diff --git a/R/combine-plots.R b/R/combine-plots.R index bcaa772d5..87de9b46a 100644 --- a/R/combine-plots.R +++ b/R/combine-plots.R @@ -3,8 +3,8 @@ #' #' @description #' -#' Wrapper around `patchwork::wrap_plots()` that will return a combined grid of -#' plots with annotations. In case you want to create a grid of plots, it is +#' Wrapper around [`patchwork::wrap_plots()`] that will return a combined grid +#' of plots with annotations. In case you want to create a grid of plots, it is #' **highly recommended** that you use `{patchwork}` package directly and not #' this wrapper around it which is mostly useful with `{ggstatsplot}` plots. It #' is exported only for backward compatibility. @@ -13,10 +13,10 @@ #' #' @param plotlist A list containing `ggplot` objects. #' @param plotgrid.args A `list` of additional arguments passed to -#' `patchwork::wrap_plots()`, except for `guides` argument which is already +#' [`patchwork::wrap_plots()`], except for `guides` argument which is already #' separately specified here. #' @param annotation.args A `list` of additional arguments passed to -#' `patchwork::plot_annotation()`. +#' [`patchwork::plot_annotation()`]. #' @param ... Currently ignored. #' @inheritParams patchwork::wrap_plots #' diff --git a/R/data.R b/R/data.R index 751e8fb8e..fd81c052b 100644 --- a/R/data.R +++ b/R/data.R @@ -66,7 +66,8 @@ #' - id. Dummy identity number for each flower (150 flowers in total). #' - Species. The species are *Iris setosa*, *versicolor*, and *virginica*. #' - condition. Factor giving a detailed description of the attribute -#' (Four levels: `"Petal.Length"`, `"Petal.Width"`, `"Sepal.Length"`, `"Sepal.Width"`). +#' (Four levels: `"Petal.Length"`, `"Petal.Width"`, `"Sepal.Length"`, +#' `"Sepal.Width"`). #' - attribute. What attribute is being measured (`"Sepal"` or `"Pepal"`). #' - measure. What aspect of the attribute is being measured (`"Length"` or `"Width"`). #' - value. Value of the measurement. diff --git a/R/extract-stats.R b/R/extract-stats.R index 5e568a96a..9c77cf2b8 100644 --- a/R/extract-stats.R +++ b/R/extract-stats.R @@ -12,7 +12,7 @@ #' #' The only exception is the `ggcorrmat()` function. But, if a data frame is #' what you want, you shouldn't be using `ggcorrmat()` anyway. You can use -#' `correlation::correlation()` function which provides tidy data frames by +#' [`correlation::correlation()`] function which provides tidy data frames by #' default. #' #' @returns diff --git a/R/ggbarstats.R b/R/ggbarstats.R index eb33746c4..b6084c65e 100644 --- a/R/ggbarstats.R +++ b/R/ggbarstats.R @@ -13,8 +13,8 @@ #' #' @inheritParams ggpiestats #' @inheritParams ggbetweenstats -#' @param sample.size.label.args Additional aesthetic arguments that will be passed to -#' `ggplot2::geom_text()`. +#' @param sample.size.label.args Additional aesthetic arguments that will be +#' passed to [`ggplot2::geom_text()`]. #' #' @inheritSection statsExpressions::contingency_table Contingency table analyses #' diff --git a/R/ggbetweenstats-helpers.R b/R/ggbetweenstats-helpers.R index e03340a60..399f3dcef 100644 --- a/R/ggbetweenstats-helpers.R +++ b/R/ggbetweenstats-helpers.R @@ -83,7 +83,7 @@ #' @param ... Currently ignored. #' @param plot A `ggplot` object on which `geom_signif` needed to be added. #' @param mpc_df A data frame containing results from pairwise comparisons -#' (produced by `pairwise_comparisons()` function). +#' (produced by [`pairwise_comparisons()`] function). #' @inheritParams ggbetweenstats #' #' @autoglobal diff --git a/R/ggbetweenstats.R b/R/ggbetweenstats.R index b881306b1..7ffd80a23 100644 --- a/R/ggbetweenstats.R +++ b/R/ggbetweenstats.R @@ -61,11 +61,11 @@ #' #' Just as `type` argument, abbreviations are also accepted. #' @param point.args A list of additional aesthetic arguments to be passed to -#' the `ggplot2::geom_point()` displaying the raw data. +#' the [`ggplot2::geom_point()`]. #' @param boxplot.args A list of additional aesthetic arguments passed on to -#' `ggplot2::geom_boxplot()`. +#' [`ggplot2::geom_boxplot()`]. #' @param violin.args A list of additional aesthetic arguments to be passed to -#' the `ggplot2::geom_violin()`. +#' the [`ggplot2::geom_violin()`]. #' @param 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 @@ -76,18 +76,18 @@ #' @param ... Currently ignored. #' @inheritParams theme_ggstatsplot #' @param centrality.point.args,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. +#' arguments to be passed to [`ggplot2::geom_point()`] and +#' [`ggrepel::geom_label_repel()`] geoms, which are involved in mean plotting. #' @param ggsignif.args A list of additional aesthetic -#' arguments to be passed to `ggsignif::geom_signif`. +#' arguments to be passed to [`ggsignif::geom_signif()`]. #' @param 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. +#' [`ggstatsplot::theme_ggstatsplot()`]. Any of the `{ggplot2}` themes (e.g., +#' [`ggplot2::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. #' @inheritParams statsExpressions::oneway_anova diff --git a/R/ggcoefstats.R b/R/ggcoefstats.R index 7af6eda6d..2fc9e9eb2 100644 --- a/R/ggcoefstats.R +++ b/R/ggcoefstats.R @@ -13,14 +13,14 @@ #' ``` #' #' @param x A model object to be tidied, or a tidy data frame from a regression -#' model. Function internally uses `parameters::model_parameters()` to get a +#' model. Function internally uses [`parameters::model_parameters()`] to get a #' tidy data frame. If a data frame, it *must* contain at the minimum two #' columns named `term` (names of predictors) and `estimate` (corresponding #' estimates of coefficients or other quantities of interest). #' @param statistic Relevant statistic for the model (`"t"`, `"f"`, `"z"`, or #' `"chi"`) in the label. Relevant only if `x` is a *data frame*. #' @param effectsize.type This is the same as `es_type` argument of -#' `parameters::model_parameters()`. Defaults to `"eta"`, and relevant for +#' [`parameters::model_parameters()`]. Defaults to `"eta"`, and relevant for #' ANOVA-like objects. #' @param bf.message Logical that decides whether results from running a #' Bayesian meta-analysis assuming that the effect size *d* varies across @@ -28,9 +28,6 @@ #' should be displayed in caption. Defaults to `TRUE`. #' @param subtitle The text for the plot subtitle. The input to this argument #' will be ignored if `meta.analytic.effect` is set to `TRUE`. -#' @param point.args Additional arguments that will be passed to -#' `geom_point` geom. Please see documentation for that function to -#' know more about these arguments. #' @param conf.int Logical. Decides whether to display confidence intervals as #' error bars (Default: `TRUE`). #' @param conf.level Numeric deciding level of confidence or credible intervals @@ -41,13 +38,13 @@ #' relevant if a data frame with estimates and their standard errors is #' entered. #' @param meta.type Type of statistics used to carry out random-effects -#' meta-analysis. If `"parametric"` (default), `metafor::rma` function will be -#' used. If `"robust"`, `metaplus::metaplus` function will be used. If -#' `"bayes"`, `metaBMA::meta_random` function will be used. +#' meta-analysis. If `"parametric"` (default), [`metafor::rma()`] will be +#' used. If `"robust"`, [`metaplus::metaplus()`] will be used. If `"bayes"`, +#' [`metaBMA::meta_random()`] will be used. #' @param exclude.intercept Logical that decides whether the intercept should be #' excluded from the plot (Default: `FALSE`). #' @param errorbar.args Additional arguments that will be passed to -#' `geom_errorbarh` geom. Please see documentation for that function +#' `geom_errorbarh()` geom. Please see documentation for that function #' to know more about these arguments. #' @param