make external package links explicit to fix note on devel

R/cut_cdf_qi.R

@@ -16,7 +16,7 @@
 #'
 #' @param p A numeric vector of values from a cumulative distribution function,
 #' such as values returned by `p`-prefixed distribution functions in base R (e.g. [pnorm()]),
-#' the [cdf()] function, or values of the `cdf` computed aesthetic from the
+#' the [`cdf()`][distributional::cdf] function, or values of the `cdf` computed aesthetic from the
 #' [stat_slabinterval()] family of stats.
 #' @param .width vector of probabilities to use that determine the widths of the resulting intervals.
 #' @param labels One of:

R/geom.R

@@ -142,7 +142,7 @@ define_orientation_variables = function(orientation) {
 
 #' Base ggproto classes for ggdist
 #'
-#' @seealso [ggproto]
+#' @seealso [`ggproto()`][ggplot2::ggproto]
 #' @keywords internal
 #' @name ggdist-ggproto
 NULL

R/geom_dotsinterval.R

@@ -366,7 +366,7 @@ draw_slabs_dots = function(
 #' @inheritParams geom_slabinterval
 #' @author Matthew Kay
 #' @return A [ggplot2::Geom] or [ggplot2::Stat] representing a dotplot or combined dotplot+interval geometry which can
-#' be added to a [ggplot()] object.
+#' be added to a [`ggplot()`][ggplot2::ggplot] object.
 #' @seealso See the [stat_slabinterval()] family for other
 #' stats built on top of [geom_slabinterval()].
 #' See `vignette("dotsinterval")` for a variety of examples of use.

R/geom_lineribbon.R

@@ -13,31 +13,32 @@ globalVariables(c(".lower", ".upper", ".width"))
 
 #' Line + multiple-ribbon plots (ggplot geom)
 #'
-#' A combination of [geom_line()] and [geom_ribbon()] with default aesthetics
-#' designed for use with output from [point_interval()].
+#' A combination of [`geom_line()`][ggplot2::geom_line] and [`geom_ribbon()`][ggplot2::geom_ribbon]
+#' with default aesthetics designed for use with output from [point_interval()].
 #'
 #' @details
-#' [geom_lineribbon()] is a combination of a [geom_line()] and [geom_ribbon()] designed for use
-#' with output from [point_interval()]. This geom sets some default aesthetics equal to the `.width`
-#' column generated by the [point_interval()] family of functions, making them
-#' often more convenient than a vanilla [geom_ribbon()] + [geom_line()].
+#' [geom_lineribbon()] is a combination of a [`geom_line()`][ggplot2::geom_line] and
+#' [`geom_ribbon()`][ggplot2::geom_ribbon] designed for use with output from [point_interval()].
+#' This geom sets some default aesthetics equal to the `.width` column generated by the
+#' [point_interval()] family of functions, making them often more convenient than a vanilla
+#' [`geom_ribbon()`][ggplot2::geom_ribbon] + [`geom_line()`][ggplot2::geom_line].
 #'
 #' Specifically, [geom_lineribbon()] acts as if its default aesthetics are
 #' `aes(fill = forcats::fct_rev(ordered(.width)))`.
 #'
 #' @eval rd_layer_params("lineribbon")
 #' @eval rd_lineribbon_aesthetics("lineribbon")
 #' @inheritParams ggplot2::geom_line
-#' @param ...  Other arguments passed to [layer()]. These are often aesthetics, used to set an aesthetic
+#' @param ...  Other arguments passed to [`layer()`][ggplot2::layer]. These are often aesthetics, used to set an aesthetic
 #' to a fixed value, like `colour = "red"` or `linewidth = 3` (see **Aesthetics**, below). They may also be
 #' parameters to the paired geom/stat.
 #' @return A [ggplot2::Geom] representing a combined line + multiple-ribbon geometry which can
-#' be added to a [ggplot()] object.
+#' be added to a [`ggplot()`][ggplot2::ggplot] object.
 #' @author Matthew Kay
 #' @seealso See [stat_lineribbon()] for a version that does summarizing of samples into points and intervals
 #' within ggplot. See [geom_pointinterval()] for a similar geom intended
-#' for point summaries and intervals. See [geom_ribbon()] and [geom_line()] for the geoms this is
-#' based on.
+#' for point summaries and intervals. See [`geom_line()`][ggplot2::geom_line] and
+#' [`geom_ribbon()`][ggplot2::geom_ribbon] and  for the geoms this is based on.
 #' @examples
 #'
 #' library(dplyr)

