ggbetweenstats

From ggstatsplot v0.6.6 by Indrajeet Patil

Box/Violin plots for group or condition comparisons in between-subjects designs.

A combination of box and violin plots along with jittered data points for between-subjects designs with statistical details included in the plot as a subtitle.

Usage

ggbetweenstats(
  data,
  x,
  y,
  plot.type = "boxviolin",
  type = "parametric",
  pairwise.comparisons = TRUE,
  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,
  sample.size.label = TRUE,
  k = 2L,
  var.equal = FALSE,
  conf.level = 0.95,
  nboot = 100L,
  tr = 0.1,
  mean.plotting = TRUE,
  mean.ci = FALSE,
  mean.point.args = list(size = 5, color = "darkred"),
  mean.label.args = list(size = 3),
  notch = FALSE,
  notchwidth = 0.5,
  outlier.tagging = FALSE,
  outlier.label = NULL,
  outlier.coef = 1.5,
  outlier.shape = 19,
  outlier.color = "black",
  outlier.label.args = list(size = 3),
  point.args = list(position = ggplot2::position_jitterdodge(dodge.width = 0.6), alpha
    = 0.4, size = 3, stroke = 0),
  violin.args = list(width = 0.5, alpha = 0.2),
  ggsignif.args = list(textsize = 3, tip_length = 0.01),
  ggtheme = ggplot2::theme_bw(),
  ggstatsplot.layer = TRUE,
  package = "RColorBrewer",
  palette = "Dark2",
  ggplot.component = NULL,
  output = "plot",
  ...
)

