Move UI and server functions to a "For developers" section in the ref…

…erence index.
Boehringer-Ingelheim · Feb 25, 2025 · 3137a1e · 3137a1e
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diff --git a/R/mod_boxplot.R b/R/mod_boxplot.R
@@ -82,13 +82,15 @@ BP <- poc( # nolint
 #' It also includes a set of listings with information about the population, distribution and statistical comparisons.
 #'
 #' @name mod_boxplot
+#' @inheritParams boxplot_server
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_boxplot UI
+#' Boxplot UI function
 #' @param id Shiny ID `[character(1)]`
+#' @keywords developers
 #' @export
 boxplot_UI <- function(id) { # nolint
   # id assert ---- It goes on its own as id is used to provide context to the other assertions
@@ -188,7 +190,8 @@ boxplot_UI <- function(id) { # nolint
   }
 }
 
-#' @describeIn mod_boxplot Server
+#' Boxplot server function
+#' @keywords developers
 #'
 #' @description
 #'
@@ -727,6 +730,8 @@ boxplot_server <- function(id,
 #' Shiny ID of the module receiving the selected subject ID in the data listing. This ID must
 #' be present in the app or be NULL.
 #'
+#' inheritParams boxplot_server
+#'
 #' @name mod_boxplot
 #'
 #' @keywords main
@@ -861,7 +866,8 @@ dataset_info_boxplot <- function(bm_dataset_name, group_dataset_name, ...) {
 
 mod_boxplot <- CM$module(mod_boxplot, check_mod_boxplot, dataset_info_boxplot)
 
-#' @describeIn mod_boxplot Boxplot wrapper when its output is fed into papo module
+#' Boxplot wrapper when its output is fed into the papo module
+#' @keywords main
 #' @export
 mod_boxplot_papo <- function(...) {
   .Deprecated("mod_boxplot_papo", msg = "'mod_boxplot_papo' is no longer required and should be replaced by 'mod_boxplot'. It is still available for compatibility purposes") # nolint

diff --git a/R/mod_corr_hm.R b/R/mod_corr_hm.R
@@ -71,23 +71,21 @@ CH_MSG <- poc( # nolint
 
 #' Correlation Heatmap module
 #'
-#' @param id Shiny ID `[character(1)]`
-#'
 #' @param default_cat Default selected categories
 #'
 #' @param default_par Default selected parameters
 #'
 #' @param default_visit Default selected visits
 #'
-#' @param default_corr_method Name of default correlation method
-#'
 #' @name mod_corr_hm
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_corr_hm UI
+#' Correlation heatmap UI function
+#'
+#' @keywords developers
 #'
 #' @param id `[character(1)]`
 #'
@@ -462,7 +460,9 @@ scatter_plot <- function(df, x_var, y_var) {
 }
 
 
-#' @describeIn mod_corr_hm Server
+#' Correlation heatmap server function
+#'
+#' @keywords developers
 #'
 #' @param id `[character(1)]`
 #'
@@ -862,6 +862,8 @@ ch_subset_data <- function(sel, cat_col, par_col, val_col, vis_col, bm_ds, subj_
 #'
 #' @name mod_corr_hm
 #'
+#' @inheritParams corr_hm_server
+#'
 #' @keywords main
 #'
 #' @export

diff --git a/R/mod_forest.R b/R/mod_forest.R
@@ -99,15 +99,16 @@ FP_MSG <- poc(
 
 #' Forest plot module
 #'
-#' @param id Shiny ID `[character(1)]`
-#'
 #' @name mod_forest
+#' @inheritParams forest_server
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_forest UI
+#' Forest plot UI function
+#'
+#' @keywords developers
 #'
 #' @param id `[character(1)]`
 #'
@@ -461,7 +462,9 @@ gen_result_table_fun_ <- function(ds, sl, fun, label) {
 gen_result_table_fun <- strict(gen_result_table_fun_)
 
 
-#' @describeIn mod_forest Server
+#' Forest plot server function
+#'
+#' @keywords developers
 #'
 #' @param id `[character(1)]`
 #'

diff --git a/R/mod_lineplot.R b/R/mod_lineplot.R
@@ -97,8 +97,9 @@ LP_CNT <- poc(
 
