Move two saem fits from setup script to skipped tests

Save winbuilder/CRAN check time...

6 files changed, 40 insertions, 34 deletions

diff --git a/log/test.log b/log/test.log
index 8fdaec48..897bf896 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.4s]
+✔ |         5 | Analytical solutions for coupled models [3.5s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.2s]
-✔ |     1  12 | Dimethenamid data from 2018 [34.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [33.2s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [5.4s]
+✔ |        14 | Error model fitting [5.0s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
-✔ |         1 | Fitting the logistic model [0.3s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [25.8s]
-✔ |     1  13 | Nonlinear mixed-effects models [0.4s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ |         1 | Fitting the logistic model [0.2s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s]
+✔ |     1  11 | Nonlinear mixed-effects models [13.1s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:79'): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:77'): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.6s]
+✔ |        10 | Special cases of mkinfit calls [0.4s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |         9 | Multistart method for saem.mmkin models [38.2s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [9.2s]
-✔ |        16 | Plotting [10.5s]
+✔ |         3 | Model predictions with mkinpredict [0.3s]
+✔ |        12 | Multistart method for saem.mmkin models [49.5s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
+✔ |        15 | Plotting [10.3s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [75.0s]
+✔ |     1  36 | saemix parent models [72.5s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ────────────────────────────────────────────────────────────────────────────────
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [4.0s]
+✔ |        10 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s]
-✔ |         9 | Hypothesis tests [9.0s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [8.2s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 229.5 s
+Duration: 246.1 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
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)