Add a test for saemix with deSolve

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

3 files changed, 32 insertions, 17 deletions

diff --git a/test.log b/test.log
index 13fa7e70..186ec590 100644
--- a/test.log
+++ b/test.log
@@ -6,7 +6,7 @@ Testing mkin
 ✔ |   2       | Export dataset for reading into CAKE
 ✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
-✔ |   7       | Fitting the SFORB model [3.7 s]
+✔ |   7       | Fitting the SFORB model [3.6 s]
 ✔ |   5       | Analytical solutions for coupled models [3.3 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  14       | Confidence intervals and p-values [1.2 s]
@@ -14,24 +14,31 @@ Testing mkin
 ✔ |   3       | Time step normalisation
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
-✔ |  31       | Nonlinear mixed effects models [27.4 s]
+✔ |  33     1 | Nonlinear mixed effects models [27.8 s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_mixed.R:137:3): saem results are reproducible for biphasic fits
+Reason: Fitting with saemix takes around 10 minutes when using deSolve
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   2       | Test dataset classes mkinds and mkindsg
 ✔ |   1       | mkinfit features [0.3 s]
 ✔ |  12       | Special cases of mkinfit calls [0.8 s]
-✔ |   8       | mkinmod model generation and printing [0.2 s]
+✔ |   8       | mkinmod model generation and printing [0.3 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.6 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.7 s]
 ✔ |   9       | Nonlinear mixed-effects models [7.9 s]
 ✔ |  16       | Plotting [1.9 s]
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
 ✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ |   9       | Hypothesis tests [7.5 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
+✔ |   9       | Hypothesis tests [7.3 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 69.5 s
+Duration: 69.7 s
 
-[ FAIL 0 | WARN 0 | SKIP 0 | PASS 204 ]
+── Skipped tests  ──────────────────────────────────────────────────────────────
+● Fitting with saemix takes around 10 minutes when using deSolve (1)
+
+[ FAIL 0 | WARN 0 | SKIP 1 | PASS 206 ]
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]))
 })