 # UI and server functions
 
-#' @describeIn mod_lineplot UI
-# NOTE: id documented in lineplot_server
+#' Lineplot UI function
+#' @inheritParams lineplot_server
+#' @keywords developers 
 #' @export
 lineplot_UI <- function(id) {
   # UI ----
@@ -545,7 +546,7 @@ generate_ref_line_data <- function(df, show_all_ref_vals) {
 }
 
 
-#' @describeIn mod_lineplot Server
+#' Lineplot server function
 #'
 #' @param id Shiny ID `[character(1)]`
 #'
@@ -635,6 +636,8 @@ generate_ref_line_data <- function(df, show_all_ref_vals) {
 #'
 #' Default projection for the Y axis
 #'
+#' @keywords developers
+#'
 #' @export
 #'
 lineplot_server <- function(id,
@@ -1548,6 +1551,8 @@ lineplot_server <- function(id,
 #' Shiny ID of the module receiving the selected subject ID in the single subject listing. This ID must
 #' be present in the app or be NULL.
 #'
+#' @inheritParams lineplot_server
+#'
 #' @name mod_lineplot
 #'
 #' @keywords main

diff --git a/R/mod_roc.R b/R/mod_roc.R
@@ -147,15 +147,17 @@ ROC_PLOT_VAL <- poc(
 
 #' ROC module
 #'
-#' @param id Shiny ID `[character(1)]`
+#' @inheritParams roc_server
 #'
 #' @name mod_roc
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_roc UI
+#' ROC UI function
+#' @keywords developers
+#' @inheritParams roc_server
 #' @export
 roc_UI <- function(id) {
   # id assert  It goes on its own as id is used to provide context to the other assertions
@@ -354,8 +356,8 @@ roc_UI <- function(id) {
   }
 }
 
-#' @describeIn mod_roc Server
-#'
+#' ROC server function
+#' @keywords developers
 #' @description
 #'
 #' ## Input dataframes:
@@ -387,6 +389,7 @@ roc_UI <- function(id) {
 #' one record per subject
 #'
 #' It expects to contain, at least, `subjid_var`
+#' @param id Shiny ID `[character(1)]`
 #'
 #' @param pred_dataset,resp_dataset,group_dataset `[data.frame()]`
 #'

diff --git a/R/mod_scatter.R b/R/mod_scatter.R
@@ -86,13 +86,16 @@ SP <- poc( # nolint
 #' It also includes a set of listings with information about the population and the regression and correlation
 #' estimates.
 #'
+#' @inheritParams scatterplot_server
+#'
 #' @name mod_scatterplot
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_scatterplot UI
+#' Scatter plot UI function
+#' @keywords developers
 #' @param id Shiny ID `[character(1)]`
 #' @export
 scatterplot_UI <- function(id) { # nolint
@@ -194,7 +197,9 @@ scatterplot_UI <- function(id) { # nolint
   }
 }
 
-#' @describeIn mod_scatterplot Server
+#' Scatter plot server function
+#'
+#' @keywords developers
 #'
 #' @description
 #'

diff --git a/R/mod_scatter_matrix.R b/R/mod_scatter_matrix.R
@@ -68,12 +68,14 @@ SPM <- poc( # nolint
 #'  of grouping. It also includes correlation stats.
 #'
 #' @name mod_scatterplotmatrix
+#' @inheritParams scatterplotmatrix_server
 #'
 #' @keywords main
 #'
 NULL
 
-#' @describeIn mod_scatterplotmatrix UI
+#' Scatter plot matrix UI function
+#' @keywords developers
 #' @param id Shiny ID `[character(1)]`
 #' @export
 scatterplotmatrix_UI <- function(id) { # nolint
@@ -134,8 +136,8 @@ scatterplotmatrix_UI <- function(id) { # nolint
   }
 }
 
-#' @describeIn mod_scatterplotmatrix Server
-#'
+#' Scatter plot matrix server function
+#' @keywords developers
 #' @description
 #'
 #' ## Input dataframes:

diff --git a/R/mod_wfphm.R b/R/mod_wfphm.R
@@ -264,7 +264,8 @@ WFPHM_MSG <- pack_of_constants( # nolint
 #'
 NULL
 
-#' @describeIn wfphm_wf UI
+#' Waterfall UI function
+#' @keywords developers
 wfphm_wf_UI <- function(id) { # nolintr
 
