Merge branch 'main' into custom_lsoda_call

1 files changed, 31 insertions, 15 deletions

diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R
index c1a10d10..dda0ea23 100644
--- a/tests/testthat/test_multistart.R
+++ b/tests/testthat/test_multistart.R
@@ -1,41 +1,57 @@
 context("Multistart method for saem.mmkin models")
 
 test_that("multistart works for saem.mmkin models", {
+  skip_on_cran() # Save CRAN time
   set.seed(123456)
-  saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores,
-    no_random_effect = "parent_0")
+  saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores)
+
   anova_sfo <- anova(sfo_saem_1,
     sfo_saem_1_reduced,
     best(saem_sfo_s_multi),
     test = TRUE
   )
-  expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.5)
+  expect_equal(round(anova_sfo, 1)["sfo_saem_1_reduced", "AIC"], 1302.2)
+  expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1302.2)
+  expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, win-builder: 0.4
+
+  saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE)
+  dfop_sfo_pop <- attr(ds_dfop_sfo, "pop")
+
+  # k2 is not fitted well (compare saem_dfop_sfo_s in test_mixed.R)
+  ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back
+  no_k1 <- c(1, 2, 3, 5, 6)
+  no_k2 <- c(1, 2, 3, 4, 6)
+  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]))
+
 
-  skip_on_cran() # Save CRAN time
   set.seed(123456)
-  saem_biphasic_m_multi <- multistart(saem_biphasic_m, n = 8,
+  saem_dfop_sfo_m_multi <- multistart(saem_dfop_sfo_m, n = 8,
     cores = n_cores)
-  expect_known_output(print(saem_biphasic_m_multi),
-    file = "print_multistart_biphasic.txt")
+  expect_known_output(print(saem_dfop_sfo_m_multi),
+    file = "print_multistart_dfop_sfo.txt")
 
-  anova_biphasic <- anova(saem_biphasic_m,
-    best(saem_biphasic_m_multi))
+  anova_dfop_sfo <- anova(saem_dfop_sfo_m,
+    best(saem_dfop_sfo_m_multi))
 
   # With the new starting parameters we do not improve
   # with multistart any more
-  expect_equal(anova_biphasic[2, "AIC"], anova_biphasic[1, "AIC"],
+  expect_equal(anova_dfop_sfo[2, "AIC"], anova_dfop_sfo[1, "AIC"],
     tolerance = 1e-4)
   skip_on_travis() # Plots are platform dependent
 
+  plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m)
+  vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m)
+
   llhist_sfo <- function() llhist(saem_sfo_s_multi)
   parplot_sfo <- function() parplot(saem_sfo_s_multi, ylim = c(0.5, 2))
   vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo)
   vdiffr::expect_doppelganger("parplot for sfo fit", parplot_sfo)
 
-  llhist_biphasic <- function() llhist(saem_biphasic_m_multi)
-  parplot_biphasic <- function() parplot(saem_biphasic_m_multi,
-    ylim = c(0.5, 2))
+  llhist_dfop_sfo <- function() llhist(saem_dfop_sfo_m_multi)
+  parplot_dfop_sfo <- function() parplot(saem_dfop_sfo_m_multi,
+    ylim = c(0.5, 2), llquant = 0.5)
 
-  vdiffr::expect_doppelganger("llhist for biphasic saemix fit", llhist_biphasic)
-  vdiffr::expect_doppelganger("parplot for biphasic saemix fit", parplot_biphasic)
+  vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo)
+  vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo)
 })