diff options
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 39 |
1 files changed, 25 insertions, 14 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index fd9635d1..2071e05c 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -156,7 +156,7 @@ DFOP_SFO <- mkinmod( m1 = mkinsub("SFO"), quiet = TRUE) dfop_sfo_pop <- list(parent_0 = 100, - k_m1 = 0.002, f_parent_to_m1 = 0.5, + k_m1 = 0.005, f_parent_to_m1 = 0.5, k1 = 0.05, k2 = 0.01, g = 0.5) syn_biphasic_parms <- as.matrix(data.frame( k1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k1), log_sd), @@ -178,19 +178,27 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { }) # Mixed model fits -mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc") -sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") +saemix_available <- FALSE +if (requireNamespace("saemix", quietly = TRUE)) { + if(packageVersion("saemix") > "3.1.9000") saemix_available <- TRUE +} +mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores) +mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores) +mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores) +mmkin_biphasic_mixed <- mixed(mmkin_biphasic) -mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE) -dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") -dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") dfop_nlme_1 <- nlme(mmkin_dfop_1) - -mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE) -mmkin_biphasic_mixed <- mixed(mmkin_biphasic) nlme_biphasic <- nlme(mmkin_biphasic) -saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) -saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) + +if (saemix_available) { + sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") + + dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") + dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") + + saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) + saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) +} ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")])) @@ -200,7 +208,10 @@ sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"), dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO"), quiet = TRUE) f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba), - ds_uba, quiet = TRUE) + ds_uba, quiet = TRUE, cores = n_cores) f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ]) -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") + +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") +} |