Merge branch 'main' into fail-on-lints

Author: IndrajeetPatil

.github/workflows/pkgdown.yaml

@@ -48,7 +48,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].1
+        uses: JamesIves/[email protected].3
         with:
           branch: gh-pages
           folder: docs

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "ggstatsplot" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'ggstatsplot: ''ggplot2'' Based Plots with Statistical Details'
-version: 0.12.3.9000
+version: 0.12.4.9000
 doi: 10.21105/joss.03167
 abstract: 'Extension of ''ggplot2'', ''ggstatsplot'' creates graphics with details
   from statistical tests included in the plots themselves. It provides an easier syntax
@@ -76,7 +76,7 @@ references:
   abstract: 'correlation: Methods for Correlation Analysis'
   notes: Imports
   url: https://easystats.github.io/correlation/
-  repository: https://easystats.r-universe.dev
+  repository: https://CRAN.R-project.org/package=correlation
   authors:
   - family-names: Makowski
     given-names: Dominique
@@ -103,13 +103,13 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4315-6788
   year: '2024'
-  version: '>= 0.8.4'
+  version: '>= 0.8.5'
 - type: software
   title: datawizard
   abstract: 'datawizard: Easy Data Wrangling and Statistical Transformations'
   notes: Imports
   url: https://easystats.github.io/datawizard/
-  repository: https://CRAN.R-project.org/package=datawizard
+  repository: https://easystats.r-universe.dev
   authors:
   - family-names: Patil
     given-names: Indrajeet
@@ -136,7 +136,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2024'
-  version: '>= 0.10.0'
+  version: '>= 0.11.0'
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -313,7 +313,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9271-5075
   year: '2024'
-  version: '>= 0.19.11'
+  version: '>= 0.20.1'
 - type: software
   title: paletteer
   abstract: 'paletteer: Comprehensive Collection of Color Palettes'
@@ -356,7 +356,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2024'
-  version: '>= 0.21.7'
+  version: '>= 0.22.0'
 - type: software
   title: patchwork
   abstract: 'patchwork: The Composer of Plots'
@@ -375,7 +375,7 @@ references:
   abstract: 'performance: Assessment of Regression Models Performance'
   notes: Imports
   url: https://easystats.github.io/performance/
-  repository: https://CRAN.R-project.org/package=performance
+  repository: https://easystats.r-universe.dev
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -406,7 +406,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4315-6788
   year: '2024'
-  version: '>= 0.11.0'
+  version: '>= 0.12.0'
 - type: software
   title: purrr
   abstract: 'purrr: Functional Programming Tools'
@@ -437,17 +437,7 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2024'
-  version: '>= 1.1.3'
-- type: software
-  title: stats
-  abstract: 'R: A Language and Environment for Statistical Computing'
-  notes: Imports
-  authors:
-  - name: R Core Team
-  institution:
-    name: R Foundation for Statistical Computing
-    address: Vienna, Austria
-  year: '2024'
+  version: '>= 1.1.4'
 - type: software
   title: statsExpressions
   abstract: 'statsExpressions: Tidy Dataframes and Expressions with Statistical Details'
@@ -459,8 +449,8 @@ references:
     given-names: Indrajeet
     email: [email protected]
     orcid: https://orcid.org/0000-0003-1995-6531
+  version: '>= 1.5.5'
   year: '2024'
-  version: '>= 1.5.4'
 - type: software
   title: tidyr
   abstract: 'tidyr: Tidy Messy Data'
@@ -580,6 +570,8 @@ references:
   - family-names: Ripley
     given-names: Brian
     email: [email protected]
+  - family-names: Venables
+    given-names: Bill
   year: '2024'
 - type: software
   title: metaBMA
@@ -620,7 +612,7 @@ references:
   authors:
   - family-names: Beath
     given-names: Ken
-    email: ken@kjbeath.com.au
+    email: ken@kjbeath.id.au
   - family-names: Bolker
     given-names: Ben
     email: [email protected]
@@ -638,6 +630,9 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4880-9610
   year: '2024'
+  identifiers:
+  - type: url
+    value: https://personality-project.org/r/psych-manual.pdf
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -700,6 +695,16 @@ references:
   - family-names: Johnson
     given-names: Andrew
   year: '2024'
+- type: software
+  title: stats
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Suggests
+  authors:
+  - name: R Core Team
+  institution:
+    name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: survival
   abstract: 'survival: Survival Analysis'

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ggstatsplot
 Title: 'ggplot2' Based Plots with Statistical Details
-Version: 0.12.3.9000
+Version: 0.12.4.9000
 Authors@R: 
     c(person(given = "Indrajeet",
              family = "Patil",
@@ -31,24 +31,23 @@ BugReports: https://github.com/IndrajeetPatil/ggstatsplot/issues
 Depends: 
     R (>= 4.1.0)
 Imports:
-    correlation (>= 0.8.4),
-    datawizard (>= 0.10.0),
+    correlation (>= 0.8.5),
+    datawizard (>= 0.11.0),
     dplyr (>= 1.1.4),
     ggcorrplot (>= 0.1.4.1),
     ggplot2 (>= 3.5.1),
     ggrepel (>= 0.9.5),
     ggside (>= 0.3.1),
     ggsignif (>= 0.6.4),
     glue (>= 1.7.0),
-    insight (>= 0.19.11),
+    insight (>= 0.20.1),
     paletteer (>= 1.6.0),
-    parameters (>= 0.21.7),
+    parameters (>= 0.22.0),
     patchwork (>= 1.2.0),
-    performance (>= 0.11.0),
+    performance (>= 0.12.0),
     purrr (>= 1.0.2),
-    rlang (>= 1.1.3),
-    stats,
-    statsExpressions (>= 1.5.4),
+    rlang (>= 1.1.4),
+    statsExpressions (>= 1.5.5),
     tidyr (>= 1.3.1),
     utils
 Suggests:
@@ -64,6 +63,7 @@ Suggests:
     psych,
     rmarkdown,
     rstantools,
+    stats,
     survival,
     testthat (>= 3.2.1),
     tibble,
@@ -79,7 +79,7 @@ Roxygen: list(
     markdown = TRUE,
     roclets = c("collate", "namespace", "rd", "pkgapi::api_roclet", "roxyglobals::global_roclet")
   )
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/check: anthonynorth/roxyglobals

NEWS.md

@@ -1,19 +1,32 @@
-# ggstatsplot 0.12.3.9000
+# ggstatsplot 0.12.4.9000
 
 N.B. All statistical analysis in `{ggstatsplot}` is carried out in
 `{statsExpressions}`. Thus, to see changes related to statistical expressions,
 read the `NEWS` for that package:
 <https://indrajeetpatil.github.io/statsExpressions/news/index.html>
 
+## BUG FIXES
+
+- `ggpiestats()` and `ggbarstats()` now respect `ratio()` argument for
+  proportion tests run in case of two-way contingency tables (#818).
+
+# ggstatsplot 0.12.4
+
 ## MAJOR CHANGES
 
-- The feature to superimpose normality curve on a histogram (in `gghistostats()`) has been removed. 
-  This feature always felt like an ad hoc addition to the plot, and has nothing to do with the key
-  statistical analysis in question (which is not about checking the normality of the distribution).
+- The feature to superimpose normality curve on a histogram (in
+  `gghistostats()`) has been removed. This feature always felt like an ad hoc
+  addition to the plot, and has nothing to do with the key statistical analysis
+  in question (which is not about checking the normality of the distribution).
+
+## MINOR CHANGES
+
+- Updates code to fix warnings coming via updates to easystats packages.
 
 ## BUG FIXES
 
-- Empty groups in factors are no longer dropped in `ggpiestats()` and `ggbarstats()` (#935).
+- Empty groups in factors are no longer dropped in `ggpiestats()` and
+  `ggbarstats()` (#935).
 
