Use SDTM as input

.lintr

@@ -11,4 +11,4 @@ linters:
     seq_linter = seq_linter()
   )
 encoding: "UTF-8"
-exclusions: list("R/PKNCA_extra_parameters.R", "tests/testthat/test-PKNCA_extra_parameters.R", "inst/www/templates/script_template.R")
+exclusions: list("R/PKNCA_extra_parameters.R", "tests/testthat/test-PKNCA_extra_parameters.R", "inst/www/templates/script_template.R", "inst/www/templates/script_template_sdtm.R")

NAMESPACE

@@ -31,6 +31,7 @@ export(create_start_impute)
 export(delete_settings_version)
 export(detect_study_types)
 export(dose_profile_duplicates)
+export(ex_to_PKNCAdose)
 export(exploration_individualplot)
 export(exploration_meanplot)
 export(export_cdisc)
@@ -57,6 +58,7 @@ export(interval_remove_impute)
 export(l_pkcl01)
 export(multiple_matrix_ratios)
 export(parse_annotation)
+export(pc_to_PKNCAconc)
 export(pivot_wider_pknca_results)
 export(pk.calc.ermax)
 export(pk.calc.ertlst)
@@ -71,6 +73,7 @@ export(read_settings)
 export(read_versioned_settings)
 export(remove_pp_not_requested)
 export(run_app)
+export(sdtm_to_PKNCAdata)
 export(settings_version_summary)
 export(simplify_unit)
 export(translate_terms)
@@ -158,6 +161,7 @@ importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
 importFrom(reactable,reactable)
 importFrom(reactable.extras,reactable_extras_dependency)
+importFrom(rlang,.data)
 importFrom(rlang,expr)
 importFrom(rlang,sym)
 importFrom(rlang,syms)

R/get_session_code.R

@@ -213,10 +213,21 @@ get_settings_code <- function(
   settings_file_path,
   data_path,
   output_path = "settings_code.R",
-  template_path = system.file("www/templates/script_template.R", package = "aNCA")
+  template_path = NULL
 ) {
   settings <- read_settings(settings_file_path)
 
+  # Auto-select template based on input_mode if not explicitly provided
+  if (is.null(template_path)) {
+    mode <- settings[["input_mode"]] %||% "adnca"
+    template_file <- if (identical(mode, "sdtm")) {
+      "www/templates/script_template_sdtm.R"
+    } else {
+      "www/templates/script_template.R"
+    }
+    template_path <- system.file(template_file, package = "aNCA")
+  }
+
   session <- list(
     settings = settings[["settings"]],
     slope_rules = settings[["slope_rules"]],
@@ -228,7 +239,8 @@ get_settings_code <- function(
     extra_vars_to_keep = c(
       settings[["mapping"]][["Grouping_Variables"]], "DOSEA", "ATPTREF", "ROUTE"
     ),
-    time_duplicate_rows = settings[["time_duplicate_keys"]]
+    time_duplicate_rows = settings[["time_duplicate_keys"]],
+    sdtm_metabolites = settings[["sdtm_metabolites"]]
   )
 
   get_code(