vline Decides whether to display a vertical line (Default: `"TRUE"`). #' @param vline.args Additional arguments that will be passed to @@ -58,18 +55,17 @@ #' coefficient value. #' @param stats.labels Logical. Decides whether the statistic and *p*-values for #' each coefficient are to be attached to each dot as a text label using -#' `ggrepel` (Default: `TRUE`). +#' `{ggrepel}` (Default: `TRUE`). #' @param stats.label.color Color for the labels. If set to `NULL`, colors will #' be chosen from the specified `package` (Default: `"RColorBrewer"`) and #' `palette` (Default: `"Dark2"`). #' @param stats.label.args Additional arguments that will be passed to -#' `ggrepel::geom_label_repel()`. Please see documentation for that -#' function to know more about these arguments. +#' [`ggrepel::geom_label_repel()`]. #' @param only.significant If `TRUE`, only stats labels for significant effects #' is shown (Default: `FALSE`). This can be helpful when a large number of #' regression coefficients are to be displayed in a single plot. #' @param ... Additional arguments to tidying method. For more, see -#' `parameters::model_parameters`. +#' [`parameters::model_parameters()`]. #' @inheritParams parameters::model_parameters #' @inheritParams theme_ggstatsplot #' @inheritParams statsExpressions::meta_analysis diff --git a/R/ggcorrmat.R b/R/ggcorrmat.R index d581a7d1a..cd0108c83 100644 --- a/R/ggcorrmat.R +++ b/R/ggcorrmat.R @@ -4,8 +4,8 @@ #' @description #' Correlation matrix containing results from pairwise correlation tests. #' If you want a data frame of (grouped) correlation matrix, use -#' `correlation::correlation()` instead. It can also do grouped analysis when -#' used with output from `dplyr::group_by()`. +#' [`correlation::correlation()`] instead. It can also do grouped analysis when +#' used with output from [`dplyr::group_by()`]. #' #' @section Summary of graphics: #' @@ -34,10 +34,10 @@ #' @param pch Decides the point shape to be used for insignificant correlation #' coefficients (only valid when `insig = "pch"`). Default: `pch = "cross"`. #' @param ggcorrplot.args A list of additional (mostly aesthetic) arguments that -#' will be passed to `ggcorrplot::ggcorrplot()` function. The list should avoid -#' any of the following arguments since they are already internally being -#' used: `corr`, `method`, `p.mat`, `sig.level`, `ggtheme`, `colors`, `lab`, -#' `pch`, `legend.title`, `digits`. +#' will be passed to [`ggcorrplot::ggcorrplot()`] function. The list should +#' avoid any of the following arguments since they are already internally +#' being used: `corr`, `method`, `p.mat`, `sig.level`, `ggtheme`, `colors`, +#' `lab`, `pch`, `legend.title`, `digits`. #' @inheritParams statsExpressions::corr_test #' @inheritParams ggbetweenstats #' @inheritParams theme_ggstatsplot diff --git a/R/ggdotplotstats.R b/R/ggdotplotstats.R index 859b1fa3f..711fd56a5 100644 --- a/R/ggdotplotstats.R +++ b/R/ggdotplotstats.R @@ -13,10 +13,9 @@ #' #' @param ... Currently ignored. #' @param y Label or grouping variable. -#' @param point.args A list of additional aesthetic arguments passed to -#' `geom_point`. #' @inheritParams gghistostats #' @inheritParams ggcoefstats +#' @inheritParams ggbetweenstats #' #' @inheritSection statsExpressions::one_sample_test One-sample tests #' diff --git a/R/gghistostats.R b/R/gghistostats.R index 2d2740c62..44a1c5d01 100644 --- a/R/gghistostats.R +++ b/R/gghistostats.R @@ -21,8 +21,8 @@ #' `stat_bin` used to display the bins. Do not specify `binwidth` argument in #' this list since it has already been specified using the dedicated argument. #' @param centrality.line.args A list of additional aesthetic arguments to be -#' passed to the `geom_line` used to display the lines corresponding to the -#' centrality parameter. +#' passed to the [`ggplot2::geom_line()`] used to display the lines +#' corresponding to the centrality parameter. #' @inheritParams statsExpressions::one_sample_test #' @inheritParams ggbetweenstats #' diff --git a/R/ggpiestats-ggbarstats-helpers.R b/R/ggpiestats-ggbarstats-helpers.R index acc27ee08..d31d59a8e 100644 --- a/R/ggpiestats-ggbarstats-helpers.R +++ b/R/ggpiestats-ggbarstats-helpers.R @@ -54,7 +54,7 @@ onesample_data <- function(data, x, y, digits = 2L, ratio = NULL, ...) { #' Safer version of chi-squared test that returns `NA`s -#' Needed to work with `group_modify()` since it will not work when `NULL` is returned +#' Needed to work with `dplyr::group_modify()` since it will not work when `NULL` is returned. #' @autoglobal #' @noRd .chisq_test_safe <- function(data, x, ratio) { diff --git a/R/ggpiestats.R b/R/ggpiestats.R index 21883e52f..544f5bc3c 100644 --- a/R/ggpiestats.R +++ b/R/ggpiestats.R @@ -18,19 +18,19 @@ #' will be dropped. Default is `NULL`. If `NULL`, one-sample proportion test #' (a goodness of fit test) will be run for the `x` variable. Otherwise an #' appropriate association test will be run. This argument can not be `NULL` -#' for `ggbarstats` function. +#' for [`ggbarstats()`]. #' @param proportion.test Decides whether proportion test for `x` variable is to #' be carried out for each level of `y`. Defaults to `results.subtitle`. In -#' `ggbarstats`, only *p*-values from this test will be displayed. -#' @param digits.perc Numeric that decides number of decimal places for percentage -#' labels (Default: `0L`). +#' [`ggbarstats()`], only *p*-values from this test will be displayed. +#' @param digits.perc Numeric that decides number of decimal places for +#' percentage labels (Default: `0L`). #' @param label Character decides what information needs to be displayed #' on the label in each pie slice. Possible options are `"percentage"` #' (default), `"counts"`, `"both"`. #' @param label.args Additional aesthetic arguments that will be passed to -#' `ggplot2::geom_label()`. -#' @param label.repel Whether labels should be repelled using `{ggrepel}` package. -#' This can be helpful in case the labels are overlapping. +#' [`ggplot2::geom_label()`]. +#' @param label.repel Whether labels should be repelled using `{ggrepel}` +#' package. This can be helpful in case of overlapping labels. #' @param legend.title Title text for the legend. #' @inheritParams ggbetweenstats #' @inheritParams statsExpressions::contingency_table diff --git a/R/ggscatterstats.R b/R/ggscatterstats.R index 59bcebe34..217ddb6f7 100644 --- a/R/ggscatterstats.R +++ b/R/ggscatterstats.R @@ -16,17 +16,15 @@ #' `var1`). #' @param label.expression An expression evaluating to a logical vector that #' determines the subset of data points to label (e.g. `y < 4 & z < 20`). -#' While using this argument with `purrr::pmap()`, you will have to provide a -#' quoted expression (e.g. `quote(y < 4 & z < 20)`). +#' While using this argument with [`purrr::pmap()`], you will have to provide +#' a quoted expression (e.g. `quote(y < 4 & z < 20)`). #' @param point.label.args A list of additional aesthetic arguments to be passed -#' to `ggrepel::geom_label_repel` geom used to display the labels. +#' to [`ggrepel::geom_label_repel()`]geom used to display the labels. #' @param smooth.line.args A list of additional aesthetic arguments to be passed #' to `geom_smooth` geom used to display the regression line. -#' @param point.args A list of additional aesthetic arguments to be passed -#' to `geom_point` geom used to display the raw data points. #' @param marginal Decides whether marginal distributions will be plotted on -#' axes using `ggside` functions. The default is `TRUE`. The package -#' `ggside` must already be installed by the user. +#' axes using `{ggside}` functions. The default is `TRUE`. The package +#' `{ggside}` must already be installed by