Arguments

data: A dataframe (or a tibble) from which variables specified are to be taken. A matrix or tables will not be accepted.
x: The grouping variable from the dataframe data.
y: The response (a.k.a. outcome or dependent) variable from the dataframe data.
plot.type: Character describing the type of plot. Currently supported plots are "box" (for pure boxplots), "violin" (for pure violin plots), and "boxviolin" (for a combination of box and violin plots; default).
type: Type of statistic expected ("parametric" or "nonparametric" or "robust" or "bayes").Corresponding abbreviations are also accepted: "p" (for parametric), "np" (nonparametric), "r" (robust), or "bf"resp.
pairwise.comparisons: Logical that decides whether pairwise comparisons are to be displayed (default: TRUE). Please note that only significant comparisons will be shown by default. To change this behavior, select appropriate option with pairwise.display argument. The pairwise comparison dataframes are prepared using the pairwiseComparisons::pairwise_comparisons function. For more details about pairwise comparisons, see the documentation for that function.
pairwise.display: Decides which pairwise comparisons to display. Available options are "significant" (abbreviation accepted: "s") or "non-significant" (abbreviation accepted: "ns") or "everything"/"all". The default is "significant". You can use this argument to make sure that your plot is not uber-cluttered when you have multiple groups being compared and scores of pairwise comparisons being displayed.
p.adjust.method: Adjustment method for p-values for multiple comparisons. Possible methods are: "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
effsize.type: Type of effect size needed for parametric tests. The argument can be "eta" (partial eta-squared) or "omega" (partial omega-squared).
bf.prior: A number between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes factors.
bf.message: Logical that decides whether to display Bayes Factor in favor of the null hypothesis. This argument is relevant only for parametric test (Default: TRUE).
results.subtitle: Decides whether the results of statistical tests are to be displayed as a subtitle (Default: TRUE). If set to FALSE, only the plot will be returned.
xlab, ylab: Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.
caption: The text for the plot caption.
title: The text for the plot title.
subtitle: The text for the plot subtitle. Will work only if results.subtitle = FALSE.
sample.size.label: Logical that decides whether sample size information should be displayed for each level of the grouping variable x (Default: TRUE).
k: Number of digits after decimal point (should be an integer) (Default: k = 2L).
var.equal: a logical variable indicating whether to treat the variances in the samples as equal. If TRUE, then a simple F test for the equality of means in a one-way analysis of variance is performed. If FALSE, an approximate method of Welch (1951) is used, which generalizes the commonly known 2-sample Welch test to the case of arbitrarily many samples.
conf.level: Scalar between 0 and 1. If unspecified, the defaults return 95% confidence/credible intervals (0.95).
nboot: Number of bootstrap samples for computing confidence interval for the effect size (Default: 100).
tr: Trim level for the mean when carrying out robust tests. If you get error stating "Standard error cannot be computed because of Winsorized variance of 0 (e.g., due to ties). Try to decrease the trimming level.", try to play around with the value of tr, which is by default set to 0.1. Lowering the value might help.
mean.plotting: Logical that decides whether mean is to be highlighted and its value to be displayed (Default: TRUE).
mean.ci: Logical that decides whether 95% confidence interval for mean is to be displayed (Default: FALSE).
mean.point.args, mean.label.args: A list of additional aesthetic arguments to be passed to ggplot2::geom_point and ggrepel::geom_label_repel geoms involved mean value plotting.
notch: A logical. If FALSE (default), a standard box plot will be displayed. If TRUE, a notched box plot will be used. Notches are used to compare groups; if the notches of two boxes do not overlap, this suggests that the medians are significantly different. In a notched box plot, the notches extend 1.58 * IQR / sqrt(n), where IQR: Inter-Quartile Range. This gives a roughly 95% confidence interval for comparing medians.
notchwidth: For a notched box plot, width of the notch relative to the body (default 0.5).
outlier.tagging: Decides whether outliers should be tagged (Default: FALSE).
outlier.label: Label to put on the outliers that have been tagged. This can't be the same as x argument.
outlier.coef: Coefficient for outlier detection using Tukey's method. With Tukey's method, outliers are below (1st Quartile) or above (3rd Quartile) outlier.coef times the Inter-Quartile Range (IQR) (Default: 1.5).
outlier.shape: Hiding the outliers can be achieved by setting outlier.shape = NA. Importantly, this does not remove the outliers, it only hides them, so the range calculated for the y-axis will be the same with outliers shown and outliers hidden.
outlier.color: Default aesthetics for outliers (Default: "black").
outlier.label.args: A list of additional aesthetic arguments to be passed to ggrepel::geom_label_repel for outlier label plotting.
point.args: A list of additional aesthetic arguments to be passed to the geom_point displaying the raw data.
violin.args: A list of additional aesthetic arguments to be passed to the geom_violin.
ggsignif.args: A list of additional aesthetic arguments to be passed to ggsignif::geom_signif.
ggtheme: A function, ggplot2 theme name. Default value is ggplot2::theme_bw(). Any of the ggplot2 themes, or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.).
ggstatsplot.layer: Logical that decides whether theme_ggstatsplot theme elements are to be displayed along with the selected ggtheme (Default: TRUE). theme_ggstatsplot is an opinionated theme layer that override some aspects of the selected ggtheme.
package, palette: Name of the package from which the given palette is to be extracted. The available palettes and packages can be checked by running View(paletteer::palettes_d_names).
ggplot.component: A ggplot component to be added to the plot prepared by ggstatsplot. This argument is primarily helpful for grouped_ variant of the current function. Default is NULL. The argument should be entered as a function.
output: Character that describes what is to be returned: can be "plot" (default) or "subtitle" or "caption". Setting this to "subtitle" will return the expression containing statistical results. If you have set results.subtitle = FALSE, then this will return a NULL. Setting this to "caption" will return the expression containing details about Bayes Factor analysis, but valid only when type = "parametric" and bf.message = TRUE, otherwise this will return a NULL.
...: Currently ignored.

References

https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggbetweenstats.html

Examples

# NOT RUN {
# to get reproducible results from bootstrapping
set.seed(123)
library(ggstatsplot)

# simple function call with the defaults
ggstatsplot::ggbetweenstats(
  data = mtcars,
  x = am,
  y = mpg,
  title = "Fuel efficiency by type of car transmission",
  caption = "Transmission (0 = automatic, 1 = manual)"
)

# more detailed function call
ggstatsplot::ggbetweenstats(
  data = datasets::morley,
  x = Expt,
  y = Speed,
  type = "nonparametric",
  plot.type = "box",
  xlab = "The experiment number",
  ylab = "Speed-of-light measurement",
  pairwise.comparisons = TRUE,
  p.adjust.method = "fdr",
  outlier.tagging = TRUE,
  outlier.label = Run,
  ggtheme = ggplot2::theme_grey(),
  ggstatsplot.layer = FALSE
)
# }

Documentation reproduced from package ggstatsplot, version 0.6.6, License: GPL-3 | file LICENSE

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