diff options
| -rw-r--r-- | tests/testthat/test_dmta.R | 80 |
1 files changed, 41 insertions, 39 deletions
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R index 46a4fdcc..22fa9d95 100644 --- a/tests/testthat/test_dmta.R +++ b/tests/testthat/test_dmta.R @@ -111,7 +111,7 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d ints_nlme$varStruct[, "upper"])) # nlmixr focei vs. nlme - # We only test for the proportional part (rsd_high), as the + # We only test for the proportional part (rsd_high), as the # constant part (sigma_low) obtained with nlmixr/FOCEI is below the lower # bound of the confidence interval obtained with nlme expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] > @@ -120,48 +120,50 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d ints_nlme$varStruct["prop", "upper"]) }) -# Model definition from the 2020 paper https://doi.org/10.3390/environments8080071 -# But note the data are different, as we did not pool the data from the same soils -# for the paper -# The model is called DFOP-SFO3+ in the paper -dfop_sfo3p <- mkinmod( - DMTA = mkinsub("DFOP", c("M23", "M27", "M31")), +# Compared to the 2020 paper https://doi.org/10.3390/environments8080071 +# the data are different, as there was an error in the handling of the +# Borstel data in the mkin package at the time. +# The model called DFOP-SFO3+ in the paper appears to be overparameterised with +# the corrected data, we get lots of problems trying to use it with mmkin, nlme +# and saemix +sfo_sfo3p <- mkinmod( + DMTA = mkinsub("SFO", c("M23", "M27", "M31")), M23 = mkinsub("SFO"), M27 = mkinsub("SFO"), M31 = mkinsub("SFO", "M27", sink = FALSE), quiet = TRUE ) -dfop_sfo3 <- mkinmod( - DMTA = mkinsub("DFOP", c("M23", "M27", "M31")), - M23 = mkinsub("SFO"), - M27 = mkinsub("SFO"), - M31 = mkinsub("SFO"), - quiet = TRUE -) -# The following is work in progress -#dmta_dfop_sfo3p_tc <- mmkin(list("DFOP-SFO3+" = dfop_sfo3p), -# dmta_ds, error_model = "tc", quiet = TRUE) -# The Borstel dataset give false convergence -#dmta_dfop_sfo3_tc <- mmkin(list("DFOP-SFO3" = dfop_sfo3), -# dmta_ds, error_model = "tc", quiet = TRUE) -# We get convergence in all soils - -#test_that("Different backends get consistent results for DFOP-SFO3+, dimethenamid data", { - - # nlme needs some help to converge -# nlme_dfop_sfo3p_tc <- nlme(dmta_dfop_sfo3p_tc, -# control = list(pnlsMaxIter = 30, tolerance = 3e-3)) -# ints_nlme_dfop_sfo3p_tc <- intervals(nlme_dfop_sfo3p_tc, which = "fixed") - - # saemix does not succeed with these data, we get problems - # with the deSolve solutions, depending on the seed: - # Error in lsoda(y, times, func, parms, ...) : - # illegal input detected before taking any integration steps - see - # written message - # or: - # Error in out[available, var] : (subscript) logical subscript too long - #saem_saemix_dfop_sfo3p_tc <- saem(dmta_dfop_sfo3p_tc) - -#}) +dmta_sfo_sfo3p_tc <- mmkin(list("SFO-SFO3+" = sfo_sfo3p), + dmta_ds, error_model = "tc", quiet = TRUE) + +test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid data", { + + nlme_sfo_sfo3p_tc <- nlme(dmta_sfo_sfo3p_tc, + start = mean_degparms(dmta_sfo_sfo3p_tc, test_log_parms = TRUE)) + ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed") + + 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. + # saem_saemix_sfo_sfo3p_tc <- saem(dmta_sfo_sfo3p_tc) + # The fit above, using SFO for the parent leads to low values of DMTA_0 + # (confidence interval from 84.4 to 92.8) which is not consistent with what + # we know about this value. Therefore, we fix it to the initial estimate + # obtained from the separate fits (95.6) + saem_saemix_sfo_sfo3p_tc_DMTA_0_fixed <- saem(dmta_sfo_sfo3p_tc, + 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 + # 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") + +}) |