diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-07 12:03:40 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-07 14:55:21 +0100 |
| commit | 7035cde3a53781721fe15a8893fdf328c789bdd2 (patch) | |
| tree | a1e4929faf9d645caedc0ed4dcc5036252497c63 /tests/testthat/setup_script.R | |
| parent | 77c248ca40b82ec00a756cd82f12968131f78959 (diff) | |
Remove nlmixr interface for release of mkin 1.1.0
I am postponing my attempts to get the nlmixr interface to CRAN, given
some problems with nlmixr using R-devel under Windows, see
https://github.com/nlmixrdevelopment/nlmixr/issues/596
and
https://github.com/r-hub/rhub/issues/512,
which is fixed by the removal of nlmixr from the testsuite.
For the tests to be more platform independent, the biphasic mixed
effects models test dataset was defined in a way that fitting
should be more robust (less ill-defined).
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 14 |
1 files changed, 4 insertions, 10 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index ec96fbc2..10696082 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -160,8 +160,8 @@ DFOP_SFO <- mkinmod( m1 = mkinsub("SFO"), quiet = TRUE) dfop_sfo_pop <- list(parent_0 = 100, - k_m1 = 0.005, f_parent_to_m1 = 0.5, - k1 = 0.05, k2 = 0.01, g = 0.5) + k_m1 = 0.007, f_parent_to_m1 = 0.5, + k1 = 0.1, k2 = 0.02, g = 0.5) syn_biphasic_parms <- as.matrix(data.frame( k1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k1), log_sd), k2 = rlnorm(n_biphasic, log(dfop_sfo_pop$k2), log_sd), @@ -186,11 +186,12 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores) mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores) mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores, + control = list(eval.max = 500, iter.max = 400), error_model = "tc") # nlme dfop_nlme_1 <- nlme(mmkin_dfop_1) -nlme_biphasic <- nlme(mmkin_biphasic) +nlme_biphasic <- suppressWarnings(nlme(mmkin_biphasic)) # saemix sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") @@ -201,13 +202,6 @@ dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) -# nlmixr saem -tmp <- suppressMessages(capture.output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem", - control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)))) -# The FOCEI fit takes too long... -#tmp <- capture_output(nlmixr_focei_biphasic <- nlmixr(mmkin_biphasic, est = "focei", -# control = nlmixr::foceiControl(print = 0))) - # UBA datasets ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")])) |