diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 13:11:49 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 13:11:49 +0100 |
| commit | 351248d07f810ccb6c497633a02cd48ee35526e6 (patch) | |
| tree | a033446050d342d09c3a443583173ae4babccd66 /tests | |
| parent | 6468bc31254baeac7dad90a38715714291be30ae (diff) | |
Fix nlmixr fits with parallel metabolites
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/testthat/test_dmta.R | 17 |
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") }) |