diff options
Diffstat (limited to 'tests/testthat/test_saemix_parent.R')
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 40 |
1 files changed, 15 insertions, 25 deletions
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 79c5fa69..20889c6c 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -73,40 +73,36 @@ test_that("Parent fits using saemix are correctly implemented", { # FOMC mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE, transformations = "saemix", no_random_effect = "parent_0") - fomc_saem_2 <- update(fomc_saem_1, transformations = "mkin") - ci_fomc_s1 <- summary(fomc_saem_1)$confint_back fomc_pop <- as.numeric(fomc_pop) + ci_fomc_s1 <- summary(fomc_saem_1)$confint_back expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop)) expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop)) - expect_equal(endpoints(fomc_saem_1), endpoints(fomc_saem_2), tol = 0.01) - mmkin_fomc_2 <- update(mmkin_fomc_1, state.ini = 100, fixed_initials = "parent") - fomc_saem_2 <- saem(mmkin_fomc_2, quiet = TRUE, transformations = "mkin") + fomc_saem_2 <- update(fomc_saem_1, transformations = "mkin") ci_fomc_s2 <- summary(fomc_saem_2)$confint_back + expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop)) + expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop)) - expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop[2:3])) - expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop[2:3])) + expect_equal(endpoints(fomc_saem_1), endpoints(fomc_saem_2), tol = 0.01) # DFOP dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix", no_random_effect = "parent_0") - s_dfop_s1 <- summary(dfop_saemix_1) - s_dfop_s2 <- summary(dfop_saemix_2) + s_dfop_s1 <- summary(dfop_saemix_1) # mkin transformations + s_dfop_s2 <- summary(dfop_saemix_2) # saemix transformations s_dfop_n <- summary(dfop_nlme_1) dfop_pop <- as.numeric(dfop_pop) - # When using DFOP with mkin transformations, k1 and k2 are sometimes swapped - swap_k1_k2 <- function(p) c(p[1], p[3], p[2], 1 - p[4]) - expect_true(all(s_dfop_s1$confint_back[, "lower"] < swap_k1_k2(dfop_pop))) - expect_true(all(s_dfop_s1$confint_back[, "upper"] > swap_k1_k2(dfop_pop))) + expect_true(all(s_dfop_s1$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$confint_back[, "upper"] > dfop_pop)) - # We get < 20% deviations with transformations made in mkin (need to swap k1 and k2) - rel_diff_1 <- (swap_k1_k2(s_dfop_s1$confint_back[, "est."]) - dfop_pop) / dfop_pop + # We get < 20% deviations with transformations made in mkin + rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop expect_true(all(rel_diff_1 < 0.20)) # We get < 20% deviations with transformations made in saemix @@ -123,27 +119,21 @@ test_that("Parent fits using saemix are correctly implemented", { transformations = "saemix") expect_equal( log(endpoints(dfop_saemix_1)$distimes[1:2]), - log(endpoints(sforb_saemix_1)$distimes[1:2]), tolerance = 0.03) + log(endpoints(sforb_saemix_1)$distimes[1:2]), tolerance = 0.01) expect_equal( log(endpoints(sforb_saemix_1)$distimes[1:2]), log(endpoints(sforb_saemix_2)$distimes[1:2]), tolerance = 0.01) mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores) - hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE) - hs_saem_2 <- saem(mmkin_hs_1, quiet = TRUE, transformations = "mkin") + hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE, no_random_effect = "parent_0") + hs_saem_2 <- saem(mmkin_hs_1, quiet = TRUE, transformations = "mkin", + no_random_effect = "parent_0") expect_equal(endpoints(hs_saem_1), endpoints(hs_saem_2), tol = 0.01) ci_hs_s1 <- summary(hs_saem_1)$confint_back hs_pop <- as.numeric(hs_pop) #expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated expect_true(all(ci_hs_s1[, "upper"] > hs_pop)) - - mmkin_hs_2 <- update(mmkin_hs_1, state.ini = 100, fixed_initials = "parent") - hs_saem_3 <- saem(mmkin_hs_2, quiet = TRUE) - ci_hs_s3 <- summary(hs_saem_3)$confint_back - - #expect_true(all(ci_hs_s3[, "lower"] < hs_pop[2:4])) # k1 again overestimated - expect_true(all(ci_hs_s3[, "upper"] > hs_pop[2:4])) }) test_that("We can also use mkin solution methods for saem", { |