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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-14 20:03:42 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-14 20:03:42 +0100
commit21ad91256dc29423bd905de5c298fd23862b1f3b (patch)
tree225e2f69ed75b96e5528bcf7b8f25eb3864b75da /tests/testthat/test_saemix_parent.R
parent0db7df4bf632a013099b17d5e817a7dc7146c394 (diff)
Automatic starting parameters for saem.mmkin
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
Diffstat (limited to 'tests/testthat/test_saemix_parent.R')
-rw-r--r--tests/testthat/test_saemix_parent.R40
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", {

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