diff options
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 30 |
1 files changed, 28 insertions, 2 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 9da8b90d..4a343bc5 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -95,7 +95,6 @@ fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE error_model_algorithm = "threestep") # Mixed models data and -set.seed(123456) sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) n <- n_biphasic <- 15 log_sd <- 0.3 @@ -103,6 +102,7 @@ err_1 = list(const = 1, prop = 0.05) tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop) const <- function(value) 2 +set.seed(123456) SFO <- mkinmod(parent = mkinsub("SFO")) k_parent = rlnorm(n, log(0.03), log_sd) ds_sfo <- lapply(1:n, function(i) { @@ -111,6 +111,19 @@ ds_sfo <- lapply(1:n, function(i) { add_err(ds_mean, tc, n = 1)[[1]] }) +set.seed(123456) +FOMC <- mkinmod(parent = mkinsub("FOMC")) +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))) +ds_fomc <- lapply(1:3, function(i) { + ds_mean <- mkinpredict(FOMC, fomc_parms[i, ], + c(parent = 100), sampling_times) + add_err(ds_mean, tc, n = 1)[[1]] +}) + +set.seed(123456) DFOP <- mkinmod(parent = mkinsub("DFOP")) dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4) dfop_parms <- as.matrix(data.frame( @@ -124,6 +137,19 @@ ds_dfop <- lapply(1:n, function(i) { }) set.seed(123456) +HS <- mkinmod(parent = mkinsub("HS")) +hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15) +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$tb), 0.1))) +ds_hs <- lapply(1:10, function(i) { + ds_mean <- mkinpredict(HS, hs_parms[i, ], + c(parent = hs_pop$parent_0), sampling_times) + add_err(ds_mean, const, n = 1)[[1]] +}) + +set.seed(123456) DFOP_SFO <- mkinmod( parent = mkinsub("DFOP", "m1"), m1 = mkinsub("SFO"), @@ -152,7 +178,7 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { # Mixed model fits mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc") -sfo_saemix_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") +sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE) dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") |