Merge branch 'main' into fail-on-lints

IndrajeetPatil · May 25, 2024 · 5886278 · 5886278
2 parents 61606cf + 5617a05
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -48,7 +48,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].0
+        uses: JamesIves/[email protected].1
         with:
           branch: gh-pages
           folder: docs
diff --git a/API b/API
@@ -11,7 +11,7 @@ ggbetweenstats(data, x, y, type = "parametric", pairwise.display = "significant"
 ggcoefstats(x, statistic = NULL, conf.int = TRUE, conf.level = 0.95, digits = 2L, exclude.intercept = FALSE, effectsize.type = "eta", meta.analytic.effect = FALSE, meta.type = "parametric", bf.message = TRUE, sort = "none", xlab = NULL, ylab = NULL, title = NULL, subtitle = NULL, caption = NULL, only.significant = FALSE, point.args = list(size = 3, color = "blue", na.rm = TRUE), errorbar.args = list(height = 0, na.rm = TRUE), vline = TRUE, vline.args = list(linewidth = 1, linetype = "dashed"), stats.labels = TRUE, stats.label.color = NULL, stats.label.args = list(size = 3, direction = "y", min.segment.length = 0, na.rm = TRUE), package = "RColorBrewer", palette = "Dark2", ggtheme = ggstatsplot::theme_ggstatsplot(), ...)
 ggcorrmat(data, cor.vars = NULL, cor.vars.names = NULL, matrix.type = "upper", type = "parametric", tr = 0.2, partial = FALSE, digits = 2L, sig.level = 0.05, conf.level = 0.95, bf.prior = 0.707, p.adjust.method = "holm", pch = "cross", ggcorrplot.args = list(method = "square", outline.color = "black", pch.cex = 14), package = "RColorBrewer", palette = "Dark2", colors = c("#E69F00", "white", "#009E73"), ggtheme = ggstatsplot::theme_ggstatsplot(), ggplot.component = NULL, title = NULL, subtitle = NULL, caption = NULL, ...)
 ggdotplotstats(data, x, y, xlab = NULL, ylab = NULL, title = NULL, subtitle = NULL, caption = NULL, type = "parametric", test.value = 0, bf.prior = 0.707, bf.message = TRUE, effsize.type = "g", conf.level = 0.95, tr = 0.2, digits = 2L, results.subtitle = TRUE, point.args = list(color = "black", size = 3, shape = 16), centrality.plotting = TRUE, centrality.type = type, centrality.line.args = list(color = "blue", linewidth = 1, linetype = "dashed"), ggplot.component = NULL, ggtheme = ggstatsplot::theme_ggstatsplot(), ...)
-gghistostats(data, x, binwidth = NULL, xlab = NULL, title = NULL, subtitle = NULL, caption = NULL, type = "parametric", test.value = 0, bf.prior = 0.707, bf.message = TRUE, effsize.type = "g", conf.level = 0.95, tr = 0.2, digits = 2L, ggtheme = ggstatsplot::theme_ggstatsplot(), results.subtitle = TRUE, bin.args = list(color = "black", fill = "grey50", alpha = 0.7), centrality.plotting = TRUE, centrality.type = type, centrality.line.args = list(color = "blue", linewidth = 1, linetype = "dashed"), normal.curve = FALSE, normal.curve.args = list(linewidth = 2), ggplot.component = NULL, ...)
