UI: Consolidate parameter-related settings into Parameter Selection tab

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: aNCA
 Title: (Pre-)Clinical NCA in a Dynamic Shiny App
-Version: 0.1.0.9156
+Version: 0.1.0.9157
 Authors@R: c(
     person("Ercan", "Suekuer", email = "ercan.suekuer@roche.com", role = "aut",
            comment = c(ORCID = "0009-0001-1626-1526")),

inst/shiny/modules/tab_nca/nca_setup.R

@@ -20,7 +20,7 @@ nca_setup_ui <- function(id) {
   navset_pill_list(
     widths = c(2, 10),
     nav_panel(
-      "Settings",
+      "NCA Settings",
       fluidRow(
         actionButton(
           ns("open_save_settings_modal"),
@@ -29,17 +29,17 @@ nca_setup_ui <- function(id) {
           class = "btn-primary"
         )
       ),
-      fluidRow(units_table_ui(ns("units_table"))),
-      settings_ui(ns("nca_settings")),
-      accordion(
-        accordion_panel(
-          title = "Ratio Calculations",
-          ratios_table_ui(ns("ratio_calculations_table"))
-        ),
-        open = c("General Settings", "Parameter Selection")
+      settings_ui(ns("nca_settings"))
+    ),
+    nav_panel(
+      "Parameter Selection",
+      parameter_selection_ui(
+        ns("nca_setup_parameter"),
+        units_ui = units_table_ui(ns("units_table")),
+        intervals_ui = partial_intervals_ui(ns("nca_settings")),
+        ratios_ui = ratios_table_ui(ns("ratio_calculations_table"))
       )
     ),
-    nav_panel("Parameter Selection", parameter_selection_ui(ns("nca_setup_parameter"))),
     nav_panel("Slope Selector", slope_selector_ui(ns("slope_selector"))),
     nav_panel("General Exclusions", general_exclusions_ui(ns("general_exclusions")))
   )

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

@@ -17,7 +17,10 @@
 #'     `list("Study Type A" = c("p1", "p2"))`.}
 #'   \item{types_df}{A `reactive` data frame containing the study type detection results.}
 
-parameter_selection_ui <- function(id) {
+parameter_selection_ui <- function(id,
+                                   units_ui = NULL,
+                                   intervals_ui = NULL,
+                                   ratios_ui = NULL) {
   ns <- NS(id)
   tagList(
     # Header row with help button
@@ -31,10 +34,14 @@ parameter_selection_ui <- function(id) {
       ),
       column(
         width = 8,
-        actionButton(ns("show_param_ref"),
-          label = "PK parameter details",
-          icon = icon("book"),
-          class = "btn-sm btn-outline-primary"
+        div(
+          class = "d-flex gap-2",
+          actionButton(ns("show_param_ref"),
+            label = "PK parameter details",
+            icon = icon("book"),
+            class = "btn-sm btn-outline-primary"
+          ),
+          units_ui
         )
       ),
       column(
@@ -55,9 +62,19 @@ parameter_selection_ui <- function(id) {
                 "for that study type. Hover a column header to see the ",
                 "full parameter name."
               ),
+              tags$li(
+                tags$b("Partial interval calculations"),
+                ": Define custom time intervals for partial AUC ",
+                "and related parameters."
+              ),
+              tags$li(
+                tags$b("Ratio calculations"),
+                ": Configure parameter ratio calculations ",
+                "between analytes."
+              ),
               tags$li(
                 tags$b("Detected study types"),
-                ": Expandable section showing detected study types ",
+                ": Study types detected in the data ",
                 "and the number of subjects."
               )
             )
@@ -113,6 +130,16 @@ parameter_selection_ui <- function(id) {
 
     br(),
     accordion(
+      accordion_panel(
+        title = "Partial Interval Calculations",
+        icon = icon("clock"),
+        intervals_ui
+      ),
+      accordion_panel(
+        title = "Ratio Calculations",
+        icon = icon("divide"),
+        ratios_ui
+      ),
       accordion_panel(
         title = "Detected Study Types",
         icon = icon("microscope"),
@@ -430,7 +457,7 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       can_exc <- params$can_excretion[i]
       locs <- character(0)
       if (type %in% c("Standard", "IV")) {
-        locs <- c(locs, "Setup > Parameter Selection")
+        locs <- c(locs, "Parameter Selection > Matrix")
       }
       if (type == "Urine" || identical(can_exc, "T")) {
         locs <- c(
@@ -439,10 +466,10 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       }
       if (type == "PKNCA-not-covered" && cat == "Ratio") {
         locs <- c(
-          locs, "Additional Analysis > Ratios"
+          locs, "Parameter Selection > Ratio Calculations"
         )
       }
-      if (length(locs) == 0) "Setup > Parameter Selection"
+      if (length(locs) == 0) "Parameter Selection > Matrix"
       else paste(locs, collapse = "; ")
     },
     character(1)

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

@@ -13,6 +13,83 @@
 #'
 #' @returns A reactive with a list with all settings.
 
