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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
commit48c463680b51fa767b4cd7bd62865f192d0354ac (patch)
tree5b66eb08a7fd5e29fb7e6d3a9a8258ccdcaea73e /tests/testthat/setup_script.R
parent2ee20b257e34210e2d1f044431f3bfe059c9c5e7 (diff)
Reintroduce interface to saemix
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
Diffstat (limited to 'tests/testthat/setup_script.R')
-rw-r--r--tests/testthat/setup_script.R18
1 files changed, 18 insertions, 0 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 547b2d6c..9229c198 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -178,6 +178,10 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
})
# Mixed model fits
+saemix_available <- FALSE
+if (requireNamespace("saemix", quietly = TRUE)) {
+ if(packageVersion("saemix") >= "3.1.9000") saemix_available <- TRUE
+}
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)
@@ -186,6 +190,16 @@ mmkin_biphasic_mixed <- mixed(mmkin_biphasic)
dfop_nlme_1 <- nlme(mmkin_dfop_1)
nlme_biphasic <- nlme(mmkin_biphasic)
+if (saemix_available) {
+ sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
+
+ dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
+ 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)
+}
+
ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
function(x) subset(x$data[c("name", "time", "value")]))
names(ds_uba) <- paste("Dataset", 6:10)
@@ -197,3 +211,7 @@ f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
ds_uba, quiet = TRUE, cores = n_cores)
f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
+if (saemix_available) {
+ f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
+ f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
+}

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