R/geom_slabinterval.R

@@ -354,7 +354,7 @@ transform_size = function(size, size_domain, size_range) {
 #' specify the endpoints of the interval. A scaling factor for interval line width and point size is applied
 #' through the `interval_size_domain`, `interval_size_range`, and `fatten_point` parameters.
 #' These scaling factors are designed to give multiple uncertainty intervals reasonable
-#' scaling at the default settings for [scale_size_continuous()].
+#' scaling at the default settings for [`scale_size_continuous()`][ggplot2::scale_size_continuous].
 #'
 #' As a combination geom, this geom expects a `datatype` aesthetic specifying which part of the geom a given
 #' row in the input data corresponds to: `"slab"` or `"interval"`. However, specifying this aesthetic
@@ -376,14 +376,14 @@ transform_size = function(size, size_domain, size_range) {
 #' @eval rd_layer_params("slabinterval")
 #' @eval rd_slabinterval_aesthetics()
 #' @inheritParams ggplot2::layer
-#' @param ...  Other arguments passed to [layer()]. These are often aesthetics, used to set an aesthetic
+#' @param ...  Other arguments passed to [`layer()`][ggplot2::layer]. These are often aesthetics, used to set an aesthetic
 #' to a fixed value, like `colour = "red"` or `linewidth = 3` (see **Aesthetics**, below). They may also be
 #' parameters to the paired geom/stat.
 #' @param position Position adjustment, either as a string, or the result of a call to a position adjustment function.
-#' Setting this equal to `"dodge"` ([position_dodge()]) or `"dodgejust"` ([position_dodgejust()]) can be useful if
+#' Setting this equal to `"dodge"` ([`position_dodge()`][ggplot2::position_dodge]) or `"dodgejust"` ([position_dodgejust()]) can be useful if
 #' you have overlapping geometries.
 #' @return A [ggplot2::Geom] representing a slab or combined slab+interval geometry which can
-#' be added to a [ggplot()] object.
+#' be added to a [`ggplot()`][ggplot2::ggplot] object.
 #' @author Matthew Kay
 #' @seealso See [geom_lineribbon()] for a combination geom designed for fit curves plus probability bands.
 #' See [geom_dotsinterval()] for a combination geom designed for plotting dotplots with intervals.
@@ -652,16 +652,17 @@ GeomSlabinterval = ggproto("GeomSlabinterval", AbstractGeom,
       documentation for that argument.)
       '),
     interval_size_range = glue_doc('
-      A length-2 numeric vector. This geom scales the raw size aesthetic values when drawing interval and point
-      sizes, as they tend to be too thick when using the default settings of [scale_size_continuous()], which give
-      sizes with a range of `c(1, 6)`. The `interval_size_domain` value indicates the input domain of raw size
-      values (typically this should be equal to the value of the `range` argument of the [scale_size_continuous()]
-      function), and `interval_size_range` indicates the desired output range of the size values (the min and max of
-      the actual sizes used to draw intervals). Most of the time it is not recommended to change the value of this
-      argument, as it may result in strange scaling of legends; this argument is a holdover from earlier versions
-      that did not have size aesthetics targeting the point and interval separately. If you want to adjust the
-      size of the interval or points separately, you can also use the `linewidth` or `point_size`
-      aesthetics; see [sub-geometry-scales].
+      A length-2 numeric vector. This geom scales the raw size aesthetic values when drawing interval
+      and point sizes, as they tend to be too thick when using the default settings of [`scale_size_continuous()`][ggplot2::scale_size_continuous],
+      which give sizes with a range of `c(1, 6)`. The `interval_size_domain` value indicates the
+      input domain of raw size values (typically this should be equal to the value of the `range`
+      argument of the [`scale_size_continuous()`][ggplot2::scale_size_continuous] function), and
+      `interval_size_range` indicates the desired output range of the size values (the min and max
+      of the actual sizes used to draw intervals). Most of the time it is not recommended to change
+      the value of this argument, as it may result in strange scaling of legends; this argument is
+      a holdover from earlier versions that did not have size aesthetics targeting the point and
+      interval separately. If you want to adjust the size of the interval or points separately,
+      you can also use the `linewidth` or `point_size` aesthetics; see [sub-geometry-scales].
       '),
     fatten_point = glue_doc('
       A multiplicative factor used to adjust the size of the point relative to the size of the

