frame first
 #' diamonds_short <- ggplot2::diamonds %>%
 #'   filter(cut %in% c("Very Good", "Ideal")) %>%
 #'   filter(clarity %in% c("SI1", "SI2", "VS1", "VS2")) %>%
 #'   sample_frac(size = 0.05)
 #'
-#' # plot
 #' grouped_ggbarstats(
 #'   data          = diamonds_short,
 #'   x             = color,

R/ggpiestats.R

@@ -109,8 +109,8 @@ ggpiestats <- function(
   # untable the data frame based on the count for each observation
   if (".counts" %in% names(data)) data %<>% tidyr::uncount(weights = .counts)
 
-  # x and y need to be a factor; also drop the unused levels of the factors
-  data %<>% mutate(across(.cols = everything(), .fns = ~ droplevels(as.factor(.x))))
+  # x and y need to be a factor
+  data %<>% mutate(across(.cols = everything(), .fns = ~ as.factor(.x)))
   x_levels <- nlevels(pull(data, {{ x }}))
   y_levels <- ifelse(test == "one.way", 0L, nlevels(pull(data, {{ y }})))
 

codemeta.json

@@ -407,7 +407,7 @@
       "@type": "SoftwareApplication",
       "identifier": "insight",
       "name": "insight",
-      "version": ">= 0.19.10",
+      "version": ">= 0.19.11",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -433,7 +433,7 @@
       "@type": "SoftwareApplication",
       "identifier": "parameters",
       "name": "parameters",
-      "version": ">= 0.21.6",
+      "version": ">= 0.21.7",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",