Make links more precise and avoid URLs

R/arrange_natural.R

@@ -15,7 +15,7 @@
 #' \href{https://en.wikipedia.org/wiki/Natural_sort_order}{natural sorting}
 #' (sorting of strings with both letters and numerals). The underlying
 #' implementation for natural sorting is based on the
-#' \href{https://stringi.gagolewski.com/}{`stringi`} library.
+#' [stringi][stringi::about_stringi] library.
 #'
 #' @param .data A data frame, data frame extension (e.g. a tibble), or a lazy
 #'   data frame (e.g. from dbplyr or dtplyr).

R/mutation-frequency.R

@@ -32,8 +32,8 @@ new_mut_freq <- function(x) {
 #'   filtered out from the analysis.
 #'
 #' @return
-#' A [tibble][tibble::tibble()] with the extra class `mut_freq`. The output has
-#' the following columns:
+#' A [tibble][tibble::tibble-package] with the extra class `mut_freq`. The
+#' output has the following columns:
 #'
 #' * `mutation_name`: The unique mutation sequenced.
 #' * `frequency`: The frequency of the mutation.

R/mutation-prevalence.R

@@ -32,8 +32,8 @@ new_mut_prev <- function(x) {
 #'   filtered out from the analysis.
 #'
 #' @return
-#' A [tibble][tibble::tibble()] with the extra class `mutation_prev`. The output
-#' has the following columns:
+#' A [tibble][tibble::tibble-package] with the extra class `mutation_prev`. The
+#' output has the following columns:
 #'
 #' * `mutation_name`: The unique mutation sequenced.
 #' * `n_total`: The number of samples for which a mutation site was sequenced.

R/read-deprecated.R

@@ -46,23 +46,23 @@
 #' @param .ref_file File path to the reference table.
 #' @param .alt_file File path to the alternate table.
 #' @param .cov_file File path to the coverage table.
-#' @param ...
-#'   <[`data-masking`](https://dplyr.tidyverse.org/reference/dplyr_data_masking.html)>
-#'   Expressions that return a logical value and are used to filter the data. If
-#'   multiple expressions are included, they are combined with the `&` operator.
-#'   Only rows for which all conditions evaluate to `TRUE` are kept.
+#' @param ... [`data-masking`][dplyr::dplyr_data_masking] Expressions that
+#'   return a logical value and are used to filter the data. If multiple
+#'   expressions are included, they are combined with the `&` operator. Only
+#'   rows for which all conditions evaluate to `TRUE` are kept.
 #' @param chrom `r lifecycle::badge("deprecated")`: The chromosome(s) to filter
 #'   to.
 #' @param gene `r lifecycle::badge("deprecated")`: The gene(s) to filter to.
 #' @param .file File path to a file.
 #' @param .name The information contained in the specific file. For example
 #'   `"coverage"` or `"ref_umi_count"`.
 #'
-#' @return A [`tibble()`][tibble::tibble()]. The first six columns contain the
-#'   metadata associated with each sample and mutation. Columns `ref_umi_count`
-#'   and `alt_umi_count` contain the umi count of the reference and alternate
-#'   allele, respectively. Column `coverage` contains the coverage for each data
-#'   point.
+#' @return
+#' A [`tibble()`][tibble::tibble-package]. The first six columns contain the
+#' metadata associated with each sample and mutation. Columns `ref_umi_count`
+#' and `alt_umi_count` contain the umi count of the reference and alternate
+#' allele, respectively. Column `coverage` contains the coverage for each data
+#' point.
 #'
 #' @seealso [vroom::vroom()] [dplyr::filter()]
 #' @keywords internal

R/read-tbl.R

@@ -30,11 +30,10 @@
 #' * [`between()`][dplyr::between()], [`near()`][dplyr::near()]
 #'
 #' @param .tbl File path to the table.
-#' @param ...
-#'   <[`data-masking`](https://dplyr.tidyverse.org/reference/dplyr_data_masking.html)>
-#'   Expressions that return a logical value and are used to filter the data. If
-#'   multiple expressions are included, they are combined with the `&` operator.
-#'   Only rows for which all conditions evaluate to `TRUE` are kept.
+#' @param ... [`data-masking`][dplyr::dplyr_data_masking] Expressions that
+#'   return a logical value and are used to filter the data. If multiple
+#'   expressions are included, they are combined with the `&` operator. Only
+#'   rows for which all conditions evaluate to `TRUE` are kept.
 #' @param .col_select One or more selection expressions, like in
 #'   [`dplyr::select()`][dplyr::select()]. Use `c()` or `list()` to use more
 #'   than one expression. See [`?dplyr::select`][dplyr::select()] for details on
@@ -46,11 +45,12 @@
 #'   to.
 #' @param gene `r lifecycle::badge("deprecated")` The gene(s) to filter to.
 #'
-#' @return A [`tibble()`][tibble::tibble()]. The first six columns contain the
-#'   metadata associated with each sample and mutation. The last column contains
-#'   the information parsed from the table. In some cases, this may be the
-#'   umi_count and in other cases it may be the coverage of the associated data
-#'   point.
+#' @return
+#' A [`tibble()`][tibble::tibble-package]. The first six columns contain the
+#' metadata associated with each sample and mutation. The last column contains
+#' the information parsed from the table. In some cases, this may be the
+#' umi_count and in other cases it may be the coverage of the associated data
+#' point.
 #'
 #' @seealso [vroom::vroom()] [dplyr::filter()]
 #' @name read-tbl