+gghistostats(data, x, binwidth = NULL, xlab = NULL, title = NULL, subtitle = NULL, caption = NULL, type = "parametric", test.value = 0, bf.prior = 0.707, bf.message = TRUE, effsize.type = "g", conf.level = 0.95, tr = 0.2, digits = 2L, ggtheme = ggstatsplot::theme_ggstatsplot(), results.subtitle = TRUE, bin.args = list(color = "black", fill = "grey50", alpha = 0.7), centrality.plotting = TRUE, centrality.type = type, centrality.line.args = list(color = "blue", linewidth = 1, linetype = "dashed"), ggplot.component = NULL, ...)
 ggpiestats(data, x, y = NULL, counts = NULL, type = "parametric", paired = FALSE, results.subtitle = TRUE, label = "percentage", label.args = list(direction = "both"), label.repel = FALSE, digits = 2L, proportion.test = results.subtitle, digits.perc = 0L, bf.message = TRUE, ratio = NULL, conf.level = 0.95, sampling.plan = "indepMulti", fixed.margin = "rows", prior.concentration = 1, title = NULL, subtitle = NULL, caption = NULL, legend.title = NULL, ggtheme = ggstatsplot::theme_ggstatsplot(), package = "RColorBrewer", palette = "Dark2", ggplot.component = NULL, ...)
 ggscatterstats(data, x, y, type = "parametric", conf.level = 0.95, bf.prior = 0.707, bf.message = TRUE, tr = 0.2, digits = 2L, results.subtitle = TRUE, label.var = NULL, label.expression = NULL, marginal = TRUE, point.args = list(size = 3, alpha = 0.4, stroke = 0), point.width.jitter = 0, point.height.jitter = 0, point.label.args = list(size = 3, max.overlaps = 1e+06), smooth.line.args = list(linewidth = 1.5, color = "blue", method = "lm", formula = y ~ x), xsidehistogram.args = list(fill = "#009E73", color = "black", na.rm = TRUE), ysidehistogram.args = list(fill = "#D55E00", color = "black", na.rm = TRUE), xlab = NULL, ylab = NULL, title = NULL, subtitle = NULL, caption = NULL, ggtheme = ggstatsplot::theme_ggstatsplot(), ggplot.component = NULL, ...)
 ggwithinstats(data, x, y, type = "parametric", pairwise.display = "significant", p.adjust.method = "holm", effsize.type = "unbiased", bf.prior = 0.707, bf.message = TRUE, results.subtitle = TRUE, xlab = NULL, ylab = NULL, caption = NULL, title = NULL, subtitle = NULL, digits = 2L, conf.level = 0.95, nboot = 100L, tr = 0.2, centrality.plotting = TRUE, centrality.type = type, centrality.point.args = list(size = 5, color = "darkred"), centrality.label.args = list(size = 3, nudge_x = 0.4, segment.linetype = 4), centrality.path = TRUE, centrality.path.args = list(linewidth = 1, color = "red", alpha = 0.5), point.args = list(size = 3, alpha = 0.5, na.rm = TRUE), point.path = TRUE, point.path.args = list(alpha = 0.5, linetype = "dashed"), boxplot.args = list(width = 0.2, alpha = 0.5, na.rm = TRUE), violin.args = list(width = 0.5, alpha = 0.2, na.rm = TRUE), ggsignif.args = list(textsize = 3, tip_length = 0.01, na.rm = TRUE), ggtheme = ggstatsplot::theme_ggstatsplot(), package = "RColorBrewer", palette = "Dark2", ggplot.component = NULL, ...)

