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-rw-r--r--tests/testthat/test_saemix_parent.R56
1 files changed, 29 insertions, 27 deletions
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 39f69f51..4504e573 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -5,6 +5,7 @@ test_that("Parent fits using saemix are correctly implemented", {
skip_on_cran()
expect_error(saem(fits), "Only row objects")
+ # SFO
# mmkin_sfo_1 was generated in the setup script
# We did not introduce variance of parent_0 in the data generation
# This is correctly detected
@@ -53,9 +54,16 @@ test_that("Parent fits using saemix are correctly implemented", {
expect_equal(round(s_sfo_nlme_1$confint_back["k_parent", "est."], 3),
round(s_sfo_saem_1$confint_back["k_parent", "est."], 3))
+ # Compare fits
+ expect_known_output(anova(sfo_saem_1, sfo_saem_1_reduced,
+ sfo_saem_1_mkin, sfo_saem_1_reduced_mkin, test = TRUE),
+ file = "anova_sfo_saem.txt"
+ )
+
+ # 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")
- fomc_saem_2 <- saem(mmkin_fomc_1, quiet = TRUE, transformations = "mkin")
+ 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)$confint_back
fomc_pop <- as.numeric(fomc_pop)
@@ -70,45 +78,39 @@ test_that("Parent fits using saemix are correctly implemented", {
expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop[2:3]))
expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop[2:3]))
+ # DFOP
+ dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix",
+ no_random_effect = "parent_0")
+
s_dfop_s1 <- summary(dfop_saemix_1)
s_dfop_s2 <- summary(dfop_saemix_2)
s_dfop_n <- summary(dfop_nlme_1)
dfop_pop <- as.numeric(dfop_pop)
- expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop))
- expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop))
+
+ # When using DFOP with mkin transformations, k1 and k2 are sometimes swapped
+ swap_k1_k2 <- function(p) c(p[1], p[3], p[2], 1 - p[4])
+ expect_true(all(s_dfop_s1$confint_back[, "lower"] < swap_k1_k2(dfop_pop)))
+ expect_true(all(s_dfop_s1$confint_back[, "upper"] > swap_k1_k2(dfop_pop)))
expect_true(all(s_dfop_s2$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$mkinmod)
-
- # We get < 20% deviations for parent_0 and k1 by averaging the transformed parameters
- # If we average only parameters passing the t-test, the deviation for k2 is also < 20%
- rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop
- rel_diff_mmkin_tested <- (dfop_mmkin_means_tested - dfop_pop) / dfop_pop
- expect_true(all(rel_diff_mmkin[c("parent_0", "k1")] < 0.20))
- expect_true(all(rel_diff_mmkin_tested[c("parent_0", "k1", "k2")] < 0.20))
-
- # We get < 20% deviations with transformations made in mkin
- rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / 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$confint_back[, "est."]) - dfop_pop) / dfop_pop
expect_true(all(rel_diff_1 < 0.20))
# We get < 20% deviations with transformations made in saemix
rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
expect_true(all(rel_diff_2 < 0.2))
- # We use constant error for SFORB because tc is overparameterised (b.1 is ill-defined in saem)
- mmkin_sforb_2 <- mmkin("SFORB", ds_dfop, quiet = TRUE, error_model = "const", cores = n_cores)
- sforb_saemix_1 <- saem(mmkin_sforb_2, quiet = TRUE,
- no_random_effect = c("parent_free_0", "k_parent_free_bound"),
- transformations = "saemix")
- sforb_saemix_2 <- saem(mmkin_sforb_2, quiet = TRUE,
- no_random_effect = c("parent_free_0", "log_k_parent_free_bound"),
+ # SFORB
+ mmkin_sforb_1 <- mmkin("SFORB", ds_dfop, quiet = TRUE, cores = n_cores)
+ sforb_saemix_1 <- saem(mmkin_sforb_1, quiet = TRUE,
+ no_random_effect = c("parent_free_0"),
transformations = "mkin")
+ sforb_saemix_2 <- saem(mmkin_sforb_1, quiet = TRUE,
+ no_random_effect = c("parent_free_0"),
+ transformations = "saemix")
expect_equal(
log(endpoints(dfop_saemix_1)$distimes[1:2]),
log(endpoints(sforb_saemix_1)$distimes[1:2]), tolerance = 0.03)
@@ -140,7 +142,7 @@ test_that("We can also use mkin solution methods for saem", {
)
skip_on_cran() # This still takes almost 2.5 minutes although we do not solve ODEs
dfop_saemix_3 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin",
- solution_type = "analytical")
+ solution_type = "analytical", no_random_effect = "parent_0")
distimes_dfop <- endpoints(dfop_saemix_1)$distimes
distimes_dfop_analytical <- endpoints(dfop_saemix_3)$distimes
rel_diff <- abs(distimes_dfop_analytical - distimes_dfop) / distimes_dfop

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