From 24780530d539f5d35925618d99e29d1687ae275f Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Fri, 14 Jul 2023 15:21:43 -0400
Subject: [PATCH 1/3] Add failing test

---
 tests/testthat/test-simplify.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/testthat/test-simplify.R b/tests/testthat/test-simplify.R
index a31cdfc..3bf2875 100644
--- a/tests/testthat/test-simplify.R
+++ b/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))
+  )
+})

From 56b62b93ab44be942ac85f228cee68d22e6fdad1 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Fri, 14 Jul 2023 15:40:16 -0400
Subject: [PATCH 2/3] Ensure that covariate columns are found for fitted
 objects

---
 R/simplify.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/simplify.R b/R/simplify.R
index c39ad75..e3dace6 100644
--- a/R/simplify.R
+++ b/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.

From 22284e0e946ec207173438e4750e3b5a04fc90fe Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Fri, 14 Jul 2023 16:28:57 -0400
Subject: [PATCH 3/3] Fix R cmd check issues

---
 .Rbuildignore | 1 +
 R/simplify.R  | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 8b9b94f..5ee7385 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,5 +1,6 @@
 ^nlmixrtargets\.Rproj$
 ^\.Rproj\.user$
+^LICENSE$
 ^LICENSE\.md$
 ^README\.Rmd$
 ^cran-comments\.md$
diff --git a/R/simplify.R b/R/simplify.R
index e3dace6..5853d9f 100644
--- a/R/simplify.R
+++ b/R/simplify.R
@@ -43,7 +43,7 @@ nlmixr_object_simplify_zero_initial <- function(object) {
 }
 
 nlmixr_object_simplify_zero_initial_helper <- function(object) {
-  if (rxode2:::.matchesLangTemplate(object, str2lang(".name(initial) <- ."))) {
+  if (rxode2::.matchesLangTemplate(object, str2lang(".name(initial) <- ."))) {
     object[[2]][[2]] <- 0
   } else if (is.call(object)) {
     for (idx in seq_along(object)) {