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -70,8 +70,6 @@ Suggests:
     vdiffr (>= 1.0.7),
     withr,
     WRS2
-Remotes:
-    tidyverse/ggplot2
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,12 @@ 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>
 
+## 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).
+
 ## BUG FIXES
 
 - Empty groups in factors are no longer dropped in `ggpiestats()` and `ggbarstats()` (#935).

diff --git a/R/ggdotplotstats.R b/R/ggdotplotstats.R
@@ -8,7 +8,7 @@
 #'
 #' @section Summary of graphics:
 #'
-#' ```{r child="man/rmd-fragments/gghistostats_graphics.Rmd"}
+#' ```{r child="man/rmd-fragments/ggdotplotstats_graphics.Rmd"}
 #' ```
 #'
 #' @param ... Currently ignored.

diff --git a/R/gghistostats.R b/R/gghistostats.R
@@ -12,10 +12,6 @@
 #' ```
 #'
 #' @param ... Currently ignored.
-#' @param normal.curve A logical value that decides whether to super-impose a
-#'   normal curve using `stats::dnorm(mean(x), stats::sd(x))`. Default is `FALSE`.
-#' @param normal.curve.args A list of additional aesthetic arguments to be
-#'   passed to the normal curve.
 #' @param binwidth The width of the histogram bins. Can be specified as a
 #'   numeric value, or a function that calculates width from `x`. The default is
 #'   to use the `max(x) - min(x) / sqrt(N)`. You should always check this value
@@ -80,8 +76,6 @@ gghistostats <- function(
     centrality.plotting = TRUE,
     centrality.type = type,
     centrality.line.args = list(color = "blue", linewidth = 1, linetype = "dashed"),
-    normal.curve = FALSE,
-    normal.curve.args = list(linewidth = 2),
     ggplot.component = NULL,
     ...) {
   # data -----------------------------------
@@ -134,17 +128,6 @@ gghistostats <- function(
     ) +
     guides(fill = "none")
 
-  # if normal curve overlay needs to be displayed
-  if (normal.curve) {
-    plot_hist <- plot_hist +
-      exec(
-        stat_function,
-        fun  = function(x, mean, sd, n, bw) stats::dnorm(x, mean, sd) * n * bw,
-        args = list(mean = mean(x_vec), sd = stats::sd(x_vec), n = length(x_vec), bw = binwidth %||% .binwidth(x_vec)),
-        !!!normal.curve.args
-      )
-  }
-
   # centrality plotting -------------------------------------
 
   if (isTRUE(centrality.plotting)) {

diff --git a/R/ggscatterstats.R b/R/ggscatterstats.R
@@ -3,12 +3,12 @@
 #'
 #' @description
 #'
-#' Scatterplots from `{ggplot2}` combined with marginal densigram (density +
-#' histogram) plots with statistical details.
+#' Scatterplots from `{ggplot2}` combined with marginal distributions plots
+#' with statistical details.
 #'
 #' @section Summary of graphics:
 #'
-#' ```{r child="man/rmd-fragments/gghistostats_graphics.Rmd"}
+#' ```{r child="man/rmd-fragments/ggscatterstats_graphics.Rmd"}
 #' ```
 #'
 #' @param ... Currently ignored.

diff --git a/README.Rmd b/README.Rmd
@@ -330,8 +330,6 @@ grouped_gghistostats(
   type              = "nonparametric",
   xlab              = "Movies budget (in million US$)",
   grouping.var      = genre,
-  normal.curve      = TRUE,
-  normal.curve.args = list(color = "red", size = 1),
   ggtheme           = ggthemes::theme_tufte(),
   ## modify the defaults from `{ggstatsplot}` for each plot
   plotgrid.args     = list(nrow = 1),

diff --git a/README.md b/README.md
@@ -3,10 +3,10 @@
 
 ## `{ggstatsplot}`: `{ggplot2}` Based Plots with Statistical Details
 
-| Status                                                                                                                                            | Usage                                                                                                                                      | Miscellaneous                                                                                                                                                     |
-|---------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Status | Usage | Miscellaneous |
+|----|----|----|
 | [![R build status](https://github.com/IndrajeetPatil/ggstatsplot/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/ggstatsplot) | [![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot) | [![codecov](https://codecov.io/gh/IndrajeetPatil/ggstatsplot/branch/main/graph/badge.svg?token=ddrxwt0bj8)](https://app.codecov.io/gh/IndrajeetPatil/ggstatsplot) |
-| [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)                        | [![Daily downloads](https://cranlogs.r-pkg.org/badges/last-day/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot)    | [![DOI](https://joss.theoj.org/papers/10.21105/joss.03167/status.svg)](https://doi.org/10.21105/joss.03167)                                                       |
+| [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) | [![Daily downloads](https://cranlogs.r-pkg.org/badges/last-day/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot) | [![DOI](https://joss.theoj.org/papers/10.21105/joss.03167/status.svg)](https://doi.org/10.21105/joss.03167) |
 
 ## Raison d’être <img src="man/figures/logo.png" align="right" width="360" />
 
@@ -27,10 +27,10 @@ makes data exploration simpler and faster.
 
 ## Installation
 
-| Type        | Source                                                                                                             | Command                                  |
-|-------------|--------------------------------------------------------------------------------------------------------------------|------------------------------------------|
-| Release     | [![CRAN Status](https://www.r-pkg.org/badges/version/ggstatsplot)](https://cran.r-project.org/package=ggstatsplot) | `install.packages("ggstatsplot")`        |
-| Development | [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/##active)      | `pak::pak("IndrajeetPatil/ggstatsplot")` |
+| Type | Source | Command |
+|----|----|----|
+| Release | [![CRAN Status](https://www.r-pkg.org/badges/version/ggstatsplot)](https://cran.r-project.org/package=ggstatsplot) | `install.packages("ggstatsplot")` |
+| Development | [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/##active) | `pak::pak("IndrajeetPatil/ggstatsplot")` |
 
 ## Citation
 
@@ -95,17 +95,17 @@ To see the detailed documentation for each function in the stable
 
 ## Summary of available plots
 
-| Function           | Plot                      | Description                                     |
-|:-------------------|:--------------------------|:------------------------------------------------|
-| `ggbetweenstats()` | **violin plots**          | for comparisons *between* groups/conditions     |
-| `ggwithinstats()`  | **violin plots**          | for comparisons *within* groups/conditions      |
-| `gghistostats()`   | **histograms**            | for distribution about numeric variable         |
-| `ggdotplotstats()` | **dot plots/charts**      | for distribution about labeled numeric variable |
-| `ggscatterstats()` | **scatterplots**          | for correlation between two variables           |
-| `ggcorrmat()`      | **correlation matrices**  | for correlations between multiple variables     |
-| `ggpiestats()`     | **pie charts**            | for categorical data                            |
-| `ggbarstats()`     | **bar charts**            | for categorical data                            |
-| `ggcoefstats()`    | **dot-and-whisker plots** | for regression models and meta-analysis         |
+| Function | Plot | Description |
+|:---|:---|:---|
+| `ggbetweenstats()` | **violin plots** | for comparisons *between* groups/conditions |
+| `ggwithinstats()` | **violin plots** | for comparisons *within* groups/conditions |
+| `gghistostats()` | **histograms** | for distribution about numeric variable |
+| `ggdotplotstats()` | **dot plots/charts** | for distribution about labeled numeric variable |
+| `ggscatterstats()` | **scatterplots** | for correlation between two variables |
+| `ggcorrmat()` | **correlation matrices** | for correlations between multiple variables |
+| `ggpiestats()` | **pie charts** | for categorical data |
+| `ggbarstats()` | **bar charts** | for categorical data |
+| `ggcoefstats()` | **dot-and-whisker plots** | for regression models and meta-analysis |
 
 In addition to these basic plots, `{ggstatsplot}` also provides
 **`grouped_`** versions (see below) that makes it easy to repeat the
@@ -116,17 +116,17 @@ same analysis for any grouping variable.
 The table below summarizes all the different types of analyses currently
 supported in this package-
 
