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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /tests/testthat/test_mixed.R
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'tests/testthat/test_mixed.R')
-rw-r--r--tests/testthat/test_mixed.R131
1 files changed, 0 insertions, 131 deletions
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index e9af10e6..ca0072ef 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,98 +1,9 @@
context("Nonlinear mixed-effects models")
-test_that("Parent fits using saemix are correctly implemented", {
- skip_if(!saemix_available)
-
- expect_error(saem(fits), "Only row objects")
- # Some fits were done in the setup script
- mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
- expect_error(update(mmkin_sfo_1, models = c("SFOOO")), "Please supply models.*")
-
- sfo_saem_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
- sfo_saem_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
- s_sfo_s1 <- summary(sfo_saem_1)
- s_sfo_s2 <- summary(sfo_saem_2)
-
- sfo_nlme_1 <- expect_warning(nlme(mmkin_sfo_1), "not converge")
- s_sfo_n <- summary(sfo_nlme_1)
-
- # Compare with input
- expect_equal(round(s_sfo_s2$confint_ranef["SD.log_k_parent", "est."], 1), 0.3)
- # k_parent is a bit different from input 0.03 here
- expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), 0.035)
- expect_equal(round(s_sfo_s2$confint_back["k_parent", "est."], 3), 0.035)
-
- # But the result is pretty unanimous between methods
- expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
- round(s_sfo_s2$confint_back["k_parent", "est."], 3))
- expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
- round(s_sfo_n$confint_back["k_parent", "est."], 3))
-
- mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores)
- fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE)
- ci_fomc_s1 <- summary(fomc_saem_1)$confint_back
-
- fomc_pop <- as.numeric(fomc_pop)
- expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop))
- expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop))
-
- mmkin_fomc_2 <- update(mmkin_fomc_1, state.ini = 100, fixed_initials = "parent")
- fomc_saem_2 <- saem(mmkin_fomc_2, quiet = TRUE, transformations = "mkin")
- ci_fomc_s2 <- summary(fomc_saem_2)$confint_back
-
- expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop[2:3]))
- expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop[2:3]))
-
- s_dfop_s1 <- summary(dfop_saemix_1)
- s_dfop_s2 <- summary(dfop_saemix_2)
- s_dfop_n <- summary(dfop_nlme_1)
-
- dfop_pop <- as.numeric(dfop_pop)
- expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop))
- expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop))
- expect_true(all(s_dfop_s2$confint_back[, "lower"] < dfop_pop))
- expect_true(all(s_dfop_s2$confint_back[, "upper"] > dfop_pop))
-
- dfop_mmkin_means_trans <- apply(parms(mmkin_dfop_1, transformed = TRUE), 1, mean)
- dfop_mmkin_means <- backtransform_odeparms(dfop_mmkin_means_trans, mmkin_dfop_1$mkinmod)
-
- # We get < 22% deviations by averaging the transformed parameters
- rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop
- expect_true(all(rel_diff_mmkin < 0.22))
-
- # We get < 50% deviations with transformations made in mkin
- rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop
- expect_true(all(rel_diff_1 < 0.5))
-
- # We get < 12% deviations with transformations made in saemix
- rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
- expect_true(all(rel_diff_2 < 0.12))
-
- mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores)
- hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE)
- ci_hs_s1 <- summary(hs_saem_1)$confint_back
-
- hs_pop <- as.numeric(hs_pop)
- # expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated
- expect_true(all(ci_hs_s1[, "upper"] > hs_pop))
-
- mmkin_hs_2 <- update(mmkin_hs_1, state.ini = 100, fixed_initials = "parent")
- hs_saem_2 <- saem(mmkin_hs_2, quiet = TRUE)
- ci_hs_s2 <- summary(hs_saem_2)$confint_back
-
- #expect_true(all(ci_hs_s2[, "lower"] < hs_pop[2:4])) # k1 again overestimated
- expect_true(all(ci_hs_s2[, "upper"] > hs_pop[2:4]))
-
- # HS would likely benefit from implemenation of transformations = "saemix"
-})
-
test_that("Print methods work", {
expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt")
expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
-
- skip_if(!saemix_available)
- expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
})
test_that("nlme results are reproducible to some degree", {
@@ -112,45 +23,3 @@ test_that("nlme results are reproducible to some degree", {
# expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop)) # k2 is overestimated
expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop))
})
-
-test_that("saem results are reproducible for biphasic fits", {
-
- skip_if(!saemix_available)
- test_summary <- summary(saem_biphasic_s)
- test_summary$saemixversion <- "Dummy 0.0 for testing"
- test_summary$mkinversion <- "Dummy 0.0 for testing"
- test_summary$Rversion <- "Dummy R version for testing"
- test_summary$date.fit <- "Dummy date for testing"
- test_summary$date.summary <- "Dummy date for testing"
- test_summary$time <- c(elapsed = "test time 0")
-
- expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_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)
-
- ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
- expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
- expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
-
- # k1 and k2 are not fitted well
- ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$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",
- # 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)
-
- # As with the analytical solution, k1 and k2 are not fitted well
- ci_dfop_sfo_s_d <- summary(saem_biphasic_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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