Make mixed model test data permanent to ensure reproducibility

To ensure that tests on different platforms work on the same data, the
mixed modelling test data previosly generated in
tests/testthat/setup_script.R were generated once using the script in
inst/dataset/generation/ds_mixed.R, and are now distributed with the
package.

1 files changed, 16 insertions, 16 deletions

diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 2d53c6dd..ab8dfc27 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,22 +1,23 @@
 context("Nonlinear mixed-effects models")
 
+
 # Round error model parameters as they are not rounded in print methods
 dfop_nlme_1$modelStruct$varStruct$const <-
   signif(dfop_nlme_1$modelStruct$varStruct$const, 3)
 dfop_nlme_1$modelStruct$varStruct$prop <-
   signif(dfop_nlme_1$modelStruct$varStruct$prop, 4)
 
+dfop_sfo_pop <- attr(ds_dfop_sfo, "pop")
+
 test_that("Print methods work", {
   expect_known_output(print(fits[, 2:3], digits = 2), "print_mmkin_parent.txt")
   expect_known_output(print(mixed(mmkin_sfo_1), digits = 2), "print_mmkin_sfo_1_mixed.txt")
   expect_known_output(print(dfop_nlme_1, digits = 1), "print_dfop_nlme_1.txt")
+  expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt")
 
-  # In order to address the platform dependence of the results, we round to two
-  # significant digits before printing
-  dfop_saemix_1_print <- dfop_saemix_1
-  dfop_saemix_1_print$so@results@conf.int[c("estimate", "lower", "upper")] <-
-    signif(dfop_saemix_1_print$so@results@conf.int[c("estimate", "lower", "upper")], 2)
-  expect_known_output(print(dfop_saemix_1_print, digits = 1), "print_dfop_saemix_1.txt")
+  skip_on_cran() # The following test is platform dependent and fails on
+  # win-builder with current (18 Nov 2022) R-devel and on the Fedora CRAN check systems
+  expect_known_output(print(dfop_saem_1, digits = 1), "print_dfop_saem_1.txt")
 })
 
 test_that("nlme results are reproducible to some degree", {
@@ -36,17 +37,16 @@ test_that("nlme results are reproducible to some degree", {
   # k1 and k2 just fail the first test (lower bound of the ci), so we need to exclude it
   dfop_no_k1_k2 <- c("parent_0", "k_m1", "f_parent_to_m1", "g")
   dfop_sfo_pop_no_k1_k2 <- as.numeric(dfop_sfo_pop[dfop_no_k1_k2])
-  dfop_sfo_pop <- as.numeric(dfop_sfo_pop) # to remove names
 
-  ci_dfop_sfo_n <- summary(nlme_biphasic)$confint_back
+  ci_dfop_sfo_n <- summary(nlme_dfop_sfo)$confint_back
 
   expect_true(all(ci_dfop_sfo_n[dfop_no_k1_k2, "lower"] < dfop_sfo_pop_no_k1_k2))
-  expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop))
+  expect_true(all(ci_dfop_sfo_n[, "upper"] > as.numeric(dfop_sfo_pop)))
 })
 
 test_that("saemix results are reproducible for biphasic fits", {
 
-  test_summary <- summary(saem_biphasic_s)
+  test_summary <- summary(saem_dfop_sfo_s)
   test_summary$saemixversion <- "Dummy 0.0 for testing"
   test_summary$mkinversion <- "Dummy 0.0 for testing"
   test_summary$Rversion <- "Dummy R version for testing"
@@ -54,33 +54,33 @@ test_that("saemix results are reproducible for biphasic fits", {
   test_summary$date.summary <- "Dummy date for testing"
   test_summary$time <- c(elapsed = "test time 0")
 
-  expect_known_output(print(test_summary, digits = 1), "summary_saem_biphasic_s.txt")
+  expect_known_output(print(test_summary, digits = 1), "summary_saem_dfop_sfo_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)
   no_k1_k2 <- c(1, 2, 3, 6)
 
-  ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
+  ci_dfop_sfo_s_s <- summary(saem_dfop_sfo_s)$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))
 
   # k2 is not fitted well
-  ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
+  ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$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)
-  #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve",
+  #saem_dfop_sfo_2 <- saem(mmkin_biphasic, solution_type = "deSolve",
   # control = list(nbiter.saemix = c(10, 5), nbiter.burn = 5), quiet = TRUE)
 
   skip("Fitting with saemix takes around 10 minutes when using deSolve")
-  saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
+  saem_dfop_sfo_2 <- saem(mmkin_dfop_sfo, 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)$confint_back
+  ci_dfop_sfo_s_d <- summary(saem_dfop_sfo_2)$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]))
 })