diff options
Diffstat (limited to 'tests/testthat/test_dmta.R')
| -rw-r--r-- | tests/testthat/test_dmta.R | 66 |
1 files changed, 0 insertions, 66 deletions
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R index 2927b711..7f0a3a67 100644 --- a/tests/testthat/test_dmta.R +++ b/tests/testthat/test_dmta.R @@ -32,20 +32,6 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d saem_saemix_dfop_tc_mkin <- saem(dmta_dfop_tc, transformations = "mkin") ints_saemix_mkin <- intervals(saem_saemix_dfop_tc_mkin) - # nlmixr saem - saem_nlmixr_dfop_tc <- nlmixr(dmta_dfop_tc, est = "saem", - control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)) - ints_nlmixr_saem <- intervals(saem_nlmixr_dfop_tc) - - # nlmixr focei - # We get three warnings about nudged etas, the initial optimization and - # gradient problems with initial estimate and covariance - # We need to capture output, otherwise it pops up in testthat output - expect_warning(tmp <- capture_output(focei_nlmixr_dfop_tc <- nlmixr( - dmta_dfop_tc, est = "focei", - control = nlmixr::foceiControl(print = 0), all = TRUE))) - ints_nlmixr_focei <- intervals(focei_nlmixr_dfop_tc) - # Fixed effects ## saemix vs. nlme expect_true(all(ints_saemix$fixed[, "est."] > @@ -59,18 +45,6 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d expect_true(all(ints_saemix_mkin$fixed[, "est."] < backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod))) - ## nlmixr saem vs. nlme - expect_true(all(ints_nlmixr_saem$fixed[, "est."] > - backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod))) - expect_true(all(ints_nlmixr_saem$fixed[, "est."] < - backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod))) - - ## nlmixr focei vs. nlme - expect_true(all(ints_nlmixr_focei$fixed[, "est."] > - backtransform_odeparms(ints_nlme$fixed[, "lower"], dmta_dfop$mkinmod))) - expect_true(all(ints_nlmixr_focei$fixed[, "est."] < - backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod))) - # Random effects ## for saemix with saemix transformations, the comparison would be complicated... ## saemix mkin vs. nlme @@ -79,18 +53,6 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d expect_true(all(ints_saemix$fixed[, "est."] < backtransform_odeparms(ints_nlme$fixed[, "upper"], dmta_dfop$mkinmod))) - ## nlmixr saem vs. nlme - expect_true(all(ints_nlmixr_saem$random[, "est."] > - backtransform_odeparms(ints_nlme$reStruct$ds[, "lower"], dmta_dfop$mkinmod))) - expect_true(all(ints_nlmixr_saem$random[, "est."] < - backtransform_odeparms(ints_nlme$reStruct$ds[, "upper"], dmta_dfop$mkinmod))) - - ## nlmixr focei vs. nlme - expect_true(all(ints_nlmixr_focei$random[, "est."] > - backtransform_odeparms(ints_nlme$reStruct$ds[, "lower"], dmta_dfop$mkinmod))) - expect_true(all(ints_nlmixr_focei$random[, "est."] < - backtransform_odeparms(ints_nlme$reStruct$ds[, "upper"], dmta_dfop$mkinmod))) - # Variance function # Some of these tests on error model parameters fail on Travis and Winbuilder skip_on_travis() @@ -106,21 +68,6 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d ints_nlme$varStruct[, "lower"])) expect_true(all(ints_saemix_mkin[[3]][, "est."] < ints_nlme$varStruct[, "upper"])) - - # nlmixr saem vs. nlme - expect_true(all(ints_nlmixr_saem[[3]][, "est."] > - ints_nlme$varStruct[, "lower"])) - expect_true(all(ints_nlmixr_saem[[3]][, "est."] < - ints_nlme$varStruct[, "upper"])) - - # nlmixr focei vs. nlme - # We only test for the proportional part (rsd_high), as the - # constant part (sigma_low) obtained with nlmixr/FOCEI is below the lower - # bound of the confidence interval obtained with nlme - expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] > - ints_nlme$varStruct["prop", "lower"]) - expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] < - ints_nlme$varStruct["prop", "upper"]) }) # Compared to the 2020 paper https://doi.org/10.3390/environments8080071 @@ -148,19 +95,6 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid "Iteration 5, LME step.*not converge") ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed") - # The saem fit with nlmixr takes only about 15 seconds - tmp <- capture.output( - saem_nlmixr_sfo_sfo3p_tc <- nlmixr(dmta_sfo_sfo3p_tc, est = "saem", - control = nlmixr::saemControl(print = 0))) - ints_nlmixr_saem_mets <- intervals(saem_nlmixr_sfo_sfo3p_tc) - - # We need to exclude the ilr transformed formation fractions in these - # tests, as they do not have a one to one relation in the transformations - expect_true(all(ints_nlmixr_saem_mets$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. |