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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /tests/testthat/test_mixed.R
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'tests/testthat/test_mixed.R')
-rw-r--r--tests/testthat/test_mixed.R34
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]))
})

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