diff options
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 19 |
1 files changed, 17 insertions, 2 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 9229c198..96e865d4 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -106,6 +106,7 @@ const <- function(value) 2 set.seed(123456) SFO <- mkinmod(parent = mkinsub("SFO")) k_parent = rlnorm(n, log(0.03), log_sd) +set.seed(123456) ds_sfo <- lapply(1:n, function(i) { ds_mean <- mkinpredict(SFO, c(k_parent = k_parent[i]), c(parent = 100), sampling_times) @@ -118,6 +119,7 @@ fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8) fomc_parms <- as.matrix(data.frame( alpha = rlnorm(n, log(fomc_pop$alpha), 0.4), beta = rlnorm(n, log(fomc_pop$beta), 0.2))) +set.seed(123456) ds_fomc <- lapply(1:3, function(i) { ds_mean <- mkinpredict(FOMC, fomc_parms[i, ], c(parent = 100), sampling_times) @@ -131,6 +133,7 @@ dfop_parms <- as.matrix(data.frame( k1 = rlnorm(n, log(dfop_pop$k1), log_sd), k2 = rlnorm(n, log(dfop_pop$k2), log_sd), g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd)))) +set.seed(123456) ds_dfop <- lapply(1:n, function(i) { ds_mean <- mkinpredict(DFOP, dfop_parms[i, ], c(parent = dfop_pop$parent_0), sampling_times) @@ -144,6 +147,7 @@ hs_parms <- as.matrix(data.frame( k1 = rlnorm(n, log(hs_pop$k1), log_sd), k2 = rlnorm(n, log(hs_pop$k2), log_sd), tb = rlnorm(n, log(hs_pop$tb), 0.1))) +set.seed(123456) ds_hs <- lapply(1:10, function(i) { ds_mean <- mkinpredict(HS, hs_parms[i, ], c(parent = hs_pop$parent_0), sampling_times) @@ -171,6 +175,7 @@ ds_biphasic_mean <- lapply(1:n_biphasic, c(parent = 100, m1 = 0), sampling_times) } ) +set.seed(123456) ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { add_err(ds, sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2), @@ -193,8 +198,18 @@ 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") + # With default control parameters, we do not get good results with mkin + # transformations here + dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", + control = list( + displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE, + rw.init = 1, nbiter.saemix = c(600, 100)) + ) + dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix", + control = list( + displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE, + rw.init = 0.5, nbiter.saemix = c(600, 100)) + ) saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) |