+#' Partial Interval Calculations UI
+#'
+#' Extracted so it can be placed in the Parameter Selection tab
+#' while keeping its server logic in settings_server.
+#'
+#' @param id The settings module namespace ID (same as settings_ui).
+partial_intervals_ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    fluidRow(
+      column(
+        width = 10,
+        actionButton(ns("addRow"), "(+) Add Row", class = "btn-success"),
+      ),
+      column(
+        width = 2,
+        dropdown(
+          div(
+            tags$h2("Partial Interval Calculations Help"),
+            p(
+              "Define custom time intervals for calculating partial area",
+              "and related parameters. Add a row for each interval you need."
+            ),
+            p("For each row, specify:"),
+            tags$ul(
+              tags$li(
+                tags$b("Parameter"),
+                ": The interval calculation to perform (e.g., AUCINT, AUCINTA, CAVGINT)."
+              ),
+              tags$li(
+                tags$b("Start"),
+                ": Start time of the interval."
+              ),
+              tags$li(
+                tags$b("End"),
+                ": End time of the interval."
+              )
+            ),
+            p(
+              tags$b("Note:"),
+              " Rows with missing Start or End values will be ignored."
+            ),
+            tags$table(
+              class = "imputation-help-table",
+              tags$thead(
+                tags$tr(
+                  tags$th("Parameter"),
+                  tags$th("Description")
+                )
+              ),
+              tags$tbody(
+                tr("AUCINT", "AUC from T1 to T2 (based on AUClast extrapolation)"),
+                tr("AUCINTD", "AUC from T1 to T2 Normalized by Dose"),
+                tr("AUCINTA", "AUCint (based on AUCall extrapolation)"),
+                tr("AUCINTAD", "AUCint (based on AUCall extrapolation, dose-aware)"),
+                tr("AUCINTIS", "AUCint (based on AUCinf,obs extrapolation)"),
+                tr("AUCINTID", "AUCint (based on AUCinf,obs extrapolation, dose-aware)"),
+                tr("AUCINTIP", "AUCint (based on AUCinf,pred extrapolation)"),
+                tr("AUCINTPD", "AUCint (based on AUCinf,pred extrapolation, dose-aware)"),
+                tr("CAVGINT", "Average Concentration from T1 to T2"),
+                tr("RCAMINT", "Amount Recovered from T1 to T2"),
+                tr("FREXINT", "Fraction Excreted from T1 to T2")
+              )
+            )
+          ),
+          style = "unite",
+          right = TRUE,
+          icon = icon("question"),
+          status = "primary",
+          width = "600px"
+        )
+      )
+    ),
+    reactableOutput(ns("int_parameters_table"))
+  )
+}
+
 settings_ui <- function(id) {
   ns <- NS(id)
 
@@ -100,74 +177,6 @@ settings_ui <- function(id) {
         # Moved input_switch for should_impute_c0 into the data_imputation module
         data_imputation_ui(ns("data_imputation"))
       ),
-      accordion_panel(
-        title = "Partial Interval Calculations",
-        fluidRow(
-          column(
-            width = 10,
-            actionButton(ns("addRow"), "(+) Add Row", class = "btn-success"),
-          ),
-          column(
-            width = 2,
-            dropdown(
-              div(
-                tags$h2("Partial Interval Calculations Help"),
-                p(
-                  "Define custom time intervals for calculating partial area",
-                  "and related parameters. Add a row for each interval you need."
-                ),
-                p("For each row, specify:"),
-                tags$ul(
-                  tags$li(
-                    tags$b("Parameter"),
-                    ": The interval calculation to perform (e.g., AUCINT, AUCINTA, CAVGINT)."
-                  ),
-                  tags$li(
-                    tags$b("Start"),
-                    ": Start time of the interval."
-                  ),
-                  tags$li(
-                    tags$b("End"),
-                    ": End time of the interval."
-                  )
-                ),
-                p(
-                  tags$b("Note:"),
-                  " Rows with missing Start or End values will be ignored."
-                ),
-                tags$table(
-                  class = "imputation-help-table",
-                  tags$thead(
-                    tags$tr(
-                      tags$th("Parameter"),
-                      tags$th("Description")
-                    )
-                  ),
-                  tags$tbody(
-                    tr("AUCINT", "AUC from T1 to T2 (based on AUClast extrapolation)"),
-                    tr("AUCINTD", "AUC from T1 to T2 Normalized by Dose"),
-                    tr("AUCINTA", "AUCint (based on AUCall extrapolation)"),
-                    tr("AUCINTAD", "AUCint (based on AUCall extrapolation, dose-aware)"),
-                    tr("AUCINTIS", "AUCint (based on AUCinf,obs extrapolation)"),
-                    tr("AUCINTID", "AUCint (based on AUCinf,obs extrapolation, dose-aware)"),
-                    tr("AUCINTIP", "AUCint (based on AUCinf,pred extrapolation)"),
-                    tr("AUCINTPD", "AUCint (based on AUCinf,pred extrapolation, dose-aware)"),
-                    tr("CAVGINT", "Average Concentration from T1 to T2"),
-                    tr("RCAMINT", "Amount Recovered from T1 to T2"),
-                    tr("FREXINT", "Fraction Excreted from T1 to T2")
-                  )
-                )
-              ),
-              style = "unite",
-              right = TRUE,
-              icon = icon("question"),
-              status = "primary",
-              width = "600px"
-            )
-          )
-        ),
-        reactableOutput(ns("int_parameters_table"))
-      ),
       accordion_panel(
         title = "Flag Rule Sets",
         fluidRow(
@@ -220,7 +229,7 @@ settings_ui <- function(id) {
           tooltip = "Minimum required half-life span ratio for lambda-z related parameters"
         )
       ),
-      open = c("General Settings", "Parameter Selection")
+      open = "General Settings"
     )
   )
 }