the user. #' @param point.width.jitter,point.height.jitter Degree of jitter in `x` and `y` #' direction, respectively. Defaults to `0` (0%) of the resolution of the #' data. Note that the jitter should not be specified in the `point.args` @@ -52,7 +50,7 @@ #' #' #' @note -#' The plot uses `ggrepel::geom_label_repel()` to attempt to keep labels +#' The plot uses [`ggrepel::geom_label_repel()`] to attempt to keep labels #' from over-lapping to the largest degree possible. As a consequence plot #' times will slow down massively (and the plot file will grow in size) if you #' have a lot of labels that overlap. @@ -130,7 +128,6 @@ ggscatterstats <- function( subtitle_df <- .eval_f(corr_test, !!!.f.args, type = type) subtitle <- .extract_expression(subtitle_df) - # BF message for null hypothesis support if (type == "parametric" && bf.message) { caption_df <- .eval_f(corr_test, !!!.f.args, type = "bayes") caption <- .extract_expression(caption_df) @@ -139,10 +136,8 @@ ggscatterstats <- function( # basic plot ------------------------------------------ - # creating jittered positions pos <- position_jitter(width = point.width.jitter, height = point.height.jitter) - # scatterplot plot_scatter <- ggplot(data, mapping = aes({{ x }}, {{ y }})) + exec(geom_point, position = pos, !!!point.args) + exec(geom_smooth, level = conf.level, !!!smooth.line.args, na.rm = TRUE) diff --git a/R/ggstatsplot-package.R b/R/ggstatsplot-package.R index f8f1e0a9a..727c3f63d 100644 --- a/R/ggstatsplot-package.R +++ b/R/ggstatsplot-package.R @@ -48,7 +48,7 @@ #' - `ggcoefstats()` function to visualize results from regression analyses. #' #' - `combine_plots()` helper function to combine multiple `{ggstatsplot}` -#' plots using `patchwork::wrap_plots()`. +#' plots using [`patchwork::wrap_plots()`]. #' #' References: Patil (2021) \doi{10.21105/joss.03236}. #' diff --git a/R/ggwithinstats.R b/R/ggwithinstats.R index 7da2cf978..c8bea260e 100644 --- a/R/ggwithinstats.R +++ b/R/ggwithinstats.R @@ -15,12 +15,12 @@ #' @inheritParams ggbetweenstats #' @param point.path,centrality.path Logical that decides whether individual #' data points and means, respectively, should be connected using -#' `ggplot2::geom_path()`. Both default to `TRUE`. Note that `point.path` +#' [`ggplot2::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. #' @param centrality.path.args,point.path.args A list of additional aesthetic -#' arguments passed on to `ggplot2::geom_path()` connecting raw data points +#' arguments passed on to [`ggplot2::geom_path()`] connecting raw data points #' and mean points. #' @inheritParams statsExpressions::oneway_anova #' diff --git a/R/theme-ggstatsplot.R b/R/theme-ggstatsplot.R index db3ce5d43..58e1b7b34 100644 --- a/R/theme-ggstatsplot.R +++ b/R/theme-ggstatsplot.R @@ -3,13 +3,13 @@ #' @description #' #' Common theme used across all plots generated in `{ggstatsplot}` and *assumed* -#' by the author to be aesthetically pleasing to the user/reader. The theme is a -#' wrapper around `theme_bw()`. +#' by the author to be aesthetically pleasing to the user. The theme is a +#' wrapper around [`ggplot2::theme_bw()`]. #' #' All `{ggstatsplot}` functions have a `ggtheme` parameter that let you choose #' a different theme. #' -#' @returns A `ggplot` object with the `theme_ggstatsplot` theme overlaid. +#' @returns A `ggplot` object. #' #' @examples #' library(ggplot2) diff --git a/man/combine_plots.Rd b/man/combine_plots.Rd index 62006ac4d..ed56d7580 100644 --- a/man/combine_plots.Rd +++ b/man/combine_plots.Rd @@ -16,11 +16,11 @@ combine_plots( \item{plotlist}{A list containing \code{ggplot} objects.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} \item{guides}{A string specifying how guides should be treated in the layout. \code{'collect'} will collect guides below to the given nesting level, removing @@ -37,8 +37,8 @@ patchwork (see example).} A combined plot with annotation labels. } \description{ -Wrapper around \code{patchwork::wrap_plots()} that will return a combined grid of -plots with annotations. In case you want to create a grid of plots, it is +Wrapper around \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}} that will return a combined grid +of plots with annotations. In case you want to create a grid of plots, it is \strong{highly recommended} that you use \code{{patchwork}} package directly and not this wrapper around it which is mostly useful with \code{{ggstatsplot}} plots. It is exported only for backward compatibility. diff --git a/man/extract_stats.Rd b/man/extract_stats.Rd index a6125423a..cf45175f2 100644 --- a/man/extract_stats.Rd +++ b/man/extract_stats.Rd @@ -33,7 +33,7 @@ using that package. The only exception is the \code{ggcorrmat()} function. But, if a data frame is what you want, you shouldn't be using \code{ggcorrmat()} anyway. You can use -\code{correlation::correlation()} function which provides tidy data frames by +\code{\link[correlation:correlation]{correlation::correlation()}} function which provides tidy data frames by default. } \examples{ diff --git a/man/ggbarstats.Rd b/man/ggbarstats.Rd index 58a61ddf2..3e5a8d760 100644 --- a/man/ggbarstats.Rd +++ b/man/ggbarstats.Rd @@ -52,7 +52,7 @@ Please note that if there are empty factor levels in your variable, they will be dropped. Default is \code{NULL}. If \code{NULL}, one-sample proportion test (a goodness of fit test) will be run for the \code{x} variable. Otherwise an appropriate association test will be run. This argument can not be \code{NULL} -for \code{ggbarstats} function.} +for \code{\link[=ggbarstats]{ggbarstats()}}.} \item{counts}{The variable in data containing counts, or \code{NULL} if each row represents a single observation.} @@ -79,10 +79,10 @@ on the label in each pie slice. Possible options are \code{"percentage"} (default), \code{"counts"}, \code{"both"}.} \item{label.args}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_label()}.} +\code{\link[ggplot2:geom_text]{ggplot2::geom_label()}}.} -\item{sample.size.label.args}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_text()}.} +\item{sample.size.label.args}{Additional aesthetic arguments that will be +passed to \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.} \item{digits}{Number of digits for rounding or significant figures. May also be \code{"signif"} to return significant figures or \code{"scientific"} @@ -93,10 +93,10 @@ significant figures (see also \code{\link[=signif]{signif()}}).} \item{proportion.test}{Decides whether proportion test for \code{x} variable is to be carried out for each level of \code{y}. Defaults to \code{results.subtitle}. In -\code{ggbarstats}, only \emph{p}-values from this test will be displayed.} +\code{\link[=ggbarstats]{ggbarstats()}}, only \emph{p}-values from this test will be displayed.} -\item{digits.perc}{Numeric that decides number of decimal places for percentage -labels (Default: \code{0L}).} +\item{digits.perc}{Numeric that decides number of decimal places for +percentage labels (Default: \code{0L}).} \item{bf.message}{Logical that decides whether to display Bayes Factor in favor of the \emph{null} hypothesis. This argument is relevant only \strong{for @@ -142,13 +142,13 @@ variable name for \code{x} will be used.} variable name for \code{y} will be used.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} diff --git a/man/ggbetweenstats.Rd b/man/ggbetweenstats.Rd index 7bb205153..a384c75cd 100644 --- a/man/ggbetweenstats.Rd +++ b/man/ggbetweenstats.Rd @@ -169,29 +169,29 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{centrality.point.args, centrality.label.args}{A list of additional aesthetic -arguments to be passed to \code{ggplot2::geom_point()} and -\code{ggrepel::geom_label_repel} geoms, which are involved in mean plotting.