Merge pull request #10 from nlmixr2/fix-9

Ensure that covariate columns are found for fitted objects

.Rbuildignore

@@ -1,5 +1,6 @@
 ^nlmixrtargets\.Rproj$
 ^\.Rproj\.user$
+^LICENSE$
 ^LICENSE\.md$
 ^README\.Rmd$
 ^cran-comments\.md$

R/simplify.R

@@ -89,7 +89,12 @@ nlmixr_data_simplify <- function(data, object, table = list()) {
       paste0("'", nlmixr_names[mask_duplicated], "'", collapse = ", ")
     )
   }
-  cov_names <- nlmixr_data_simplify_cols(data, cols = object$all.covs, type = "covariate")
+  if (!is.null(object$ui)) {
+    covVec <- object$ui$all.covs
+  } else {
+    covVec <- object$all.covs
+  }
+  cov_names <- nlmixr_data_simplify_cols(data, cols = covVec, type = "covariate")
   keep_names <- nlmixr_data_simplify_cols(data, cols = table$keep, type = "keep")
   # Simplifying the nlmixr_names column names to always be lower case ensures
   # that upper/lower case column name changes will not affect the need to rerun.

tests/testthat/test-simplify.R

@@ -115,3 +115,20 @@ test_that("nlmixr_object_simplify_zero_initial", {
   new_model <- nlmixr_object_simplify_zero_initial(pheno)
   expect_equal(body(new_model), body(pheno_0))
 })
+
+test_that("re-estimating a model works with covariates (#9)", {
+  bad_data_lower_case <- nlmixr2data::pheno_sd
+  bad_data_lower_case$id <- bad_data_lower_case$ID
+  fit_estimated <-
+    suppressMessages(
+      nlmixr2est::nlmixr(
+        object = model_simple,
+        data = nlmixr2data::pheno_sd,
+        est = "focei",
+        control = list(eval.max = 1)
+      )
+    )
+  expect_true(
+    "WT" %in% names(nlmixr_data_simplify(data = nlmixr2data::pheno_sd, object = fit_estimated))
+  )
+})