   # id assert ---- It goes on its own as id is used to provide context to the other assertions
@@ -311,7 +312,8 @@ wfphm_wf_UI <- function(id) { # nolintr
 }
 
 # nolint start cyclocomp_linter
-#' @describeIn wfphm_wf server
+#' Waterfall server function
+#' @keywords developers
 wfphm_wf_server <- function(id,
                             bm_dataset,
                             group_dataset,
@@ -908,7 +910,8 @@ wfphm_wf_rename_cols <- function(df) {
 #'
 NULL
 
-#' @describeIn wfphm_hmcat UI
+#' Waterfall plus heatmap categorical heatmap UI function
+#' @keywords developers
 wfphm_hmcat_UI <- function(id) { # nolint
 
   # id assert ---- It goes on its own as id is used to provide context to the other assertions
@@ -943,7 +946,8 @@ wfphm_hmcat_UI <- function(id) { # nolint
   )
 }
 
-#' @describeIn wfphm_hmcat server
+#' Waterfall plus heatmap categorical heatmap server function
+#' @keywords developers
 wfphm_hmcat_server <- function(id,
                                dataset,
                                subjid_var,
@@ -1906,9 +1910,7 @@ wfphm_hmpar_subset <- function(
 #'
 #' See the subsections for each of plots particularities
 #'
-#' @param id Shiny ID `[character(1)]`
-#'
-#' @param bm_dataset `[shiny::reactive(data.frame) | shinymeta::metaReactive(data.frame)]`
+#' @param module_id Shiny ID `[character(1)]`
 #'
 #' It expects the following format:
 #'
@@ -1917,8 +1919,6 @@ wfphm_hmpar_subset <- function(
 #'  - `cat_var`, `par_var`, `visit_var` and `subjid_var` columns are factors
 #'  - It contains at least 1 row
 #'
-#' @param group_dataset `[shiny::reactive(data.frame) | shinymeta::metaReactive(data.frame)]`
-#'
 #' It expects the following format:
 #'
 #'  - it contains, at least, the columns specified in the parameters: `subjid_var`
@@ -1939,8 +1939,6 @@ wfphm_hmpar_subset <- function(
 #' named vector containing a set of transformation where the name is the string shown in the selector and the value is
 #' function to be applied according to details section.
 #'
-#' @param tr_choices the names of the entries in tr_mapper
-#'
 #' @param bar_group_palette `[list(palettes)]`
 #'
 #' list of custom palettes to apply to bar_grouping. It receives the values used for grouping and must return a DaVinci
@@ -1980,8 +1978,12 @@ wfphm_hmpar_subset <- function(
 #'
 NULL
 
-#' @describeIn wfphm UI
+#' Waterfall plus heatmap UI function
+#'
+#' @param id Shiny ID `[character(1)]`
+#' @param tr_choices the names of the entries in tr_mapper
 #'
+#' @keywords developers
 #' @export
 
 wfphm_UI <- function(id, tr_choices = names(tr_mapper_def())) { # nolint
@@ -2066,8 +2068,14 @@ wfphm_UI <- function(id, tr_choices = names(tr_mapper_def())) { # nolint
   wfphm_mainpanel
 }
 
-#' @describeIn wfphm server
+#' Waterfall plus heatmap server function
+#' @keywords developers
+#' @param bm_dataset `[shiny::reactive(data.frame) | shinymeta::metaReactive(data.frame)]`
+#' @param group_dataset `[shiny::reactive(data.frame) | shinymeta::metaReactive(data.frame)]`
 #'
+#' @keywords developers
+#' @inheritParams wfphm_UI
+#' @inheritParams mod_wfphm
 #' @export
 wfphm_server <- function(id,
                          bm_dataset,
@@ -2244,7 +2252,6 @@ tr_mapper_def <- function() {
 
 #' @describeIn wfphm dv.manager wrapper for the module
 #'
-#' @param module_id Shiny id
 #' @param bm_dataset_name,group_dataset_name
 #'
 #' The name of the dataset

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -18,6 +18,9 @@ reference:
   - title: Mock Applications
   - contents: 
     - has_keyword("mock")
+  - title: For developers
+  - contents: 
+    - has_keyword("developers")
   - title: Additional Documentation
   - subtitle: Lineplot
   - contents: