check that ipred exists before adding to table

R/add_default_output_tables.R

@@ -66,7 +66,15 @@ add_default_output_tables <- function(
   ## goodness of fit, all rows
   if("fit" %in% tables && !(default_table_names[["fit"]] %in% existing_tables)) {
     if(verbose) cli::cli_alert_info("Adding output table for goodness of fit")
-    cols <- c("DV", "EVID", "MDV", "PRED", "IPRED", "CWRES", "NPDE")
+    optional_vars <- c("MDV", "IPRED")
+    add_optional <- c()
+    for(variab in optional_vars) {
+      check_var <- check_nm_table_variables(model, variab, throw_error = FALSE)
+      if(is.null(check_var)) { # i.e. IPRED is declared as variable and we can safely add to table
+        add_optional <- c(add_optional, variab)
+      }
+    }
+    cols <- c("DV", "EVID", add_optional, "PRED", "CWRES", "NPDE")
     if(full_tables) {
       cols <- unique(c(cols, model$datainfo$names))
     }

R/add_table_to_model.R

@@ -50,9 +50,13 @@ add_table_to_model <- function(
 #' Check NONMEM table variables
 #'
 #' @inheritParams add_table_to_model
+#' @param throw_error should throw error? If FALSE, will return vector of 
+#' invalid variables.
 #'
-#' @returns `NULL` if all variables are valid, otherwise an error.
-check_nm_table_variables <- function(model, variables) {
+#' @returns `NULL` if all variables are valid, otherwise an error (or return
+#' all invalid variables if `throw_error` is FALSE).
+#' 
+check_nm_table_variables <- function(model, variables, throw_error = TRUE) {
   is_data_variable <- variables %in% model$datainfo$names
   is_lhs_variable <- variables %in% get_lhs_variables(model)
   is_defined_pk_parameter <- variables %in% get_defined_pk_parameters(model)
@@ -67,15 +71,18 @@ check_nm_table_variables <- function(model, variables) {
   if (all(is_valid)) return()
 
   invalid_variables <- variables[!is_valid]
-  cli::cli_abort(c(
-    paste0(
-      "$TABLE variables must be any of the following: ",
-      "A data variable, a left-hand side variable in the model, ",
-      "or a reserved NONMEM $TABLE variable."
-    ),
-    "x" = "{.field {invalid_variables}} {?is/are} not {?a/} valid variable{?s}.",
-    "i" = "Did you make a typo?"
-  ))
+  if(throw_error) {
+    cli::cli_abort(c(
+      paste0(
+        "$TABLE variables must be any of the following: ",
+        "A data variable, a left-hand side variable in the model, ",
+        "or a reserved NONMEM $TABLE variable."
+      ),
+      "x" = "{.field {invalid_variables}} {?is/are} not {?a/} valid variable{?s}.",
+      "i" = "Did you make a typo?"
+    ))
+  }
+  invalid_variables
 }
 
 get_lhs_variables <- function(model) {

R/create_model.R

@@ -288,7 +288,21 @@ create_model <- function(
       parameter_uncertainty_method = toupper(uncertainty_method)
     )
   }
-
+
+  ## Convert to TDMDD model?
+  if(!is.null(tmdd_type)) {
+    allowed_tmdd_types <- c("full", "ib", "crib", "cr", "qss", "mmapp")
+    if(!tmdd_type %in% allowed_tmdd_types) {
+      cli::cli_abort("Specified `tmdd_type` not allowed, select one of: {allowed_tmdd_types}.")
+    }
+    cli::cli_alert_info("Converting model into TMDD structure ({tmdd_type}).")
+    mod <- mod |>
+      pharmr::set_tmdd(type = tmdd_type)
+  }
+
+  ## Add metabolite compartment?
+  mod <- add_metabolite_compartment(mod, metabolite, route)
+
   ## Add $TABLEs
   if(tool == "nonmem") {
     if(!is.null(tables)) {
@@ -323,20 +337,6 @@ create_model <- function(
     )
   }
 
-  ## Convert to TDMDD model?
-  if(!is.null(tmdd_type)) {
-    allowed_tmdd_types <- c("full", "ib", "crib", "cr", "qss", "mmapp")
-    if(!tmdd_type %in% allowed_tmdd_types) {
-      cli::cli_abort("Specified `tmdd_type` not allowed, select one of: {allowed_tmdd_types}.")
-    }
-    cli::cli_alert_info("Converting model into TMDD structure ({tmdd_type}).")
-    mod <- mod |>
-      pharmr::set_tmdd(type = tmdd_type)
-  }
-
-  ## Add metabolite compartment?
-  mod <- add_metabolite_compartment(mod, metabolite, route)
-
   ## Handle BLQ
   if(!is.null(blq_method)) {
     blq_method <- tolower(blq_method)