} +arguments to be passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} and +\code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}} geoms, which are involved in mean plotting.} \item{point.args}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_point()} displaying the raw data.} +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{boxplot.args}{A list of additional aesthetic arguments passed on to -\code{ggplot2::geom_boxplot()}.} +\code{\link[ggplot2:geom_boxplot]{ggplot2::geom_boxplot()}}.} \item{violin.args}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_violin()}.} +the \code{\link[ggplot2:geom_violin]{ggplot2::geom_violin()}}.} \item{ggsignif.args}{A list of additional aesthetic -arguments to be passed to \code{ggsignif::geom_signif}.} +arguments to be passed to \code{\link[ggsignif:stat_signif]{ggsignif::geom_signif()}}.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} diff --git a/man/ggcoefstats.Rd b/man/ggcoefstats.Rd index 1cad8bafe..23241e02a 100644 --- a/man/ggcoefstats.Rd +++ b/man/ggcoefstats.Rd @@ -38,7 +38,7 @@ ggcoefstats( } \arguments{ \item{x}{A model object to be tidied, or a tidy data frame from a regression -model. Function internally uses \code{parameters::model_parameters()} to get a +model. Function internally uses \code{\link[parameters:model_parameters]{parameters::model_parameters()}} to get a tidy data frame. If a data frame, it \emph{must} contain at the minimum two columns named \code{term} (names of predictors) and \code{estimate} (corresponding estimates of coefficients or other quantities of interest).} @@ -63,7 +63,7 @@ significant figures (see also \code{\link[=signif]{signif()}}).} excluded from the plot (Default: \code{FALSE}).} \item{effectsize.type}{This is the same as \code{es_type} argument of -\code{parameters::model_parameters()}. Defaults to \code{"eta"}, and relevant for +\code{\link[parameters:model_parameters]{parameters::model_parameters()}}. Defaults to \code{"eta"}, and relevant for ANOVA-like objects.} \item{meta.analytic.effect}{Logical that decides whether subtitle for @@ -73,9 +73,9 @@ relevant if a data frame with estimates and their standard errors is entered.} \item{meta.type}{Type of statistics used to carry out random-effects -meta-analysis. If \code{"parametric"} (default), \code{metafor::rma} function will be -used. If \code{"robust"}, \code{metaplus::metaplus} function will be used. If -\code{"bayes"}, \code{metaBMA::meta_random} function will be used.} +meta-analysis. If \code{"parametric"} (default), \code{\link[metafor:rma.uni]{metafor::rma()}} will be +used. If \code{"robust"}, \code{\link[metaplus:metaplus]{metaplus::metaplus()}} will be used. If \code{"bayes"}, +\code{\link[metaBMA:meta_random]{metaBMA::meta_random()}} will be used.} \item{bf.message}{Logical that decides whether results from running a Bayesian meta-analysis assuming that the effect size \emph{d} varies across @@ -104,12 +104,11 @@ if \code{bf.message = FALSE}.} is shown (Default: \code{FALSE}). This can be helpful when a large number of regression coefficients are to be displayed in a single plot.} -\item{point.args}{Additional arguments that will be passed to -\code{geom_point} geom. Please see documentation for that function to -know more about these arguments.} +\item{point.args}{A list of additional aesthetic arguments to be passed to +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{errorbar.args}{Additional arguments that will be passed to -\code{geom_errorbarh} geom. Please see documentation for that function +\code{geom_errorbarh()} geom. Please see documentation for that function to know more about these arguments.} \item{vline}{Decides whether to display a vertical line (Default: \code{"TRUE"}).} @@ -120,33 +119,32 @@ know more about these arguments.} \item{stats.labels}{Logical. Decides whether the statistic and \emph{p}-values for each coefficient are to be attached to each dot as a text label using -\code{ggrepel} (Default: \code{TRUE}).} +\code{{ggrepel}} (Default: \code{TRUE}).} \item{stats.label.color}{Color for the labels. If set to \code{NULL}, colors will be chosen from the specified \code{package} (Default: \code{"RColorBrewer"}) and \code{palette} (Default: \code{"Dark2"}).} \item{stats.label.args}{Additional arguments that will be passed to -\code{ggrepel::geom_label_repel()}. Please see documentation for that -function to know more about these arguments.} +\code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}}.} \item{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 \code{View(paletteer::palettes_d_names)}.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{...}{Additional arguments to tidying method. For more, see -\code{parameters::model_parameters}.} +\code{\link[parameters:model_parameters]{parameters::model_parameters()}}.} } \description{ Plot with the regression coefficients' point estimates as dots with diff --git a/man/ggcorrmat.Rd b/man/ggcorrmat.Rd index 9fd4205cf..9329e0b3b 100644 --- a/man/ggcorrmat.Rd +++ b/man/ggcorrmat.Rd @@ -92,10 +92,10 @@ comparisons. Possible methods are: \code{"holm"} (default), \code{"hochberg"}, coefficients (only valid when \code{insig = "pch"}). Default: \code{pch = "cross"}.} \item{ggcorrplot.args}{A list of additional (mostly aesthetic) arguments that -will be passed to \code{ggcorrplot::ggcorrplot()} function. The list should avoid -any of the following arguments since they are already internally being -used: \code{corr}, \code{method}, \code{p.mat}, \code{sig.level}, \code{ggtheme}, \code{colors}, \code{lab}, -\code{pch}, \code{legend.title}, \code{digits}.} +will be passed to \code{\link[ggcorrplot:ggcorrplot]{ggcorrplot::ggcorrplot()}} function. The list should +avoid any of the following arguments since they are already internally +being used: \code{corr}, \code{method}, \code{p.mat}, \code{sig.level}, \code{ggtheme}, \code{colors}, +\code{lab}, \code{pch}, \code{legend.title}, \code{digits}.} \item{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 @@ -106,13 +106,13 @@ If set to \code{NULL}, manual specification of colors will be turned off and 3 colors from the specified \code{palette} from \code{package} will be selected.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} @@ -134,8 +134,8 @@ if \code{bf.message = FALSE}.} \description{ Correlation matrix containing results from pairwise correlation tests. If you want a data frame of (grouped) correlation matrix, use -\code{correlation::correlation()} instead. It can also do grouped analysis when -used with output from \code{dplyr::group_by()}. +\code{\link[correlation:correlation]{correlation::correlation()}} instead. It can also do grouped analysis when +used with output from \code{\link[dplyr:group_by]{dplyr::group_by()}}. } \details{ For details, see: diff --git a/man/ggdotplotstats.Rd b/man/ggdotplotstats.Rd index 80333589f..a04cf0b78 100644 --- a/man/ggdotplotstats.Rd +++ b/man/ggdotplotstats.Rd @@ -101,8 +101,8 @@ significant figures (see also \code{\link[=signif]{signif()}}).} to be displayed as a subtitle (Default: \code{TRUE}). If set to \code{FALSE}, only the plot will be returned.} -\item{point.args}{A list of additional aesthetic arguments passed to -\code{geom_point}.} +\item{point.args}{A list of additional aesthetic arguments to be passed to +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{centrality.plotting}{Logical that decides whether centrality tendency measure is to be displayed as a point with a label (Default: \code{TRUE}). @@ -131,8 +131,8 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{centrality.line.args}{A list of additional aesthetic arguments to be -passed to the \code{geom_line} used to display the lines corresponding to the -centrality parameter.} +passed to the \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} used to display the lines +corresponding to the centrality parameter.} \item{ggplot.component}{A \code{ggplot} component to be added to the plot prepared by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} @@ -140,13 +140,13 @@ variants of all primary functions. Default is \code{NULL}. The argument should be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} functions.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} diff --git a/man/gghistostats.Rd b/man/gghistostats.Rd index aa5d02b70..72324ce91 100644 --- a/man/gghistostats.Rd +++ b/man/gghistostats.Rd @@ -98,13 +98,13 @@ notation with 4 decimal places, or \code{digits = "signif5"} for 5 significant figures (see also \code{\link[=signif]{signif()}}).} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} @@ -143,8 +143,8 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{centrality.line.args}{A list of additional aesthetic arguments to be -passed to the \code{geom_line} used to display the lines corresponding to the -centrality parameter.} +passed to the \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} used to display the lines +corresponding to the centrality parameter.} \item{ggplot.component}{A \code{ggplot} component to be added to the plot prepared by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} diff --git a/man/ggpiestats.Rd b/man/ggpiestats.Rd index 3851298b8..224c05f46 100644 --- a/man/ggpiestats.Rd +++ b/man/ggpiestats.Rd @@ -50,7 +50,7 @@ Please note that if there are empty factor levels in your variable, they will be dropped. Default is \code{NULL}. If \code{NULL}, one-sample proportion test (a goodness of fit test) will be run for the \code{x} variable. Otherwise an appropriate association test will be run. This argument can not be \code{NULL} -for \code{ggbarstats} function.} +for \code{\link[=ggbarstats]{ggbarstats()}}.} \item{counts}{The variable in data containing counts, or \code{NULL} if each row represents a single observation.} @@ -77,10 +77,10 @@ on the label in each pie slice. Possible options are \code{"percentage"} (default), \code{"counts"}, \code{"both"}.} \item{label.args}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_label()}.} +\code{\link[ggplot2:geom_text]{ggplot2::geom_label()}}.} -\item{label.repel}{Whether labels should be repelled using \code{{ggrepel}} package. -This can be helpful in case the labels are overlapping.} +\item{label.repel}{Whether labels should be repelled using \code{{ggrepel}} +package. This can be helpful in case of overlapping labels.} \item{digits}{Number of digits for rounding or significant figures. May also be \code{"signif"} to return significant figures or \code{"scientific"} @@ -91,10 +91,10 @@ significant figures (see also \code{\link[=signif]{signif()}}).} \item{proportion.test}{Decides whether proportion test for \code{x} variable is to be carried out for each level of \code{y}. Defaults to \code{results.subtitle}. In -\code{ggbarstats}, only \emph{p}-values from this test will be displayed.} +\code{\link[=ggbarstats]{ggbarstats()}}, only \emph{p}-values from this test will be displayed.} -\item{digits.perc}{Numeric that decides number of decimal places for percentage -labels (Default: \code{0L}).} +\item{digits.perc}{Numeric that decides number of decimal places for +percentage labels (Default: \code{0L}).} \item{bf.message}{Logical that decides whether to display Bayes Factor in favor of the \emph{null} hypothesis. This argument is relevant only \strong{for @@ -134,13 +134,13 @@ if \code{bf.message = FALSE}.} \item{legend.title}{Title text for the legend.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} diff --git a/man/ggscatterstats.Rd b/man/ggscatterstats.Rd index de1f0a500..33aab92ba 100644 --- a/man/ggscatterstats.Rd +++ b/man/ggscatterstats.Rd @@ -93,15 +93,15 @@ the plot will be returned.} \item{label.expression}{An expression evaluating to a logical vector that determines the subset of data points to label (e.g. \code{y < 4 & z < 20}). -While using this argument with \code{purrr::pmap()}, you will have to provide a -quoted expression (e.g. \code{quote(y < 4 & z < 20)}).} +While using this argument with \code{\link[purrr:pmap]{purrr::pmap()}}, you will have to provide +a quoted expression (e.g. \code{quote(y < 4 & z < 20)}).} \item{marginal}{Decides whether marginal distributions will be plotted on -axes using \code{ggside} functions. The default is \code{TRUE}. The package -\code{ggside} must already be installed by the user.} +axes using \code{{ggside}} functions. The default is \code{TRUE}. The package +\code{{ggside}} must already be installed by the user.} -\item{point.args}{A list of additional aesthetic arguments to be passed -to \code{geom_point} geom used to display the raw data points.} +\item{point.args}{A list of additional aesthetic arguments to be passed to +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{point.width.jitter, point.height.jitter}{Degree of jitter in \code{x} and \code{y} direction, respectively. Defaults to \code{0} (0\%) of the resolution of the @@ -111,7 +111,7 @@ displaying the \strong{points} and the other displaying the *\strong{labels} for these points.} \item{point.label.args}{A list of additional aesthetic arguments to be passed -to \code{ggrepel::geom_label_repel} geom used to display the labels.} +to \code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}}geom used to display the labels.} \item{smooth.line.args}{A list of additional aesthetic arguments to be passed to \code{geom_smooth} geom used to display the regression line.} @@ -135,13 +135,13 @@ variable name for \code{y} will be used.} if \code{bf.message = FALSE}.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} @@ -161,7 +161,7 @@ For details, see: \url{https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html} } \note{ -The plot uses \code{ggrepel::geom_label_repel()} to attempt to keep labels +The plot uses \code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}} to attempt to keep labels from over-lapping to the largest degree possible. As a consequence plot times will slow down massively (and the plot file will grow in size) if you have a lot of labels that overlap. diff --git a/man/ggstatsplot-package.Rd b/man/ggstatsplot-package.Rd index 0d3c957b9..0b55e3ee9 100644 --- a/man/ggstatsplot-package.Rd +++ b/man/ggstatsplot-package.Rd @@ -42,7 +42,7 @@ displayed in the subtitle. \item \code{ggcorrmat()} function to visualize the correlation matrix. \item \code{ggcoefstats()} function to visualize results from regression analyses. \item \code{combine_plots()} helper function to combine multiple \code{{ggstatsplot}} -plots using \code{patchwork::wrap_plots()}. +plots using \code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}. } References: Patil (2021) \doi{10.21105/joss.03236}. diff --git a/man/ggwithinstats.Rd b/man/ggwithinstats.Rd index 8d10dc446..6e34c75d2 100644 --- a/man/ggwithinstats.Rd +++ b/man/ggwithinstats.Rd @@ -165,40 +165,40 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{centrality.point.args, centrality.label.args}{A list of additional aesthetic -arguments to be passed to \code{ggplot2::geom_point()} and -\code{ggrepel::geom_label_repel} geoms, which are involved in mean plotting.} +arguments to be passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} and +\code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}} geoms, which are involved in mean plotting.