Merge branch 'main' into custom_lsoda_call

1 files changed, 19 insertions, 15 deletions

diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 646b6110..39a332f5 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,17 +1,24 @@
 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")
 
-  expect_known_output(print(dfop_saemix_1, 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, on the Linux R-devel CRAN check systems
+  # and also using R-devel locally
+  expect_known_output(print(dfop_saem_1, digits = 1), "print_dfop_saem_1.txt")
 })
 
 test_that("nlme results are reproducible to some degree", {
@@ -31,17 +38,19 @@ 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)
+  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"
   test_summary$Rversion <- "Dummy R version for testing"
@@ -49,33 +58,28 @@ test_that("saemix results are reproducible for biphasic fits", {
   test_summary$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
-  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]))
 })