More linking in docs (#956)

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
 #'

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.

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

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
 #'

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

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

R/ggcoefstats.R

@@ -13,24 +13,21 @@
 #' ```
 #'
 #' @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
 #'   studies with standard deviation *t* (i.e., a random-effects analysis)
 #'   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

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

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
 #'

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
 #'

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) {

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

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 @@
 #' <https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html>
 #'
 #' @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)

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}.
 #'

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
 #'

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)