markdown itemize & links

R/alluvial-data.r

@@ -7,20 +7,17 @@
 #' subsets or amounts of observations that take the corresponding values of the
 #' corresponding variables. This function checks a data frame for either of two
 #' types of alluvial structure:
-#' \itemize{
-#'   \item One row per **lode**, wherein each row encodes a subset or
-#'         amount of observations having a specific profile of axis values, a
-#'         `key` field encodes the axis, a `value` field encodes the
-#'         value within each axis, and a `id` column identifies multiple
-#'         lodes corresponding to the same subset or amount of observations.
-#'         `is_lodes_form` tests for this structure.
-#'   \item One row per **alluvium**, wherein each row encodes a subset or
-#'         amount of observations having a specific profile of axis values and a
-#'         set `axes` of fields encodes its values at each axis variable.
-#'         `is_alluvia_form` tests for this structure.
-#' }
 #'
-
+#' - One row per **lode**, wherein each row encodes a subset or amount of
+#'   observations having a specific profile of axis values, a `key` field
+#'   encodes the axis, a `value` field encodes the value within each axis, and a
+#'   `id` column identifies multiple lodes corresponding to the same subset or
+#'   amount of observations. `is_lodes_form` tests for this structure.
+#' - One row per **alluvium**, wherein each row encodes a subset or amount of
+#'   observations having a specific profile of axis values and a set `axes` of
+#'   fields encodes its values at each axis variable. `is_alluvia_form` tests
+#'   for this structure.
+#'
 #' `to_lodes_form` takes a data frame with several designated variables to
 #' be used as axes in an alluvial diagram, and reshapes the data frame so that
 #' the axis variable names constitute a new factor variable and their values
@@ -43,22 +40,22 @@
 #'   "alluvia").
 #' @param silent Whether to print messages.
 #' @param key,value,id In `to_lodes_form`, handled as in
-#'   \code{\link[tidyr]{gather}} and used to name the new axis (key), stratum
+#'   [tidyr::gather()] and used to name the new axis (key), stratum
 #'   (value), and alluvium (identifying) variables. In `to_alluvia_form`,
-#'   handled as in \code{\link[tidyr]{spread}} and used to identify the fields
+#'   handled as in [tidyr::spread()] and used to identify the fields
 #'   of `data` to be used as the axis (key), stratum (value), and alluvium
 #'   (identifying) variables.
 #' @param axes In `*_alluvia_form`, handled as in
-#'   \code{\link[dplyr]{select}} and used to identify the field(s) of
+#'   [dplyr::select()] and used to identify the field(s) of
 #'   `data` to be used as axes.
 #' @param ... Used in `is_alluvia_form` and `to_lodes_form` as in
-#'   \code{\link[dplyr]{select}} to determine axis variables, as an alternative
+#'   [dplyr::select()] to determine axis variables, as an alternative
 #'   to `axes`. Ignored when `axes` is provided.
 #' @param weight Optional field of `data`, handled using
-#'   \code{\link[rlang]{enquo}}, to be used as heights or depths of the alluvia
+#'   [rlang::enquo()], to be used as heights or depths of the alluvia
 #'   or lodes.
 #' @param diffuse Fields of `data`, handled using
-#'   \code{\link[tidyselect]{vars_select}}, to merge into the reshapen data by
+#'   [tidyselect::vars_select()], to merge into the reshapen data by
 #'   `id`. They must be a subset of the axis variables. Alternatively, a
 #'   logical value indicating whether to merge all (`TRUE`) or none
 #'   (`FALSE`) of the axis variables.

R/data.r

@@ -4,12 +4,12 @@
 #' kindly contributed by Raffaele Vardavas.
 #'
 #' @format An alluvial data frame in lodes form.
-#' @source RAND American Life Panel \url{https://alpdata.rand.org/}
+#' @source RAND American Life Panel <https://alpdata.rand.org/>
 #' @name vaccinations
 NULL
 
 #' Student curricula across semesters
-#' 
+#'
 #' This dataset, kindly contributed by Dario Bonaretti, follows the curricula of
 #' 10 students across 8 academic semesters.
 #'

R/ggproto.r

@@ -1,6 +1,6 @@
 #' Base ggproto classes for ggalluvial
 #'
 #' @name ggalluvial-ggproto
-#' @seealso \code{\link[ggplot2]{ggplot2-ggproto}}
+#' @seealso [`ggplot2::ggplot2-ggproto`]
 #' @keywords internal
 NULL

R/lode-guidance-functions.r

@@ -1,24 +1,22 @@
 #' Lode guidance functions
 #'
 #' These functions control the order of lodes within strata in an alluvial
-#' diagram. They are invoked by \code{\link{stat_alluvium}} and can be passed to
+#' diagram. They are invoked by [stat_alluvium()] and can be passed to
 #' the `lode.guidance` parameter.
 #'
 
