ggstatsplot Files

NEW FEATURES

• ggbarstats() (and grouped_ggbarstats()) now supports one-sample goodness-of-fit tests when only x is specified (with y = NULL as the new default). This produces a single stacked bar chart with chi-squared GOF test results in the subtitle, mirroring the existing one-sample support in ggpiestats() (#532, [#697]).

• ggpiestats() and ggbarstats() now compute pairwise contingency table analyses (Fisher's exact tests via pairwise_contingency_table()) when x has more than two levels. These are available via extract_stats(plot)$pairwise_comparisons_data. A new p.adjust.method parameter controls the p-value adjustment method (default: "holm"). Pairwise results are not displayed on the plots since bar and pie charts lack a natural visual representation for pairwise significance annotations (#554).

• ggscatterstats() now sets a default number of bins for marginal histograms, suppressing the stat_bin() message about picking a better binwidth (#810).

• ggscatterstats() gains xsidehistogram.scale and ysidehistogram.scale parameters to control the scale (e.g., breaks, limits, transform) of the marginal distribution histograms (#898).

• All top-level plotting functions now include an alternative argument, which is passed down to {statsExpressions} to specify the alternative hypothesis for effect size confidence intervals (#794).

• ggbetweenstats() and ggwithinstats() now include a pairwise.alpha argument to control the alpha cutoff used for filtering displayed pairwise comparisons, and the secondary-axis label now reports the chosen alpha.

BREAKING CHANGES

• The following expert-level statistical parameters have been removed from all function signatures because their defaults are the universally recommended values and changing them requires specialist knowledge (#1087):

  • var.equal (from ggbetweenstats()): Welch's test (var.equal = FALSE) is uniformly recommended over Student's t-test.
  • nboot (from ggbetweenstats(), ggwithinstats()): 100 bootstrap resamples is adequate for trimmed-mean CIs.
  • sampling.plan, fixed.margin, prior.concentration (from ggpiestats(), ggbarstats()): Technical BayesFactor settings that virtually no one changes.
  • effsize.type (from ggbetweenstats(), ggwithinstats(), gghistostats(), ggdotplotstats()): The unbiased effect size estimator is now always used.

Users who need non-default values for these parameters should call {statsExpressions} directly.

• ggwithinstats() (and grouped_ggwithinstats()) gains a subject.id parameter. When provided, the subject identifier column is used to correctly pair observations across conditions and to remove NA observations by subject key rather than by positional row number. Plots and statistical results for unsorted repeated-measures data will differ from previous versions once subject.id is supplied. All examples and vignettes have been updated to pass subject.id explicitly, which is now the recommended practice.

• The package argument has been removed from all plotting functions. The palette argument now accepts a single "package::palette" string (e.g., palette = "ggthemes::gdoc"), matching the convention used by {paletteer} itself.

• The default palette has been changed from "RColorBrewer::Dark2" (8 colors) to "ggthemes::gdoc" (24 qualitative colors), which accommodates categorical variables with up to 24 levels without errors (#1015).

• When the chosen palette does not have enough colors for the number of levels in the data, an error is now thrown (previously a warning was issued that was silently ignored until ggplot2 crashed anyway).

BUG FIXES

• Grouped plot functions (e.g., grouped_ggbarstats()) now preserve the order of groups as they appear in the data rather than sorting them alphabetically (#792).

• combine_plots() now renders the overall annotation title in bold by default, matching the styling used for individual plot titles.

• grouped_ggbarstats() and grouped_ggpiestats() now display a single unified legend when different groups have different observed factor levels for the x variable. Previously, patchwork could not merge the per-panel fill scales, producing duplicate legends (#868).

• ggbetweenstats() and ggwithinstats() now correctly display sample size labels on the x-axis even when centrality.plotting = FALSE (#695).

• ggcoefstats() now preserves the model term order in the default top-to-bottom plot layout and in estimate-sorted displays, instead of showing terms in the reverse order (#642).

• ggcoefstats() no longer draws empty stats.labels boxes for model terms whose label expression is absent, which affected mixed-model coefficient plots such as the documented lmer() example.