} \item{centrality.path.args, point.path.args}{A list of additional aesthetic -arguments passed on to \code{ggplot2::geom_path()} connecting raw data points +arguments passed on to \code{\link[ggplot2:geom_path]{ggplot2::geom_path()}} connecting raw data points and mean points.} \item{point.args}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_point()} displaying the raw data.} +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{point.path, centrality.path}{Logical that decides whether individual data points and means, respectively, should be connected using -\code{ggplot2::geom_path()}. Both default to \code{TRUE}. Note that \code{point.path} +\code{\link[ggplot2:geom_path]{ggplot2::geom_path()}}. Both default to \code{TRUE}. Note that \code{point.path} argument is relevant only when there are two groups (i.e., in case of a \emph{t}-test). In case of large number of data points, it is advisable to set \code{point.path = FALSE} as these lines can overwhelm the plot.} \item{boxplot.args}{A list of additional aesthetic arguments passed on to -\code{ggplot2::geom_boxplot()}.} +\code{\link[ggplot2:geom_boxplot]{ggplot2::geom_boxplot()}}.} \item{violin.args}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_violin()}.} +the \code{\link[ggplot2:geom_violin]{ggplot2::geom_violin()}}.} \item{ggsignif.args}{A list of additional aesthetic -arguments to be passed to \code{ggsignif::geom_signif}.} +arguments to be passed to \code{\link[ggsignif:stat_signif]{ggsignif::geom_signif()}}.} \item{ggtheme}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} diff --git a/man/grouped_ggbarstats.Rd b/man/grouped_ggbarstats.Rd index 67ff0f11d..7985be016 100644 --- a/man/grouped_ggbarstats.Rd +++ b/man/grouped_ggbarstats.Rd @@ -21,8 +21,8 @@ ungrouped before they are entered as \code{data}.} \item{...}{ Arguments passed on to \code{\link[=ggbarstats]{ggbarstats}} \describe{ - \item{\code{sample.size.label.args}}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_text()}.} + \item{\code{sample.size.label.args}}{Additional aesthetic arguments that will be +passed to \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.} \item{\code{x}}{The variable to use as the \strong{rows} in the contingency table. Please note that if there are empty factor levels in your variable, they will be dropped.} @@ -31,17 +31,17 @@ Please note that if there are empty factor levels in your variable, they will be dropped. Default is \code{NULL}. If \code{NULL}, one-sample proportion test (a goodness of fit test) will be run for the \code{x} variable. Otherwise an appropriate association test will be run. This argument can not be \code{NULL} -for \code{ggbarstats} function.} +for \code{\link[=ggbarstats]{ggbarstats()}}.} \item{\code{proportion.test}}{Decides whether proportion test for \code{x} variable is to be carried out for each level of \code{y}. Defaults to \code{results.subtitle}. In -\code{ggbarstats}, only \emph{p}-values from this test will be displayed.} - \item{\code{digits.perc}}{Numeric that decides number of decimal places for percentage -labels (Default: \code{0L}).} +\code{\link[=ggbarstats]{ggbarstats()}}, only \emph{p}-values from this test will be displayed.} + \item{\code{digits.perc}}{Numeric that decides number of decimal places for +percentage labels (Default: \code{0L}).} \item{\code{label}}{Character decides what information needs to be displayed on the label in each pie slice. Possible options are \code{"percentage"} (default), \code{"counts"}, \code{"both"}.} \item{\code{label.args}}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_label()}.} +\code{\link[ggplot2:geom_text]{ggplot2::geom_label()}}.} \item{\code{legend.title}}{Title text for the legend.} \item{\code{bf.message}}{Logical that decides whether to display Bayes Factor in favor of the \emph{null} hypothesis. This argument is relevant only \strong{for @@ -61,13 +61,13 @@ be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} function be extracted. The available palettes and packages can be checked by running \code{View(paletteer::palettes_d_names)}.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{\code{type}}{A character specifying the type of statistical approach: @@ -116,11 +116,11 @@ variable name for \code{y} will be used.} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Helper function for \code{ggstatsplot::ggbarstats()} to apply this function across diff --git a/man/grouped_ggbetweenstats.Rd b/man/grouped_ggbetweenstats.Rd index f1ede1975..f77be1540 100644 --- a/man/grouped_ggbetweenstats.Rd +++ b/man/grouped_ggbetweenstats.Rd @@ -76,11 +76,11 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{\code{point.args}}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_point()} displaying the raw data.} +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{\code{boxplot.args}}{A list of additional aesthetic arguments passed on to -\code{ggplot2::geom_boxplot()}.} +\code{\link[ggplot2:geom_boxplot]{ggplot2::geom_boxplot()}}.} \item{\code{violin.args}}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_violin()}.} +the \code{\link[ggplot2:geom_violin]{ggplot2::geom_violin()}}.} \item{\code{ggplot.component}}{A \code{ggplot} component to be added to the plot prepared by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} variants of all primary functions. Default is \code{NULL}. The argument should @@ -89,18 +89,18 @@ be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} function be extracted. The available palettes and packages can be checked by running \code{View(paletteer::palettes_d_names)}.} \item{\code{centrality.point.args,centrality.label.args}}{A list of additional aesthetic -arguments to be passed to \code{ggplot2::geom_point()} and -\code{ggrepel::geom_label_repel} geoms, which are involved in mean plotting.} +arguments to be passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} and +\code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}} geoms, which are involved in mean plotting.} \item{\code{ggsignif.args}}{A list of additional aesthetic -arguments to be passed to \code{ggsignif::geom_signif}.} +arguments to be passed to \code{\link[ggsignif:stat_signif]{ggsignif::geom_signif()}}.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{\code{x}}{The grouping (or independent) variable from \code{data}. In case of a @@ -153,11 +153,11 @@ for the effect size (Default: \code{100L}).} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Helper function for \code{ggstatsplot::ggbetweenstats} to apply this function diff --git a/man/grouped_ggcorrmat.Rd b/man/grouped_ggcorrmat.Rd index af09b9338..d1b4bb24d 100644 --- a/man/grouped_ggcorrmat.Rd +++ b/man/grouped_ggcorrmat.Rd @@ -39,10 +39,10 @@ colors from the specified \code{palette} from \code{package} will be selected.} \item{\code{pch}}{Decides the point shape to be used for insignificant correlation coefficients (only valid when \code{insig = "pch"}). Default: \code{pch = "cross"}.} \item{\code{ggcorrplot.args}}{A list of additional (mostly aesthetic) arguments that -will be passed to \code{ggcorrplot::ggcorrplot()} function. The list should avoid -any of the following arguments since they are already internally being -used: \code{corr}, \code{method}, \code{p.mat}, \code{sig.level}, \code{ggtheme}, \code{colors}, \code{lab}, -\code{pch}, \code{legend.title}, \code{digits}.} +will be passed to \code{\link[ggcorrplot:ggcorrplot]{ggcorrplot::ggcorrplot()}} function. The list should +avoid any of the following arguments since they are already internally +being used: \code{corr}, \code{method}, \code{p.mat}, \code{sig.level}, \code{ggtheme}, \code{colors}, +\code{lab}, \code{pch}, \code{legend.title}, \code{digits}.