grouped_ggwithinstats: Violin plots for group or condition comparisons in...

grouped_ggwithinstatsR Documentation

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,
  ...,
  grouping.var,
  output = "plot",
  plotgrid.args = list(),
  annotation.args = list()
)

Arguments

data

A data frame (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted. Additionally, grouped data frames from {dplyr} should be ungrouped before they are entered as data.

...

Arguments passed on to ggwithinstats

point.path,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,point.path.args

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

boxplot.args

A list of additional aesthetic arguments passed on to geom_boxplot.

xlab

Label for x axis variable. If NULL (default), variable name for x will be used.

ylab

Labels for y axis variable. If NULL (default), variable name for y will be used.

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 pairwise_comparisons function. For more details about pairwise comparisons, see the documentation for that function.

p.adjust.method

Adjustment method for p-values for multiple comparisons. Possible methods are: "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

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.

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.

subtitle

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

caption

The text for the plot caption. This argument is relevant only if bf.message = FALSE.

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.label.args

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

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).

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.

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.

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.

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).

centrality.point.args,centrality.label.args

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

ggsignif.args

A list of additional aesthetic arguments to be passed to ggsignif::geom_signif.

ggtheme

A {ggplot2} theme. Default value is ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well.

x

The grouping (or independent) variable from data. In case of a repeated measures or within-subjects design, if subject.id argument is not available or not explicitly specified, the function assumes that the data has already been sorted by such an id by the user and creates an internal identifier. So if your data is not sorted, the results can be inaccurate when there are more than two levels in x and there are NAs present. The data is expected to be sorted by user in subject-1,subject-2, ..., pattern.

y

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

type

A character specifying the type of statistical approach:

  • "parametric"

  • "nonparametric"

  • "robust"

  • "bayes"

You can specify just the initial letter.

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).

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 and posterior estimates. In addition to numeric arguments, several named values are also recognized: "medium", "wide", and "ultrawide", corresponding to r scale values of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value corresponds to scale for fixed effects.

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.

nboot

Number of bootstrap samples for computing confidence interval for the effect size (Default: 100L).

grouping.var

A single grouping variable.

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.

See Also

ggwithinstats, ggbetweenstats, grouped_ggbetweenstats

Examples


if (require("PMCMRplus")) {
  # to get reproducible results from bootstrapping
  set.seed(123)
  library(ggstatsplot)
  library(dplyr, warn.conflicts = FALSE)
  library(ggplot2)

  # the most basic function call
  grouped_ggwithinstats(
    data             = filter(bugs_long, condition %in% c("HDHF", "HDLF")),
    x                = condition,
    y                = desire,
    grouping.var     = gender,
    type             = "np", # non-parametric test
    # additional modifications for **each** plot using `{ggplot2}` functions
    ggplot.component = scale_y_continuous(breaks = seq(0, 10, 1), limits = c(0, 10))
  )
}


ggstatsplot documentation built on May 21, 2022, 5:05 p.m.