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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-02 13:11:49 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-02 13:11:49 +0100
commit351248d07f810ccb6c497633a02cd48ee35526e6 (patch)
treea033446050d342d09c3a443583173ae4babccd66 /tests
parent6468bc31254baeac7dad90a38715714291be30ae (diff)
Fix nlmixr fits with parallel metabolites
Diffstat (limited to 'tests')
-rw-r--r--tests/testthat/test_dmta.R17
1 files changed, 14 insertions, 3 deletions
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
index 7b130999..71e68f51 100644
--- a/tests/testthat/test_dmta.R
+++ b/tests/testthat/test_dmta.R
@@ -144,6 +144,19 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid
"Iteration 5, LME step.*not converge")
ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed")
+ # The saem fit with nlmixr takes only about 15 seconds
+ tmp <- capture.output(
+ saem_nlmixr_sfo_sfo3p_tc <- nlmixr(dmta_sfo_sfo3p_tc, est = "saem",
+ control = nlmixr::saemControl(print = 0)))
+ ints_nlmixr_saem_mets <- intervals(saem_nlmixr_sfo_sfo3p_tc)
+
+ # We need to exclude the ilr transformed formation fractions in these
+ # tests, as they do not have a one to one relation in the transformations
+ expect_true(all(ints_nlmixr_saem_mets$fixed[, "est."][-c(6, 7, 8)] >
+ backtransform_odeparms(ints_nlme_mets$fixed[, "lower"][-c(6, 7, 8)], sfo_sfo3p)))
+ expect_true(all(ints_nlmixr_saem_mets$fixed[, "est."][-c(6, 7, 8)] <
+ backtransform_odeparms(ints_nlme_mets$fixed[, "upper"], sfo_sfo3p)[-c(6, 7, 8)]))
+
skip("Fitting this ODE model with saemix takes about 15 minutes on my system")
# As DFOP is overparameterised and leads to instabilities and errors, we
# need to use SFO.
@@ -156,15 +169,13 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid
fixed.estim = c(0, rep(1, 7)))
ints_saemix_mets <- intervals(saem_saemix_sfo_sfo3p_tc_DMTA_0_fixed)
- # We need to exclude the ilr transformed formation fractions in these
+ # Again, we need to exclude the ilr transformed formation fractions in these
# tests, as they do not have a one to one relation in the transformations
expect_true(all(ints_saemix_mets$fixed[, "est."][-c(6, 7, 8)] >
backtransform_odeparms(ints_nlme_mets$fixed[, "lower"][-c(6, 7, 8)], sfo_sfo3p)))
expect_true(all(ints_saemix_mets$fixed[, "est."][-c(6, 7, 8)] <
backtransform_odeparms(ints_nlme_mets$fixed[, "upper"], sfo_sfo3p)[-c(6, 7, 8)]))
- # The model is not supported by nlmixr.mmkin
- #saem_nlmixr_sfo_sfo3p_tc <- nlmixr(dmta_sfo_sfo3p_tc, est = "saem")
})

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