R/geom_spike.R

@@ -21,7 +21,7 @@
 #' thickness function.
 #' @inheritParams geom_slabinterval
 #' @return A [ggplot2::Geom] representing a spike geometry which can
-#' be added to a [ggplot()] object.
+#' be added to a [`ggplot()`][ggplot2::ggplot] object.
 #' rd_slabinterval_aesthetics(geom_name),
 #' @seealso
 #' See [stat_spike()] for the stat version, intended for

R/guide_rampbar.R

@@ -10,7 +10,7 @@
 #'
 #' A colour ramp bar guide that shows continuous colour ramp scales mapped onto
 #' values as a smooth gradient. Designed for use with [scale_fill_ramp_continuous()]
-#' and [scale_colour_ramp_continuous()]. Based on [guide_colourbar()].
+#' and [scale_colour_ramp_continuous()]. Based on [`guide_colourbar()`][ggplot2::guide_colourbar].
 #'
 #' @inheritDotParams ggplot2::guide_colourbar
 #' @param to The color to ramp to in the guide. Corresponds to `1` on the scale.

R/parse_dist.R

@@ -43,12 +43,12 @@ globalVariables("prior")
 #'   - an [environment]: use the given environment
 #' @param lb The name of an input column (for `data.frame` and `brms::prior` objects) that contains
 #'   the lower bound of the distribution, which if present will produce a truncated distribution using
-#'   [dist_truncated()]. Ignored if `lb` is `NULL` or if `object[[lb]]` is `NA` for the corresponding
-#'   input row.
+#'   [`dist_truncated()`][distributional::dist_truncated]. Ignored if `lb` is `NULL` or if `object[[lb]]`
+#'   is `NA` for the corresponding input row.
 #' @param ub The name of an input column (for `data.frame` and `brms::prior` objects) that contains
 #'   the upper bound of the distribution, which if present will produce a truncated distribution using
-#'   [dist_truncated()]. Ignored if `ub` is `NULL` or if `object[[ub]]` is `NA` for the corresponding
-#'   input row.
+#'   [`dist_truncated()`][distributional::dist_truncated]. Ignored if `ub` is `NULL` or if `object[[ub]]`
+#'   is `NA` for the corresponding input row.
 #' @param to_r_names If `TRUE` (the default), certain common aliases for distribution names are
 #'   automatically translated into names that R can recognize (i.e., names which have functions starting
 #'   with `r`, `p`, `q`, and `d` representing random number generators, distribution

R/point_interval.R

@@ -41,7 +41,7 @@ globalVariables(c("y", "ymin", "ymax"))
 #' corresponding to the interval. This behavior allows `point_interval`
 #' and its derived functions (like `median_qi`, `mean_qi`, `mode_hdi`, etc)
 #' to be easily used to plot intervals in ggplot stats using methods like
-#' [stat_eye()], [stat_halfeye()], or [stat_summary()].
+#' [stat_eye()], [stat_halfeye()], or [`stat_summary()`][ggplot2::stat_summary].
 #'
 #' `median_qi`, `mode_hdi`, etc are short forms for
 #' `point_interval(..., .point = median, .interval = qi)`, etc.

