ggstatsplot (version 0.7.2)

grouped_ggwithinstats: Violin plots for group or condition comparisons in within-subjects designs repeated across all levels of a grouping variable.

Description

A combined plot of comparison plot created for levels of a grouping variable.

Usage

grouped_ggwithinstats(
  data,
  x,
  y,
  grouping.var,
  outlier.label = NULL,
  output = "plot",
  plotgrid.args = list(),
  annotation.args = list(),
  ...
)

Arguments

data

A dataframe (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted.

x

The grouping (or independent) variable from the dataframe data.

y

The response (or outcome or dependent) variable from the dataframe data.

grouping.var

A single grouping variable (can be entered either as a bare name x or as a string "x").

outlier.label

Label to put on the outliers that have been tagged. This can't be the same as x argument.

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.

plotgrid.args

A list of additional arguments passed to patchwork::wrap_plots, except for guides argument which is already separately specified here.

annotation.args

A list of additional arguments passed to patchwork::plot_annotation.

...

Arguments passed on to ggwithinstats

point.path

Logical that decides whether individual data points and means, respectively, should be connected using geom_path. Both default to TRUE. Note that point.path argument is relevant only when there are two groups (i.e., in case of a t-test). In case of large number of data points, it is advisable to set point.path = FALSE as these lines can overwhelm the plot.

centrality.path

Logical that decides whether individual data points and means, respectively, should be connected using geom_path. Both default to TRUE. Note that point.path argument is relevant only when there are two groups (i.e., in case of a t-test). In case of large number of data points, it is advisable to set point.path = FALSE as these lines can overwhelm the plot.

centrality.path.args

A list of additional aesthetic arguments passed on to geom_path connecting raw data points and mean points.

point.path.args

A list of additional aesthetic arguments passed on to geom_path connecting raw data points and mean points.

type

A character specifying the type of statistical approach. Four possible options:

• "parametric"

• "nonparametric"

• "robust"

• "bayes"

Corresponding abbreviations are also accepted: "p" (for parametric), "np" (for nonparametric), "r" (for robust), or "bf" (for Bayesian).

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")

• "non-significant" (abbreviation accepted: "ns")

• "all"

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

Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.

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.

subtitle

The text for the plot subtitle. Will work only if results.subtitle = FALSE.

k

Number of digits after decimal point (should be an integer) (Default: k = 2L).

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. In case of an error, try reducing the value of tr, which is by default set to 0.2. Lowering the value might help.

centrality.plotting

Logical that decides whether centrality tendency measure is to be displayed as a point with a label (Default: TRUE). Function decides which central tendency measure to show depending on the type argument.

• mean for parametric statistics

• median for non-parametric statistics

• trimmed mean for robust statistics

• MAP estimator for Bayesian statistics

If you want default centrality parameter, you can specify this using centrality.type argument.

centrality.type

Decides which centrality parameter is to be displayed. The default is to choose the same as type argument. You can specify this to be:

• "parameteric" (for mean)

• "nonparametric" (for median)

• robust (for trimmed mean)

• bayes (for MAP estimator)

Just as type argument, abbreviations are also accepted.

centrality.point.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_point and ggrepel::geom_label_repel geoms, which are involved in mean plotting.

centrality.label.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_point and ggrepel::geom_label_repel geoms, which are involved in mean plotting.

outlier.tagging

Decides whether outliers should be tagged (Default: FALSE).

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.label.args

A list of additional aesthetic arguments to be passed to ggrepel::geom_label_repel for outlier label plotting.

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

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).

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_ variants of all primary functions. Default is NULL. The argument should be entered as a ggplot2 function or a list of ggplot2 functions.

References

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

See Also

ggwithinstats, ggbetweenstats, grouped_ggbetweenstats

Examples

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

# the most basic function call
grouped_ggwithinstats(
  data = VR_dilemma,
  x = modality,
  y = score,
  grouping.var = order,
  type = "np", # non-parametric test
  # additional modifications for **each** plot using `ggplot2` functions
  ggplot.component = ggplot2::scale_y_continuous(
    breaks = seq(0, 1, 0.1),
    limits = c(0, 1)
  )
)
# }