 # ggstatsplot 0.12.3
 

R/ggbarstats.R

@@ -121,7 +121,7 @@ ggbarstats <- function(
   descriptive_df <- descriptive_data(data, {{ x }}, {{ y }}, label, digits.perc)
 
   # data frame containing all details needed for prop test
-  onesample_df <- onesample_data(data, {{ x }}, {{ y }}, digits)
+  onesample_df <- onesample_data(data, {{ x }}, {{ y }}, digits, ratio)
 
   # if no. of factor levels is greater than the default palette color count
   .is_palette_sufficient(package, palette, nlevels(pull(data, {{ x }})))

R/ggcoefstats.R

@@ -19,7 +19,7 @@
 #'   estimates of coefficients or other quantities of interest).
 #' @param statistic Relevant statistic for the model (`"t"`, `"f"`, `"z"`, or
 #'   `"chi"`) in the label. Relevant only if `x` is a *data frame*.
-#' @param effectsize.type This is the same as `effectsize_type` argument of
+#' @param effectsize.type This is the same as `es_type` argument of
 #'   `parameters::model_parameters()`. Defaults to `"eta"`, and relevant for
 #'   ANOVA-like objects.
 #' @param bf.message Logical that decides whether results from running a
@@ -165,10 +165,10 @@ ggcoefstats <- function(
 
     # converting model object to a tidy data frame
     tidy_df <- tidy_model_parameters(
-      model           = x,
-      effectsize_type = effectsize.type,
-      ci              = conf.level,
-      table_wide      = TRUE,
+      model      = x,
+      es_type    = effectsize.type,
+      ci         = conf.level,
+      table_wide = TRUE,
       ...
     )
 

R/ggpiestats-ggbarstats-helpers.R

@@ -36,14 +36,14 @@ descriptive_data <- function(
 #' @title A data frame with chi-squared test results
 #' @autoglobal
 #' @noRd
-onesample_data <- function(data, x, y, digits = 2L, ...) {
+onesample_data <- function(data, x, y, digits = 2L, ratio = NULL, ...) {
   full_join(
     # descriptive summary
     x = .cat_counter(data, {{ y }}) %>%
       mutate(N = paste0("(n = ", .prettyNum(counts), ")")),
     # proportion test results
     y = group_by(data, {{ y }}) %>%
-      group_modify(.f = ~ .chisq_test_safe(., {{ x }})) %>%
+      group_modify(.f = ~ .chisq_test_safe(., {{ x }}, ratio)) %>%
       ungroup(),
     by = as_name(ensym(y))
   ) %>%
@@ -60,22 +60,16 @@ onesample_data <- function(data, x, y, digits = 2L, ...) {
 #' Needed to work with `group_modify()` since it will not work when `NULL` is returned
 #' @autoglobal
 #' @noRd
-.chisq_test_safe <- function(data, x, ...) {
-  xtab <- table(pull(data, {{ x }}))
-
-  result <- tryCatch(
-    expr = parameters::model_parameters(suppressWarnings(stats::chisq.test(xtab))),
-    error = function(e) NULL
+.chisq_test_safe <- function(data, x, ratio) {
+  tryCatch(
+    suppressWarnings(contingency_table(data, x, ratio = ratio)),
+    error = function(e) {
+      tibble(
+        statistic = NA_real_, p.value = NA_real_, df = NA_real_,
+        method = "Chi-squared test for given probabilities"
+      )
+    }
   )
-
-  if (is.null(result)) {
-    tibble(
-      statistic = NA_real_, p.value = NA_real_, df = NA_real_,
-      method = "Chi-squared test for given probabilities"
-    )
-  } else {
-    insight::standardize_names(result, style = "broom") %>% as_tibble()
-  }
 }
 
 

R/ggpiestats.R

@@ -153,7 +153,7 @@ ggpiestats <- function(
   descriptive_df <- descriptive_data(data, {{ x }}, {{ y }}, label, digits.perc)
 
   # data frame containing all details needed for proportion test
-  if (test == "two.way") onesample_df <- onesample_data(data, {{ x }}, {{ y }}, digits)
+  if (test == "two.way") onesample_df <- onesample_data(data, {{ x }}, {{ y }}, digits, ratio)
 
   # if no. of factor levels is greater than the default palette color count
   .is_palette_sufficient(package, palette, min_length = x_levels)