R/pr.R

@@ -14,7 +14,7 @@
 #' [Pr_()] and [p_()] are an **experimental** mini-language for specifying aesthetic values
 #' based on probabilities and probability densities derived from distributions
 #' supplied to \pkg{ggdist} stats (e.g., in [stat_slabinterval()],
-#' [stat_dotsinterval()], etc.). They generate expressions that use [after_stat()]
+#' [stat_dotsinterval()], etc.). They generate expressions that use [`after_stat()`][ggplot2::after_stat]
 #' and the computed variables of the stat (such as `cdf` and `pdf`; see e.g.
 #' the **Computed Variables** section of [stat_slabinterval()]) to compute
 #' the desired probabilities or densities.
@@ -36,7 +36,7 @@
 #'
 #' Where `p_(x)` is the probability density function. The use of `!!` is
 #' necessary to splice the generated expression into the `aes()` call; for
-#' more information, see [quasiquotation].
+#' more information, see [quasiquotation][rlang::quasiquotation].
 #'
 #' @section Probability expressions:
 #'
@@ -69,7 +69,7 @@
 #'   discrete). It currently does not allow any operators in the expression, and
 #'   must be passed one of `x`, `y`, or `value`.
 #' @seealso The *Computed Variables* section of [stat_slabinterval()] (especially
-#' `cdf` and `pdf`) and the [after_stat()] function.
+#' `cdf` and `pdf`) and the [`after_stat()`][ggplot2::after_stat] function.
 #' @examples
 #' library(ggplot2)
 #' library(distributional)

R/rd.R

@@ -161,7 +161,7 @@ rd_layer_params = function(geom_name, stat = NULL, as_dots = FALSE) {
   if (length(params)) {
     if (as_dots) {
       glue_doc('
-        @param ...  Other arguments passed to [layer()]. These are often aesthetics, used to set an aesthetic
+        @param ...  Other arguments passed to [`layer()`][ggplot2::layer]. These are often aesthetics, used to set an aesthetic
           to a fixed value, like `colour = "red"` or `linewidth = 3` (see **Aesthetics**, below). They may also be
           parameters to the paired geom/stat. When paired with the default geom, [geom_<<geom_name>>()],
           these include:

R/rd_dotsinterval.R

@@ -32,7 +32,7 @@ rd_dotsinterval_shortcut_geom = function(
     rd_layer_params(geom_name, as_dots = FALSE),
     glue_doc('
       @return A [ggplot2::Geom] representing a <<chart_type>> geometry which can
-      be added to a [ggplot()] object.
+      be added to a [`ggplot()`][ggplot2::ggplot] object.
       '),
     '@template details-dotsinterval-family',
     '@template references-quantile-dotplots',
@@ -108,7 +108,7 @@ rd_dotsinterval_shortcut_stat = function(
     '@template details-x-y-xdist-ydist',
     glue_doc('
       @return A [ggplot2::Stat] representing a <<chart_type>> geometry which can
-      be added to a [ggplot()] object.'),
+      be added to a [`ggplot()`][ggplot2::ggplot] object.'),
     rd_slabinterval_computed_variables(stat),
     rd_dotsinterval_aesthetics(geom_name, stat),
     glue_doc('

R/rd_lineribbon.R

@@ -41,7 +41,7 @@ rd_lineribbon_shortcut_stat = function(
     '@template details-x-y-xdist-ydist',
     glue_doc('
       @return A [ggplot2::Stat] representing a <<chart_type>> geometry which can
-      be added to a [ggplot()] object.'),
+      be added to a [`ggplot()`][ggplot2::ggplot] object.'),
     rd_slabinterval_computed_variables(stat),
     rd_lineribbon_aesthetics(geom_name, stat),
     glue_doc('

R/rd_slabinterval.R

@@ -30,7 +30,7 @@ rd_slabinterval_shortcut_geom = function(
       This geom wraps [geom_slabinterval()] with defaults designed to produce
       <<chart_type>> plots. Default aesthetic mappings are applied if the `.width` column
       is present in the input data (e.g., as generated by the [point_interval()] family of functions),
-      making this geom often more convenient than vanilla [ggplot2] geometries when used with
+      making this geom often more convenient than vanilla [ggplot2][ggplot2::ggplot2] geometries when used with
       functions like [median_qi()], [mean_qi()], [mode_hdi()], etc.
 
