Add a test for saemix with deSolve

But skip the test as it takes too long to always run

2 files changed, 16 insertions, 8 deletions

diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 4a343bc5..cfdc9277 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -34,9 +34,10 @@ f_1_mkin_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE,
 
 # mmkin object of parent fits for tests
 models <- c("SFO", "FOMC", "DFOP", "HS")
-fits <- mmkin(models,
-  list(FOCUS_A = FOCUS_2006_A, FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
-  quiet = TRUE, cores = n_cores)
+fits <- suppressWarnings( # FOCUS A FOMC was, it seems, in testthat output
+  mmkin(models,
+    list(FOCUS_A = FOCUS_2006_A, FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+    quiet = TRUE, cores = n_cores))
 
 # One metabolite
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", to = "m1"),
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 7798be8a..05632c6f 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -122,17 +122,24 @@ test_that("saem results are reproducible for biphasic fits", {
   expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
 
   dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
+  no_k1 <- c(1, 2, 3, 5, 6)
+  no_k2 <- c(1, 2, 3, 4, 6)
+
   ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
   expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
   expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
 
-  # The following does not work, as k1 and k2 are not fitted well
+  # k1 and k2 are not fitted well
   ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
-  # expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop))
-  # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
+  expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
+  expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
 
-  # Somehow this does not work at the moment. But it took forever (~ 10 min) anyways...
-  #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
+  skip("Fitting with saemix takes around 10 minutes when using deSolve")
+  saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
 
+  # As with the analytical solution, k1 and k2 are not fitted well
+  ci_dfop_sfo_s_d <- summary(saem_biphasic_2)$confint_back
+  expect_true(all(ci_dfop_sfo_s_d[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
+  expect_true(all(ci_dfop_sfo_s_d[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
 })