 #' Each function orders the numbers 1 through `n`, starting at index
-#' `i`. The choice of function made in \code{\link{stat_alluvium}}
+#' `i`. The choice of function made in [stat_alluvium()]
 #' determines the order in which the other axes contribute to the sorting of
 #' lodes within each index axis. After starting at `i`, the functions order
 #' the remaining axes as follows:
-#' \itemize{
-#'   \item `zigzag`: Zigzag outward from `i`
-#'   \item `rightward`: Increasing order
-#'   \item `leftward`: Decreasing order
-#'   \item `rightleft`: Proceed rightward from `i` to `n`, then
-#'         leftward to 1
-#'   \item `leftright`: Proceed leftward from `i` to 1, then rightward
-#'         to `n`
-#' }
+#'
+#' - `zigzag`: Zigzag outward from `i`
+#' - `rightward`: Increasing order
+#' - `leftward`: Decreasing order
+#' - `rightleft`: Proceed rightward from `i` to `n`, then leftward to 1
+#' - `leftright`: Proceed leftward from `i` to 1, then rightward to `n`
+#'
 #' @name lode-guidance-functions
 #' @param n Numeric, a positive integer
 #' @param i Numeric, a positive integer at most `n`

R/self-adjoin.r

@@ -5,27 +5,27 @@
 #' form to something similar to alluvia form.
 #'
 
-#' `self_adjoin` invokes \code{\link[dplyr]{join}} functions in order to convert
+#' `self_adjoin` invokes [`dplyr::join`] functions in order to convert
 #' a dataset with measures along a discrete `key` variable into a dataset
 #' consisting of column bindings of these measures (by any `by` variables) along
 #' adjacent values of `key`.
 #' @name self-adjoin
 #' @import tidyselect
 #' @family alluvial data manipulation
 #' @param data A data frame in lodes form (repeated measures data; see
-#'   \code{\link{alluvial-data}}).
+#'   [`alluvial-data`]).
 #' @param key Column of `data` indicating sequential collection; handled as in
 #'   [tidyr::spread()].
 #' @param by Character vector of variables to self-adjoin by; passed to
-#'   \code{\link[dplyr]{join}} functions.
+#'   [`dplyr::join`] functions.
 #' @param link Character vector of variables to adjoin. Will be replaced by
 #'   pairs of variables suffixed by `suffix`.
 #' @param keep.x,keep.y Character vector of variables to associate with the
 #'   first (respectively, second) copy of `data` after adjoining. These
 #'   variables can overlap with each other but cannot overlap with `by` or
 #'   `link`.
 #' @param suffix Suffixes to add to the adjoined `link` variables; passed to
-#'   \code{\link[dplyr]{join}} functions.
+#'   [`dplyr::join`] functions.
 #' @example inst/examples/ex-self-adjoin.r
 #' @export
 self_adjoin <- function(

R/stat-alluvium.r

@@ -23,7 +23,7 @@
 #' @param lode.guidance The function to prioritize the axis variables for
 #'   ordering the lodes within each stratum. Options are "zigzag", "rightleft",
 #'   "leftright", "rightward", and "leftward" (see
-#'   \code{\link{lode-guidance-functions}}).
+#'   [`lode-guidance-functions`]).
 #' @param lode.ordering A list (of length the number of axes) of integer vectors
 #'   (each of length the number of rows of `data`) or NULL entries
 #'   (indicating no imposed ordering), or else a numeric matrix of corresponding

man-roxygen/geom-aesthetics.r

@@ -1,17 +1,17 @@
 #' @section Aesthetics:
 #' `geom_alluvium`, `geom_flow`, `geom_lode`, and `geom_stratum` understand the
 #' following aesthetics (required aesthetics are in bold):
-#' \itemize{
-#'   \item **`x`**
-#'   \item **`y`**
-#'   \item **`ymin`**
-#'   \item **`ymax`**
-#'   \item `alpha`
-#'   \item `colour`
-#'   \item `fill`
-#'   \item `linetype`
-#'   \item `size`
-#'   \item `group`
-#' }
+#'
+#' - **`x`**
+#' - **`y`**
+#' - **`ymin`**
+#' - **`ymax`**
+#' - `alpha`
+#' - `colour`
+#' - `fill`
+#' - `linetype`
+#' - `size`
+#' - `group`
+#'
 #' `group` is used internally; arguments are ignored.
 #'

man-roxygen/stat-aesthetics.r

@@ -1,29 +1,26 @@
 #' @section Aesthetics:
 #' `stat_alluvium`, `stat_flow`, and `stat_stratum` require one
 #' of two sets of aesthetics:
-#' \itemize{
-#'   \item **`x`** and at least one of
-#'         **`alluvium`** and **`stratum`**
-#'   \item any number of **`axis[0-9]*`**
-#'         (`axis1`, `axis2`, etc.)
-#' }
+#'
+#' - **`x`** and at least one of **`alluvium`** and **`stratum`**
+#' - any number of **`axis[0-9]*`** (`axis1`, `axis2`, etc.)
+#'
 #' Use `x`, `alluvium`, and/or `stratum` for data in lodes format
-#' and `axis[0-9]*` for data in alluvia format
-#' (see [`alluvial-data`]).
+#' and `axis[0-9]*` for data in alluvia format (see [`alluvial-data`]).
 #' Arguments to parameters inconsistent with the format will be ignored.
 #' Additionally, each `stat_*` layer accepts the following optional
 #' aesthetics:
-#' \itemize{
-#'   \item `y`
-#'   \item `group`
-#' }
+#'
+#' - `y`
+#' - `group`
+#'
 #' `y` controls the heights of the alluvia
 #' and may be aggregated across equivalent observations.
 #' `group` is used internally; arguments are ignored.
 #' Finally, `stat_stratum` accepts the following optional aesthetic:
-#' \itemize{
-#'   \item `label`
-#' }
+#'
+#' - `label`
+#'
 #' `label` is used to label the strata and must take a unique value across
 #' the observations within each stratum.
 #' These and any other aesthetics are aggregated as follows: