Reintroduce interface to saemix

Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.

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")
+}