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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-01 10:19:15 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-01 10:19:15 +0100
commit1d581d24bc85402770a195b44e453a1449597faf (patch)
tree2e4a342140ccef360f7f4a7df455beb3f21ba2b0 /tests
parentd2ddca3769be6746475e3949bf7604ad193a9d70 (diff)
Add a test for the DMTA data
comparing nlme and saemix. This test shows a reasonable evaluation of the DMTA data with nlme and saemix, which was missing, as the data used in the paper are flawed.
Diffstat (limited to 'tests')
-rw-r--r--tests/testthat/test_dmta.R80
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")
+
+})

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