fix: R script and settings export missing volume unit simplification (#1190)

NEWS.md

@@ -64,6 +64,7 @@
 
 
 ## Bugs fixed
+* R script and settings export now include volume unit simplifications. Unit change detection uses value comparison (`PPSTRESU != PPORRESU`) instead of an edit-tracking flag, so automatic simplifications (e.g. `mg*L/mL` → `mg`) are captured alongside user edits (#1190)
 * Fixed ratio calculations with `Aggregate Subject = yes` or `if-needed` not aggregating reference values, and ratio parameter columns (FABS, FREL, etc.) not appearing in NCA Results (#1273)
 * Last dose interval end time now extends to the last observed sample instead of being cut off at TRTRINT (tau), ensuring all collected data points are included in NCA calculations (#1235)
 * Fixed NA `PPSTRESU` handling across NCA results: descriptive statistics no longer crash when a parameter group has all-NA units, and manual interval parameters (e.g., RCAMINT) no longer get `NA` appended to their column names (#1216)

inst/shiny/functions/zip-utils.R

@@ -523,10 +523,12 @@ prepare_export_files <- function(target_dir,
 .export_settings <- function(target_dir, session) {
   settings_list <- session$userData$settings()
 
-  if (!is.null(settings_list$units)) {
-    settings_list$units <- settings_list$units %>%
-      dplyr::filter(!default) %>%
-      dplyr::select(-default)
+  # Units are stored separately from settings() to avoid triggering
+  # the settings debounce cascade. Read directly for export.
+  units_snapshot <- session$userData$units_table()
+  if (!is.null(units_snapshot)) {
+    settings_list$units <- units_snapshot %>%
+      dplyr::filter(!is.na(PPSTRESU), !is.na(PPORRESU), PPSTRESU != PPORRESU)
   }
 
   settings_list$ratio_table <- session$userData$ratio_table()

inst/shiny/modules/tab_nca.R

@@ -203,9 +203,7 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override,
         # Update units table
         processed_pknca_data <- processed_pknca_data()
         if (!is.null(session$userData$units_table())) {
-          custom_units <- select(
-            session$userData$units_table(), -any_of("default")
-          )
+          custom_units <- session$userData$units_table()
           by_cols <- intersect(names(processed_pknca_data$units), names(custom_units))
           by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
           processed_pknca_data$units <- rows_update(
@@ -214,6 +212,11 @@ tab_nca_server <- function(id, pknca_data, extra_group_vars, settings_override,
             by = by_cols,
             unmatched = "ignore"
           )
+        } else {
+          # First NCA run: populate units_table from the data so settings
+          # export includes volume-simplified units even if the user never
+          # opens the Units modal.
+          session$userData$units_table(processed_pknca_data$units)
         }
 
         #' Calculate results

inst/shiny/modules/tab_nca/nca_setup.R

@@ -169,7 +169,23 @@ nca_setup_server <- function(id, data, adnca_data, extra_group_vars, settings_ov
       has_full_units <- all(c("PPORRESU", "conversion_factor") %in% names(imported_units))
 
       if (has_full_units) {
-        session$userData$units_table(imported_units)
+        # Imported settings contain only changed rows (PPSTRESU != PPORRESU).
+        # Merge them into the full data-derived units table so downstream code
+        # that expects the complete table (e.g. nca_results.R) works correctly.
+        observe({
+          req(processed_pknca_data())
+          data_units <- processed_pknca_data()$units
+          by_cols <- intersect(names(data_units), names(imported_units))
+          by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
+          merged <- rows_update(
+            data_units,
+            imported_units,
+            by = by_cols,
+            unmatched = "ignore"
+          )
+          session$userData$units_table(merged)
+        }) %>%
+          bindEvent(processed_pknca_data(), once = TRUE)
       } else {
         # Defaults-only format: wait for data-derived units, then resolve.
         observe({
@@ -231,10 +247,12 @@ nca_setup_server <- function(id, data, adnca_data, extra_group_vars, settings_ov
       },
       content = function(con) {
         export_settings <- final_settings()
-        if (!is.null(export_settings$units)) {
-          export_settings$units <- export_settings$units %>%
-            filter(!default) %>%
-            select(-default)
+        # Units are stored separately from settings() to avoid triggering
+        # the settings debounce cascade. Read directly for export.
+        units_snapshot <- session$userData$units_table()
+        if (!is.null(units_snapshot)) {
+          export_settings$units <- units_snapshot %>%
+            filter(!is.na(PPSTRESU), !is.na(PPORRESU), PPSTRESU != PPORRESU)
         }
         export_settings$ratio_table <- ratio_table()
         payload <- list(

inst/shiny/modules/tab_nca/setup/settings.R

@@ -502,8 +502,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
             is.checked = input$LAMZSPN_rule,
             threshold = input$LAMZSPN_threshold
           )
-        ),
-        units = session$userData$units_table()
+        )
       )
     })
 

inst/shiny/modules/tab_nca/units_table.R

@@ -26,13 +26,12 @@ units_table_server <- function(id, mydata) {
 
     modal_units_table <- reactiveVal(NULL)
     observeEvent(input$open_units_table, {
-      default_units <- mydata()$units %>%
-        dplyr::mutate(default = TRUE)
+      default_units <- mydata()$units
 
       if (!is.null(session$userData$units_table())) {
-        custom_units <- dplyr::mutate(session$userData$units_table(), default = FALSE)
+        custom_units <- session$userData$units_table()
         by_cols <- intersect(names(default_units), names(custom_units))
-        by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor", "default"))
+        by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
         dplyr::rows_update(
           default_units,
           custom_units,
@@ -102,8 +101,7 @@ units_table_server <- function(id, mydata) {
         PPORRESU = colDef(name = "Default Unit"),
         PPSTRESU = colDef(name = "Custom Unit"),
         conversion_factor = colDef(name = "Conversion Factor"),
-        is_hidden = colDef(show = FALSE),
-        default = colDef(show = FALSE)
+        is_hidden = colDef(show = FALSE)
       ),
       pagination = FALSE,
       filterable = TRUE,
@@ -156,7 +154,6 @@ units_table_server <- function(id, mydata) {
           )
         }
 
-        modal_units_table[info$row, "default"] <- FALSE
         modal_units_table[info$row, "conversion_factor"] <- conversion_factor_value
       }
 
@@ -192,22 +189,19 @@ units_table_server <- function(id, mydata) {
       }
 
       log_trace("Applying custom units specification.")
-      modal_units_table() %>%
-        dplyr::filter(!default) %>%
-        session$userData$units_table()
+      session$userData$units_table(modal_units_table())
 
       # Close the modal message window for the user
       removeModal()
     })
 
     #' Update local `modal_units_table()` if the global value changes.
     observeEvent(session$userData$units_table(), {
-      default_units <- mydata()$units %>%
-        dplyr::mutate(default = TRUE)
+      default_units <- mydata()$units
 
-      custom_units <- dplyr::mutate(session$userData$units_table(), default = FALSE)
+      custom_units <- session$userData$units_table()
       by_cols <- intersect(names(default_units), names(custom_units))
-      by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor", "default"))
+      by_cols <- setdiff(by_cols, c("PPSTRESU", "conversion_factor"))
       dplyr::rows_update(
         default_units,
         custom_units,