} \item{\code{type}}{A character specifying the type of statistical approach: \itemize{ \item \code{"parametric"} @@ -85,13 +85,13 @@ be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} function be extracted. The available palettes and packages can be checked by running \code{View(paletteer::palettes_d_names)}.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} }} @@ -99,11 +99,11 @@ thus the details as well.} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Helper function for \code{ggstatsplot::ggcorrmat()} to apply this function across diff --git a/man/grouped_ggdotplotstats.Rd b/man/grouped_ggdotplotstats.Rd index 355abc844..d2e554783 100644 --- a/man/grouped_ggdotplotstats.Rd +++ b/man/grouped_ggdotplotstats.Rd @@ -22,11 +22,9 @@ ungrouped before they are entered as \code{data}.} Arguments passed on to \code{\link[=ggdotplotstats]{ggdotplotstats}} \describe{ \item{\code{y}}{Label or grouping variable.} - \item{\code{point.args}}{A list of additional aesthetic arguments passed to -\code{geom_point}.} \item{\code{centrality.line.args}}{A list of additional aesthetic arguments to be -passed to the \code{geom_line} used to display the lines corresponding to the -centrality parameter.} +passed to the \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} used to display the lines +corresponding to the centrality parameter.} \item{\code{x}}{A numeric variable from the data frame \code{data}.} \item{\code{type}}{A character specifying the type of statistical approach: \itemize{ @@ -100,27 +98,29 @@ by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} variants of all primary functions. Default is \code{NULL}. The argument should be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} functions.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{\code{ylab}}{Labels for \code{y} axis variable. If \code{NULL} (default), variable name for \code{y} will be used.} + \item{\code{point.args}}{A list of additional aesthetic arguments to be passed to +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} }} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Helper function for \code{ggstatsplot::ggdotplotstats} to apply this function diff --git a/man/grouped_gghistostats.Rd b/man/grouped_gghistostats.Rd index 8ebf09d2b..f41aa808e 100644 --- a/man/grouped_gghistostats.Rd +++ b/man/grouped_gghistostats.Rd @@ -31,11 +31,11 @@ and explore multiple widths to find the best to illustrate the stories in your data.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} \item{...}{ Arguments passed on to \code{\link[=gghistostats]{gghistostats}} @@ -44,8 +44,8 @@ separately specified here.} \code{stat_bin} used to display the bins. Do not specify \code{binwidth} argument in this list since it has already been specified using the dedicated argument.} \item{\code{centrality.line.args}}{A list of additional aesthetic arguments to be -passed to the \code{geom_line} used to display the lines corresponding to the -centrality parameter.} +passed to the \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} used to display the lines +corresponding to the centrality parameter.} \item{\code{type}}{A character specifying the type of statistical approach: \itemize{ \item \code{"parametric"} @@ -118,13 +118,13 @@ by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} variants of all primary functions. Default is \code{NULL}. The argument should be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} functions.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} }} diff --git a/man/grouped_ggpiestats.Rd b/man/grouped_ggpiestats.Rd index 6c35a8df2..0959ddae3 100644 --- a/man/grouped_ggpiestats.Rd +++ b/man/grouped_ggpiestats.Rd @@ -29,19 +29,19 @@ Please note that if there are empty factor levels in your variable, they will be dropped. Default is \code{NULL}. If \code{NULL}, one-sample proportion test (a goodness of fit test) will be run for the \code{x} variable. Otherwise an appropriate association test will be run. This argument can not be \code{NULL} -for \code{ggbarstats} function.} +for \code{\link[=ggbarstats]{ggbarstats()}}.} \item{\code{proportion.test}}{Decides whether proportion test for \code{x} variable is to be carried out for each level of \code{y}. Defaults to \code{results.subtitle}. In -\code{ggbarstats}, only \emph{p}-values from this test will be displayed.} - \item{\code{digits.perc}}{Numeric that decides number of decimal places for percentage -labels (Default: \code{0L}).} +\code{\link[=ggbarstats]{ggbarstats()}}, only \emph{p}-values from this test will be displayed.} + \item{\code{digits.perc}}{Numeric that decides number of decimal places for +percentage labels (Default: \code{0L}).} \item{\code{label}}{Character decides what information needs to be displayed on the label in each pie slice. Possible options are \code{"percentage"} (default), \code{"counts"}, \code{"both"}.} \item{\code{label.args}}{Additional aesthetic arguments that will be passed to -\code{ggplot2::geom_label()}.} - \item{\code{label.repel}}{Whether labels should be repelled using \code{{ggrepel}} package. -This can be helpful in case the labels are overlapping.} +\code{\link[ggplot2:geom_text]{ggplot2::geom_label()}}.} + \item{\code{label.repel}}{Whether labels should be repelled using \code{{ggrepel}} +package. This can be helpful in case of overlapping labels.} \item{\code{legend.title}}{Title text for the legend.} \item{\code{bf.message}}{Logical that decides whether to display Bayes Factor in favor of the \emph{null} hypothesis. This argument is relevant only \strong{for @@ -61,13 +61,13 @@ be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} function be extracted. The available palettes and packages can be checked by running \code{View(paletteer::palettes_d_names)}.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{\code{type}}{A character specifying the type of statistical approach: @@ -112,11 +112,11 @@ hypothesis under the alternative, and corresponds to Gunel and Dickey's \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Helper function for \code{ggstatsplot::ggpiestats} to apply this diff --git a/man/grouped_ggscatterstats.Rd b/man/grouped_ggscatterstats.Rd index 2afdae091..3ece2d0ff 100644 --- a/man/grouped_ggscatterstats.Rd +++ b/man/grouped_ggscatterstats.Rd @@ -26,17 +26,15 @@ ungrouped before they are entered as \code{data}.} \code{var1}).} \item{\code{label.expression}}{An expression evaluating to a logical vector that determines the subset of data points to label (e.g. \code{y < 4 & z < 20}). -While using this argument with \code{purrr::pmap()}, you will have to provide a -quoted expression (e.g. \code{quote(y < 4 & z < 20)}).} +While using this argument with \code{\link[purrr:pmap]{purrr::pmap()}}, you will have to provide +a quoted expression (e.g. \code{quote(y < 4 & z < 20)}).} \item{\code{point.label.args}}{A list of additional aesthetic arguments to be passed -to \code{ggrepel::geom_label_repel} geom used to display the labels.} +to \code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}}geom used to display the labels.} \item{\code{smooth.line.args}}{A list of additional aesthetic arguments to be passed to \code{geom_smooth} geom used to display the regression line.} - \item{\code{point.args}}{A list of additional aesthetic arguments to be passed -to \code{geom_point} geom used to display the raw data points.} \item{\code{marginal}}{Decides whether marginal distributions will be plotted on -axes using \code{ggside} functions. The default is \code{TRUE}. The package -\code{ggside} must already be installed by the user.} +axes using \code{{ggside}} functions. The default is \code{TRUE}. The package +\code{{ggside}} must already be installed by the user.