       Specifically, if `.width` is present in the input, [geom_<<geom_name>>()] acts
@@ -40,7 +40,7 @@ rd_slabinterval_shortcut_geom = function(
     rd_layer_params(geom_name, as_dots = FALSE),
     glue_doc('
       @return A [ggplot2::Geom] representing a <<chart_type>> geometry which can
-      be added to a [ggplot()] object.'),
+      be added to a [`ggplot()`][ggplot2::ggplot] object.'),
     rd_slabinterval_aesthetics(geom_name),
     glue_doc('
       @seealso
@@ -86,7 +86,7 @@ rd_slabinterval_shortcut_stat = function(
     '@template details-x-y-xdist-ydist',
     glue_doc('
       @return A [ggplot2::Stat] representing a <<chart_type>> geometry which can
-      be added to a [ggplot()] object.'),
+      be added to a [`ggplot()`][ggplot2::ggplot] object.'),
     rd_slabinterval_computed_variables(stat),
     rd_slabinterval_aesthetics(geom_name, stat),
     glue_doc('
@@ -135,8 +135,8 @@ rd_slabinterval_computed_variables = function(stat = StatSlabinterval) {
   out = glue_doc('
       @section Computed Variables:
       The following variables are computed by this stat and made available for
-      use in aesthetic specifications ([aes()]) using the [after_stat()]
-      function or the `after_stat` argument of [stage()]:
+      use in aesthetic specifications ([`aes()`][ggplot2::aes]) using the [`after_stat()`][ggplot2::after_stat]
+      function or the `after_stat` argument of [`stage()`][ggplot2::stage]:
 
       - `x` or `y`: For slabs, the input values to the slab function.
         For intervals, the point summary from the interval function. Whether it is `x` or `y` depends on `orientation`

R/scale_.R

@@ -25,16 +25,17 @@
 #'   \item{`scale_slab_color_* `}{Slab outline color}
 #'   \item{`scale_slab_fill_* `}{Slab fill color}
 #'   \item{`scale_slab_alpha_* `}{Slab alpha level / opacity. The default settings of
-#'   `scale_slab_alpha_continuous` differ from [scale_alpha_continuous()] and
-#'   are designed for gradient plots (e.g. [stat_gradientinterval()]) by ensuring that
+#'   `scale_slab_alpha_continuous` differ from [`scale_alpha_continuous()`][ggplot2::scale_alpha_continuous]
+#'   and are designed for gradient plots (e.g. [stat_gradientinterval()]) by ensuring that
 #'   densities of 0 get mapped to 0 in the output.}
 #'   \item{`scale_slab_linewidth_* `}{Slab outline line width}
 #'   \item{`scale_slab_linetype_* `}{Slab outline line type}
 #'   \item{`scale_slab_shape_* `}{Slab dot shape (for [geom_dotsinterval()])}
 #' }
 #'
 #' See the corresponding scale documentation in ggplot for more information; e.g.
-#' [scale_color_discrete()], [scale_color_continuous()], etc.
+#' [`scale_color_discrete()`][ggplot2::scale_color_discrete],
+#' [`scale_color_continuous()`][ggplot2::scale_color_continuous], etc.
 #'
 #' Other scale functions can be used with the aesthetics/scales defined here by using the `aesthetics`
 #' argument to that scale function. For example, to use color brewer scales with the `point_color` aesthetic:
@@ -56,7 +57,7 @@
 #' @inheritParams ggplot2::continuous_scale
 #' @inheritParams ggplot2::scale_shape
 #' @param ... Arguments passed to underlying scale or guide functions. E.g. `scale_point_color_discrete`
-#' passes arguments to [scale_color_discrete()]. See those functions for more details.
+#' passes arguments to [`scale_color_discrete()`][ggplot2::scale_color_discrete]. See those functions for more details.
 #' @param aesthetics Names of aesthetics to set scales for.
 #' @param guide Guide to use for legends for an aesthetic.
 #' @param range a numeric vector of length 2 that specifies the minimum and maximum size of the plotting symbol
@@ -65,12 +66,13 @@
 #' @param na.value When `na.translate` is true, what value should be shown?
 #' @return
 #' A [ggplot2::Scale] representing one of the aesthetics used to target the appearance of specific parts of composite
-#' `ggdist` geoms. Can be added to a [ggplot()] object.
+#' `ggdist` geoms. Can be added to a [`ggplot()`][ggplot2::ggplot] object.
 #' @name sub-geometry-scales
 #' @aliases scales
 #' @author Matthew Kay
 #' @family ggdist scales
-#' @seealso Other ggplot2 scales: [scale_color_discrete()], [scale_color_continuous()], etc.
+#' @seealso Other ggplot2 scales: [`scale_color_discrete()`][ggplot2::scale_color_discrete],
+#' [`scale_color_continuous()`][ggplot2::scale_color_continuous], etc.
 #' @examples
 #'
 #' library(dplyr)