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authorJohannes Ranke <jranke@uni-bremen.de>2022-02-28 14:38:23 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-02-28 14:38:23 +0100
commit37bffdcfab0ca4e0de638b1a63e808b1d29d3f15 (patch)
treec3a8ec0df74d36fcc079dd33b66457bc91b58a20 /tests/testthat/test_saemix_parent.R
parentd68f7cc800fe2342642056780b915821dbe113e0 (diff)
Add nlmixr tests, reorganize, test intervals()
Diffstat (limited to 'tests/testthat/test_saemix_parent.R')
-rw-r--r--tests/testthat/test_saemix_parent.R91
1 files changed, 91 insertions, 0 deletions
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
new file mode 100644
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+++ b/tests/testthat/test_saemix_parent.R
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+test_that("Parent fits using saemix are correctly implemented", {
+
+ 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$confint_back[, "upper"] > dfop_pop))
+
+ dfop_mmkin_means_trans_tested <- mean_degparms(mmkin_dfop_1, test_log_parms = TRUE)
+ dfop_mmkin_means_trans <- apply(parms(mmkin_dfop_1, transformed = TRUE), 1, mean)
+
+ dfop_mmkin_means_tested <- backtransform_odeparms(dfop_mmkin_means_trans_tested, mmkin_dfop_1$mkinmod)
+ dfop_mmkin_means <- backtransform_odeparms(dfop_mmkin_means_trans, mmkin_dfop_1$mkinmod)
+
+ # We get < 20% deviations for parent_0 and k1 by averaging the transformed parameters
+ # If we average only parameters passing the t-test, the deviation for k2 is also < 20%
+ rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop
+ rel_diff_mmkin_tested <- (dfop_mmkin_means_tested - dfop_pop) / dfop_pop
+ expect_true(all(rel_diff_mmkin[c("parent_0", "k1")] < 0.20))
+ expect_true(all(rel_diff_mmkin_tested[c("parent_0", "k1", "k2")] < 0.20))
+
+ # We get < 15% deviations with transformations made in mkin
+ rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop
+ expect_true(all(rel_diff_1 < 0.15))
+
+ # We get < 20% deviations with transformations made in saemix
+ rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
+ expect_true(all(rel_diff_2 < 0.2))
+
+ mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores)
+ hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE)
+ ci_hs_s1 <- summary(hs_saem_1)$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"
+})
+

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