diff options
Diffstat (limited to 'tests/testthat/test_mixed.R')
| -rw-r--r-- | tests/testthat/test_mixed.R | 55 |
1 files changed, 47 insertions, 8 deletions
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 644cccc1..6fc6c2f0 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -1,14 +1,15 @@ context("Nonlinear mixed effects models") test_that("Parent only models can be fitted using nonlinear mixed effects models", { + 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_saemix_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin") - sfo_saemix_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters") - s_sfo_s1 <- summary(sfo_saemix_1) - s_sfo_s2 <- summary(sfo_saemix_2) + 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) @@ -25,6 +26,21 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models 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") + 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) @@ -35,14 +51,37 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models 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$mkinmod) + + # We get < 22% deviations by averaging the transformed parameters + rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop + expect_true(all(rel_diff_mmkin < 0.22)) - # We get < 20% deviations with transformations made in mkin + # We get < 50% deviations with transformations made in mkin rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_1 < 0.2)) + expect_true(all(rel_diff_1 < 0.5)) - # We get < 8% deviations with transformations made in saemix + # We get < 12% deviations with transformations made in saemix rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_2 < 0.08)) + expect_true(all(rel_diff_2 < 0.12)) + + mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const") + hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE) + ci_hs_s1 <- summary(hs_saem_1)$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", { |