-| Functions                            | Description                                       | Parametric | Non-parametric | Robust | Bayesian |
-|:-------------------------------------|:--------------------------------------------------|:-----------|:---------------|:-------|:---------|
-| `ggbetweenstats()`                   | Between group/condition comparisons               | ✅         | ✅             | ✅     | ✅       |
-| `ggwithinstats()`                    | Within group/condition comparisons                | ✅         | ✅             | ✅     | ✅       |
-| `gghistostats()`, `ggdotplotstats()` | Distribution of a numeric variable                | ✅         | ✅             | ✅     | ✅       |
-| `ggcorrmat`                          | Correlation matrix                                | ✅         | ✅             | ✅     | ✅       |
-| `ggscatterstats()`                   | Correlation between two variables                 | ✅         | ✅             | ✅     | ✅       |
-| `ggpiestats()`, `ggbarstats()`       | Association between categorical variables         | ✅         | ✅             | ❌     | ✅       |
-| `ggpiestats()`, `ggbarstats()`       | Equal proportions for categorical variable levels | ✅         | ✅             | ❌     | ✅       |
-| `ggcoefstats()`                      | Regression model coefficients                     | ✅         | ✅             | ✅     | ✅       |
-| `ggcoefstats()`                      | Random-effects meta-analysis                      | ✅         | ❌             | ✅     | ✅       |
+| Functions | Description | Parametric | Non-parametric | Robust | Bayesian |
+|:---|:---|:---|:---|:---|:---|
+| `ggbetweenstats()` | Between group/condition comparisons | ✅ | ✅ | ✅ | ✅ |
+| `ggwithinstats()` | Within group/condition comparisons | ✅ | ✅ | ✅ | ✅ |
+| `gghistostats()`, `ggdotplotstats()` | Distribution of a numeric variable | ✅ | ✅ | ✅ | ✅ |
+| `ggcorrmat` | Correlation matrix | ✅ | ✅ | ✅ | ✅ |
+| `ggscatterstats()` | Correlation between two variables | ✅ | ✅ | ✅ | ✅ |
+| `ggpiestats()`, `ggbarstats()` | Association between categorical variables | ✅ | ✅ | ❌ | ✅ |
+| `ggpiestats()`, `ggbarstats()` | Equal proportions for categorical variable levels | ✅ | ✅ | ❌ | ✅ |
+| `ggcoefstats()` | Regression model coefficients | ✅ | ✅ | ✅ | ✅ |
+| `ggcoefstats()` | Random-effects meta-analysis | ✅ | ❌ | ✅ | ✅ |
 
 Summary of Bayesian analysis
 
@@ -315,8 +315,6 @@ grouped_gghistostats(
   type              = "nonparametric",
   xlab              = "Movies budget (in million US$)",
   grouping.var      = genre,
-  normal.curve      = TRUE,
-  normal.curve.args = list(color = "red", size = 1),
   ggtheme           = ggthemes::theme_tufte(),
   ## modify the defaults from `{ggstatsplot}` for each plot
   plotgrid.args     = list(nrow = 1),
@@ -699,12 +697,18 @@ extract_subtitle(p)
 #> list(italic("F")["Welch"](2, 18.03) == "31.62", italic(p) == 
 #>     "1.27e-06", widehat(omega["p"]^2) == "0.74", CI["95%"] ~ 
 #>     "[" * "0.53", "1.00" * "]", italic("n")["obs"] == "32")
+```
+
+``` r
 
 # extracting expression present in the caption
 extract_caption(p)
 #> list(log[e] * (BF["01"]) == "-14.92", widehat(italic(R^"2"))["Bayesian"]^"posterior" == 
 #>     "0.71", CI["95%"]^HDI ~ "[" * "0.57", "0.79" * "]", italic("r")["Cauchy"]^"JZS" == 
 #>     "0.71")
+```
+
+``` r
 
 # a list of tibbles containing statistical analysis summaries
 extract_stats(p)

diff --git a/codemeta.json b/codemeta.json
@@ -349,7 +349,7 @@
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://github.com/tidyverse/ggplot2"
+      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
     },
     "7": {
       "@type": "SoftwareApplication",
@@ -532,7 +532,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "9347.226KB",
+  "fileSize": "9327.22KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/figures/README-gghistostats2-1.png b/man/figures/README-gghistostats2-1.png
diff --git a/man/ggdotplotstats.Rd b/man/ggdotplotstats.Rd