Move two saem fits from setup script to skipped tests

Save winbuilder/CRAN check time...

5 files changed, 18 insertions, 12 deletions

diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
index 69fa6a4d..69fa6a4d 100644
--- a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
+++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 2448886d..4e2f76ab 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -109,7 +109,4 @@ sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0")
 dfop_saem_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin",
   no_random_effect = c("parent_0", "g_qlogis"))
 
-saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE)
-saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE)
-
 parallel::stopCluster(cl)
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index ab8dfc27..8c257738 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -46,6 +46,9 @@ test_that("nlme results are reproducible to some degree", {
 
 test_that("saemix results are reproducible for biphasic fits", {
 
+  skip_on_cran()
+  saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE)
+
   test_summary <- summary(saem_dfop_sfo_s)
   test_summary$saemixversion <- "Dummy 0.0 for testing"
   test_summary$mkinversion <- "Dummy 0.0 for testing"
@@ -65,11 +68,6 @@ test_that("saemix results are reproducible for biphasic fits", {
   expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
   expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
 
-  # k2 is not fitted well
-  ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back
-  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]))
-
   # I tried to only do few iterations in routine tests as this is so slow
   # but then deSolve fails at some point (presumably at the switch between
   # the two types of iterations)
diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R
index 3a511e06..91ef71f0 100644
--- a/tests/testthat/test_multistart.R
+++ b/tests/testthat/test_multistart.R
@@ -4,6 +4,7 @@ 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)
+
   anova_sfo <- anova(sfo_saem_1,
     sfo_saem_1_reduced,
     best(saem_sfo_s_multi),
@@ -13,6 +14,17 @@ test_that("multistart works for saem.mmkin models", {
   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]))
+
+
   set.seed(123456)
   saem_dfop_sfo_m_multi <- multistart(saem_dfop_sfo_m, n = 8,
     cores = n_cores)
@@ -28,6 +40,9 @@ test_that("multistart works for saem.mmkin models", {
     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)
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 01b0c1ee..f5da5982 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -41,7 +41,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba),
     ds_uba, quiet = TRUE, cores = n_cores)
   f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ])
-
   f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
 
   plot_dfop_sfo_mmkin <- function() plot(f_uba_dfop_sfo_mixed, pop_curve = TRUE)
@@ -59,9 +58,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   # Biphasic fits with lots of data and fits have lots of potential for differences
   plot_dfop_sfo_nlme <- function() plot(nlme_dfop_sfo)
   #plot_dfop_sfo_saem_s <- function() plot(saem_dfop_sfo_s)
-  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)
 
   # different results when working with eigenvalues
   plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE)