docs(create_model): document route='auto' and harden detection

R/create_model.R

@@ -4,7 +4,13 @@
 #' functionality in pharmr/Pharmpy.
 #'
 #' @param data filename of dataset or data.frame as input to NONMEM / nlmixr.
-#' @param route route of administration, either `oral` or `iv`
+#' @param route route of administration. One of `"auto"` (default), `"oral"`,
+#' `"sc"`, `"im"`, `"extravascular"`, or `"iv"`. When `"auto"`, the route is
+#' inferred from `data` by comparing the `CMT` of dose events (`EVID=1`) to the
+#' `CMT` of observation events (`EVID=0`): if any dose compartment is not also
+#' an observation compartment (e.g. doses in `CMT=1`, observations in `CMT=2`),
+#' the route is set to `"oral"`; otherwise `"iv"`. Falls back to `"iv"` if `data`
+#' is `NULL` or the dataset lacks the required `CMT`/`EVID` columns.
 #' @param lag_time add a lag time, default is `FALSE`
 #' @param n_transit_compartments number of transit-compartments for absorption
 #' model. Default is `0`.
@@ -200,6 +206,7 @@ create_model <- function(
   ## Pick route
   if(route == "auto") {
     route <- get_route_from_data(data)
+    if(verbose) cli::cli_alert_info("Auto-detected route from data: {route}")
   }
 
   ## Read base model
@@ -770,6 +777,9 @@ get_route_from_data <- function(data, default = "iv") {
     return(default)
   }
   dataset <- load_data_wrapper(data)
+  if(!all(c("EVID", "CMT") %in% names(dataset))) {
+    return(default)
+  }
   dose_cmt <- dataset |>
     dplyr::filter(.data$EVID == 1) |>
     dplyr::pull("CMT") |>
@@ -778,6 +788,9 @@ get_route_from_data <- function(data, default = "iv") {
     dplyr::filter(.data$EVID == 0) |>
     dplyr::pull("CMT") |>
     unique()
+  if(length(dose_cmt) == 0 || length(obs_cmt) == 0) {
+    return(default)
+  }
   if(length(setdiff(dose_cmt, obs_cmt)) > 0) {
     route <- "oral"
   } else {

tests/testthat/test-create_model.R

@@ -54,6 +54,33 @@ test_that("create_model basic functionality works", {
   expect_true(!grepl("POP_KA", mod_iv$code))
 })
 
+test_that("route = 'auto' infers route from CMT/EVID in data", {
+  iv_data <- data.frame(
+    ID = 1,
+    TIME = c(0, 1, 2),
+    DV = c(0, 10, 5),
+    AMT = c(100, 0, 0),
+    CMT = 1,
+    EVID = c(1, 0, 0),
+    MDV = c(1, 0, 0)
+  )
+  oral_data <- iv_data
+  oral_data$CMT <- c(1, 2, 2)
+
+  expect_equal(get_route_from_data(iv_data), "iv")
+  expect_equal(get_route_from_data(oral_data), "oral")
+  expect_equal(get_route_from_data(NULL), "iv")
+  expect_equal(get_route_from_data(iv_data[, c("ID", "TIME", "DV")]), "iv")
+
+  mod_iv <- create_model(data = iv_data, verbose = FALSE)
+  expect_s3_class(mod_iv, "pharmpy.model.external.nonmem.model.Model")
+  expect_true(!grepl("POP_MAT", mod_iv$code))
+
+  mod_oral <- create_model(data = oral_data, verbose = FALSE)
+  expect_s3_class(mod_oral, "pharmpy.model.external.nonmem.model.Model")
+  expect_true(grepl("POP_MAT", mod_oral$code))
+})
+
 test_that("model features are correctly added", {
   test_data <- data.frame(
     ID = 1,