feat: add log-points for NCA user input changes

inst/shiny/functions/utils-exclusions.R

@@ -90,6 +90,12 @@ EXCL_COLOR_BOTH <- "#FFD9B3"  # orange — NCA + TLG
     exclusion_list(append(current, list_new_reason))
     updateTextInput(session, "exclusion_reason", value = "")
     updateReactable(table_id, selected = NA)
+
+    type_label <- .exclusion_type_label(nca_checked, tlg_checked)
+    log_info(
+      "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+      ", reason='", reason, "'"
+    )
   }
 }
 

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

@@ -196,6 +196,15 @@ data_imputation_server <- function(id, settings_override) {
       }
     })
 
+    observeEvent(input$select_blq_strategy, {
+      log_info("BLQ imputation strategy changed: ", input$select_blq_strategy)
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$should_impute_c0, {
+      state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
+      log_info("Start concentration imputation ", state)
+    }, ignoreInit = TRUE)
+
     blq_imputation_rule <- reactive({
       req(input$select_blq_strategy)
       rule_list <- switch(input$select_blq_strategy,

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

@@ -131,6 +131,7 @@ general_exclusions_server <- function(
 
         xbtn_counter(max(new_ids))
         exclusion_list(rehydrated_list)
+        log_info("Exclusions restored from settings: ", length(overrides), " rules loaded")
       }
     })
 
@@ -167,6 +168,7 @@ general_exclusions_server <- function(
       lapply(lst, function(item) {
         xbtn_id <- item$xbtn_id
         observeEvent(input[[xbtn_id]], {
+          log_info("Exclusion removed: reason='", item$reason, "'")
           current <- exclusion_list()
           exclusion_list(
             Filter(function(x) x$xbtn_id != xbtn_id, current)

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

@@ -93,7 +93,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_trace("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -126,7 +126,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_trace("Slope selector: removing manual slope rule")
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
       edited_slopes <- manual_slopes()[-selected, ]
@@ -138,7 +138,7 @@ manual_slopes_table_server <- function(
     # Render the manual slopes table (reactable)
     output$manual_slopes <- renderReactable({
       req(manual_slopes())
-      log_trace("{id}: rendering slope edit data table")
+      log_trace(id, ": rendering slope edit data table")
       isolate({
         data <- manual_slopes()
       })

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

@@ -286,7 +286,10 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
           params <- selection_debounce()
           n_params <- if (is.null(params)) 0 else length(params)
 
-          log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
+          log_info("Parameter selection for '", study_type, "': ", n_params, " parameters selected.")
+          if (n_params > 0) {
+            log_debug("Parameters for '", study_type, "': ", paste(params, collapse = ", "))
+          }
         }, ignoreNULL = FALSE, ignoreInit = TRUE)
       })
     })

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

@@ -258,6 +258,10 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     # A guard flag prevents infinite observer loops.
     updating_filters <- reactiveVal(FALSE)
 
+    # Guard to suppress log noise during initial data load / settings restore.
+    # Set to TRUE after the first analyte cascade completes.
+    filters_initialized <- reactiveVal(FALSE)
+
     # settings_override is consumed once during the first cascade after
     # settings upload. After that, pending_settings is set to NULL so
     # subsequent user-driven changes are not overridden by stale values.
@@ -299,7 +303,14 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       req(data(), input$select_analyte)
       if (updating_filters()) return()
       updating_filters(TRUE)
-      on.exit(updating_filters(FALSE))
+      on.exit({
+        updating_filters(FALSE)
+        if (!filters_initialized()) filters_initialized(TRUE)
+      })
+
+      if (filters_initialized()) {
+        log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+      }
 
       settings <- .consume_settings()
 
@@ -335,6 +346,10 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      if (filters_initialized()) {
+        log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+      }
+
       settings <- .consume_settings()
 
       all_analyte <- unique(data()$PARAM) %>% na.omit()
@@ -356,6 +371,25 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       .update_profile(settings)
     })
 
+    # Log profile, method, and min half-life points changes
+    observeEvent(input$select_profile, {
+      if (filters_initialized()) {
+        log_info("NCA profile changed: ", paste(input$select_profile, collapse = ", "))
+      }
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$method, {
+      if (filters_initialized()) {
+        log_info("Extrapolation method changed: ", input$method)
+      }
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$min_hl_points, {
+      if (filters_initialized()) {
+        log_info("Min. half-life points changed: ", input$min_hl_points)
+      }
+    }, ignoreInit = TRUE)
+
     # Include keyboard limits for the settings GUI display
 
     # Keyboard limits for the setting thresholds
@@ -365,6 +399,19 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "LAMZSPN_threshold", min = 0, lab = "LAMZSPN")
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
+    # Log flag rule changes
+    lapply(c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN"), function(flag) {
+      rule_id <- paste0(flag, "_rule")
+      threshold_id <- paste0(flag, "_threshold")
+      observeEvent(input[[rule_id]], {
+        state <- if (input[[rule_id]]) "enabled" else "disabled"
+        log_info("Flag rule ", flag, " ", state)
+      }, ignoreInit = TRUE)
+      observeEvent(input[[threshold_id]], {
+        log_info("Flag rule ", flag, " threshold changed: ", input[[threshold_id]])
+      }, ignoreInit = TRUE)
+    })
+
     # Reactive value to store the partial intervals data table
     # Define the parameters that can be used for partial area calculations
     PARTIAL_INT_PARAMS <- metadata_nca_parameters %>%

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

@@ -246,6 +246,9 @@ slope_selector_server <- function( # nolint
     manual_slopes <- slopes_table$manual_slopes
     refresh_reactable <- slopes_table$refresh_reactable
 
+    # Track user-initiated slope changes (buttons, plotly clicks)
+    user_changed_slopes <- reactiveVal(FALSE)
+
     # Define the click events for the point exclusion and selection in the slope plots
     last_click_data <- reactiveVal(NULL)
     observeEvent(event_data("plotly_click", priority = "event"), {
@@ -259,19 +262,33 @@ slope_selector_server <- function( # nolint
       )
       # Update reactive values: last click & manual slopes table
       last_click_data(click_result$last_click_data)
+      user_changed_slopes(TRUE)
       manual_slopes(click_result$manual_slopes)
 
       # render rectable anew #
       shinyjs::runjs("memory = {};") # needed to properly reset reactable.extras widgets
       refresh_reactable(refresh_reactable() + 1)
     })
 
+    # Also flag user-initiated changes from add/remove buttons
+    observeEvent(slopes_table$refresh_reactable(), {
+      user_changed_slopes(TRUE)
+    }, ignoreInit = TRUE)
+
     #' Separate event handling updating displayed reactable upon every change (adding and removing
     #' rows, plots selection, edits). This needs to be separate call, since simply re-rendering
     #' the table would mean losing focus on text inputs when entering values.
     observeEvent(manual_slopes(), {
       req(manual_slopes())
 
+      if (user_changed_slopes()) {
+        n_rules <- nrow(manual_slopes())
+        n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+        n_incl <- n_rules - n_excl
+        log_info("Slope rules updated: ", n_rules, " total (", n_incl, " selections, ", n_excl, " exclusions)")
+        user_changed_slopes(FALSE)
+      }
+
       # Update reactable with rules
       reactable::updateReactable(
         outputId = "manual_slopes",