} \item{\code{point.width.jitter,point.height.jitter}}{Degree of jitter in \code{x} and \code{y} direction, respectively. Defaults to \code{0} (0\%) of the resolution of the data. Note that the jitter should not be specified in the \code{point.args} @@ -91,18 +89,20 @@ the plot will be returned.} \code{results.subtitle = FALSE}.} \item{\code{caption}}{The text for the plot caption. This argument is relevant only if \code{bf.message = FALSE}.} + \item{\code{point.args}}{A list of additional aesthetic arguments to be passed to +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{\code{ggplot.component}}{A \code{ggplot} component to be added to the plot prepared by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} variants of all primary functions. Default is \code{NULL}. The argument should be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} functions.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} }} @@ -110,11 +110,11 @@ thus the details as well.} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ Grouped scatterplots from \code{{ggplot2}} combined with marginal distribution diff --git a/man/grouped_ggwithinstats.Rd b/man/grouped_ggwithinstats.Rd index d36b7368b..ed1621130 100644 --- a/man/grouped_ggwithinstats.Rd +++ b/man/grouped_ggwithinstats.Rd @@ -24,12 +24,12 @@ ungrouped before they are entered as \code{data}.} \describe{ \item{\code{point.path,centrality.path}}{Logical that decides whether individual data points and means, respectively, should be connected using -\code{ggplot2::geom_path()}. Both default to \code{TRUE}. Note that \code{point.path} +\code{\link[ggplot2:geom_path]{ggplot2::geom_path()}}. Both default to \code{TRUE}. Note that \code{point.path} argument is relevant only when there are two groups (i.e., in case of a \emph{t}-test). In case of large number of data points, it is advisable to set \code{point.path = FALSE} as these lines can overwhelm the plot.} \item{\code{centrality.path.args,point.path.args}}{A list of additional aesthetic -arguments passed on to \code{ggplot2::geom_path()} connecting raw data points +arguments passed on to \code{\link[ggplot2:geom_path]{ggplot2::geom_path()}} connecting raw data points and mean points.} \item{\code{xlab}}{Label for \code{x} axis variable. If \code{NULL} (default), variable name for \code{x} will be used.} @@ -85,11 +85,11 @@ to be: Just as \code{type} argument, abbreviations are also accepted.} \item{\code{point.args}}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_point()} displaying the raw data.} +the \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}.} \item{\code{boxplot.args}}{A list of additional aesthetic arguments passed on to -\code{ggplot2::geom_boxplot()}.} +\code{\link[ggplot2:geom_boxplot]{ggplot2::geom_boxplot()}}.} \item{\code{violin.args}}{A list of additional aesthetic arguments to be passed to -the \code{ggplot2::geom_violin()}.} +the \code{\link[ggplot2:geom_violin]{ggplot2::geom_violin()}}.} \item{\code{ggplot.component}}{A \code{ggplot} component to be added to the plot prepared by \code{{ggstatsplot}}. This argument is primarily helpful for \code{grouped_} variants of all primary functions. Default is \code{NULL}. The argument should @@ -98,18 +98,18 @@ be entered as a \code{{ggplot2}} function or a list of \code{{ggplot2}} function be extracted. The available palettes and packages can be checked by running \code{View(paletteer::palettes_d_names)}.} \item{\code{centrality.point.args,centrality.label.args}}{A list of additional aesthetic -arguments to be passed to \code{ggplot2::geom_point()} and -\code{ggrepel::geom_label_repel} geoms, which are involved in mean plotting.} +arguments to be passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} and +\code{\link[ggrepel:geom_text_repel]{ggrepel::geom_label_repel()}} geoms, which are involved in mean plotting.} \item{\code{ggsignif.args}}{A list of additional aesthetic -arguments to be passed to \code{ggsignif::geom_signif}.} +arguments to be passed to \code{\link[ggsignif:stat_signif]{ggsignif::geom_signif()}}.} \item{\code{ggtheme}}{A \code{{ggplot2}} theme. Default value is -\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g., -\code{theme_bw()}), or themes from extension packages are allowed (e.g., -\code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, etc.). -But note that sometimes these themes will remove some of the details that -\code{{ggstatsplot}} plots typically contains. For example, if relevant, -\code{ggbetweenstats()} shows details about multiple comparison test as a label -on the secondary Y-axis. Some themes (e.g. +\code{\link[=theme_ggstatsplot]{theme_ggstatsplot()}}. Any of the \code{{ggplot2}} themes (e.g., +\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}), or themes from extension packages are allowed +(e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()}, +etc.). But note that sometimes these themes will remove some of the details +that \code{{ggstatsplot}} plots typically contains. For example, if relevant, +\code{\link[=ggbetweenstats]{ggbetweenstats()}} shows details about multiple comparison test as a +label on the secondary Y-axis. Some themes (e.g. \code{ggthemes::theme_fivethirtyeight()}) will remove the secondary Y-axis and thus the details as well.} \item{\code{x}}{The grouping (or independent) variable from \code{data}. In case of a @@ -158,11 +158,11 @@ for the effect size (Default: \code{100L}).} \item{grouping.var}{A single grouping variable.} \item{plotgrid.args}{A \code{list} of additional arguments passed to -\code{patchwork::wrap_plots()}, except for \code{guides} argument which is already +\code{\link[patchwork:wrap_plots]{patchwork::wrap_plots()}}, except for \code{guides} argument which is already separately specified here.} \item{annotation.args}{A \code{list} of additional arguments passed to -\code{patchwork::plot_annotation()}.} +\code{\link[patchwork:plot_annotation]{patchwork::plot_annotation()}}.} } \description{ A combined plot of comparison plot created for levels of a grouping variable. diff --git a/man/iris_long.Rd b/man/iris_long.Rd index c52cb5e9c..878c38585 100644 --- a/man/iris_long.Rd +++ b/man/iris_long.Rd @@ -10,7 +10,8 @@ A data frame with 600 rows and 5 variables \item id. Dummy identity number for each flower (150 flowers in total). \item Species. The species are \emph{Iris setosa}, \emph{versicolor}, and \emph{virginica}. \item condition. Factor giving a detailed description of the attribute -(Four levels: \code{"Petal.Length"}, \code{"Petal.Width"}, \code{"Sepal.Length"}, \code{"Sepal.Width"}). +(Four levels: \code{"Petal.Length"}, \code{"Petal.Width"}, \code{"Sepal.Length"}, +\code{"Sepal.Width"}). \item attribute. What attribute is being measured (\code{"Sepal"} or \code{"Pepal"}). \item measure. What aspect of the attribute is being measured (\code{"Length"} or \code{"Width"}). \item value. Value of the measurement. diff --git a/man/theme_ggstatsplot.Rd b/man/theme_ggstatsplot.Rd index 860e08cde..32c7dc475 100644 --- a/man/theme_ggstatsplot.Rd +++ b/man/theme_ggstatsplot.Rd @@ -7,12 +7,12 @@ theme_ggstatsplot() } \value{ -A \code{ggplot} object with the \code{theme_ggstatsplot} theme overlaid. +A \code{ggplot} object. } \description{ Common theme used across all plots generated in \code{{ggstatsplot}} and \emph{assumed} -by the author to be aesthetically pleasing to the user/reader. The theme is a -wrapper around \code{theme_bw()}. +by the author to be aesthetically pleasing to the user. The theme is a +wrapper around \code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}. All \code{{ggstatsplot}} functions have a \code{ggtheme} parameter that let you choose a different theme.