Merge pull request #1074 from pharmaverse/1072-general-code-refactoring

General code refactoring: remove duplicates, correct docs (#1072)

Author: Gero1999

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9101
+Version: 0.1.0.9102
 Authors@R: c(
     person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
            comment = c(ORCID = "0009-0001-1626-1526")),

R/PKNCA.R

@@ -634,6 +634,8 @@ PKNCA_build_units_table <- function(o_conc, o_dose) { # nolint
 #' 1. Checks if the specified unit columns exist in the PKNCA object.
 #' 2. If a column does not exist, it creates the column and assigns default values.
 #' 3. If not default values are provided, it assigns NA to the new column.
+#' @keywords internal
+#' @noRd
 ensure_column_unit_exists <- function(pknca_obj, unit_name) {
   for (unit in unit_name) {
     if (is.null(pknca_obj$columns[[unit]])) {
@@ -659,6 +661,8 @@ ensure_column_unit_exists <- function(pknca_obj, unit_name) {
 #' @param df A data frame.
 #' @param strata_cols Column names in df whose unique combination defines the strata.
 #' @returns A data frame containing the strata columns and their minimal set of grouping columns.
+#' @keywords internal
+#' @noRd
 select_minimal_grouping_cols <- function(df, strata_cols) {
   # If there is no strata_cols specified, simply return the original df
   if (length(strata_cols) == 0) {
@@ -757,6 +761,8 @@ PKNCA_hl_rules_exclusion <- function(res, rules) { # nolint
 #' @examples
 #' # Suppose processed_pknca_data is a valid PKNCA data object
 #' # check_valid_pknca_data(processed_pknca_data)
+#' @keywords internal
+#' @noRd
 check_valid_pknca_data <- function(processed_pknca_data, check_exclusion_has_reason = TRUE) {
 
   if (check_exclusion_has_reason) {

R/PKNCA_extra_parameters.R

@@ -134,12 +134,18 @@ PKNCA::PKNCA.set.summary(
 
 
 
-# Helper to generate missing-data checking messages for paired vectors
-#
-# This function accepts two columns/vectors (for example, concentrations
-# and volumes). It computes missingness internally and produces a character
-# vector of human-readable messages describing the missingness that matches
-# the style used in the package (used previously in `pk.calc.ae`).
+#' Generate missing-data checking messages for paired vectors
+#'
+#' Accepts two columns/vectors (e.g., concentrations and volumes), computes
+#' missingness, and returns human-readable messages describing it.
+#'
+#' @param a First vector.
+#' @param b Second vector.
+#' @param name_a Label for the first vector in messages.
+#' @param name_b Label for the second vector in messages.
+#' @returns Character vector of missingness messages (empty if none).
+#' @keywords internal
+#' @noRd
 generate_missing_messages <- function(a, b,
                                       name_a = deparse(substitute(a)),
                                       name_b = deparse(substitute(b))) {

R/g_pkcg.R

@@ -651,7 +651,7 @@ g_pkcg03_lin <- function(data, ...) {
 #' Wrapper around aNCA::pkcg03() function. Calls the function with `LOG` scale argument.
 #' @param data Data to be passed into the plotting function.
 #' @param ...  Any other parameters to be passed into the plotting function.
-#' @returns ggplot2 object for pkcg01.
+#' @returns ggplot2 object for pkcg03.
 #' @export
 g_pkcg03_log <- function(data, ...) {
   pkcg03(adnca = data, scale = "LOG", ...)

R/officer-utils.R

@@ -7,6 +7,7 @@
 #' @param template Path to PowerPoint template file
 #' @importFrom officer read_pptx add_slide ph_with ph_location_type
 #' @return rpptx object
+#' @keywords internal
 create_pptx_doc <- function(path, title, template) {
   pptx <- read_pptx(template)
   add_pptx_sl_title(pptx, title)

R/pk_dose_qc_plot.R

@@ -70,7 +70,6 @@
 #'   colour_var_units = "DOSE_UNIT",
 #'   title = "Sample Dosing and PK Plot"
 #' )
-#' @export
 pk_dose_qc_plot <- function(data_conc,
                             data_dose = NULL,
                             x_var,

R/ratio_calculations.R

@@ -83,7 +83,6 @@ multiple_matrix_ratios <- function(data, matrix_col, conc_col, units_col,
 #' @param custom_pptestcd Optional character. If provided, will be used as the PPTESTCD value.
 #' @returns A data.frame result object with the calculated ratios.
 #' @export
-#' @export
 calculate_ratios <- function(
     data,
     test_parameter,
@@ -95,7 +94,6 @@ calculate_ratios <- function(
     custom_pptestcd = NULL) {
   UseMethod("calculate_ratios", data)
 }
-#' @export
 
 #' @export
 calculate_ratios.data.frame <- function(
@@ -231,7 +229,6 @@ calculate_ratios.data.frame <- function(
     select(any_of(c(names(df_test), "PPANMETH"))) %>%
     unique()
 }
-#' @export
 
 #' @export
 calculate_ratios.PKNCAresults <- function(

inst/shiny/modules/common/download_code.R

@@ -1,3 +1,10 @@
+#' Module for displaying NCA results.
+#'
+#' Provides a parameter picker, units table, interactive results table with
+#' color-coded acceptance flags and a download button for the NCA output.
+#'
+#' @param id Module namespace ID.
+
 # nca_results UI Module
 nca_results_ui <- function(id) {
   ns <- NS(id)

inst/shiny/modules/tab_nca/nca_results.R

@@ -1,3 +1,9 @@
+#' Module for viewing and downloading CDISC parameter datasets (PP, ADPP, ADNCA).
+#'
+#' Renders each dataset in an interactive table with CSV/XLSX download options.
+#'
+#' @param id Module namespace ID.
+
 parameter_datasets_ui <- function(id) {
   ns <- NS(id)
   navset_pill(