diff options
Diffstat (limited to 'tests/testthat/setup_script.R')
| -rw-r--r-- | tests/testthat/setup_script.R | 38 |
1 files changed, 13 insertions, 25 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 62cdf78e..777c998a 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -8,31 +8,18 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) { n_cores <- 1 } -# We are only allowed one core on travis, but they also set NOT_CRAN=true -if (Sys.getenv("TRAVIS") != "") n_cores = 1 +# Use the two available cores on travis +if (Sys.getenv("TRAVIS") != "") n_cores = 2 # On Windows we would need to make a cluster first if (Sys.info()["sysname"] == "Windows") n_cores = 1 -# We set up some models and fits with nls for comparisons -SFO_trans <- function(t, parent_0, log_k_parent_sink) { - parent_0 * exp(- exp(log_k_parent_sink) * t) -} -SFO_notrans <- function(t, parent_0, k_parent_sink) { - parent_0 * exp(- k_parent_sink * t) -} -f_1_nls_trans <- nls(value ~ SFO_trans(time, parent_0, log_k_parent_sink), - data = FOCUS_2006_A, - start = list(parent_0 = 100, log_k_parent_sink = log(0.1))) -f_1_nls_notrans <- nls(value ~ SFO_notrans(time, parent_0, k_parent_sink), - data = FOCUS_2006_A, - start = list(parent_0 = 100, k_parent_sink = 0.1)) - +# Very simple example fits f_1_mkin_trans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE) f_1_mkin_notrans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE, transform_rates = FALSE) -# mmkin object of parent fits for tests +# mmkin object of parent fits models <- c("SFO", "FOMC", "DFOP", "HS") fits <- suppressWarnings( # FOCUS A FOMC was, it seems, in testthat output mmkin(models, @@ -72,9 +59,8 @@ DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data f_2_mkin <- mkinfit("DFOP", DFOP_par_c, quiet = TRUE) f_2_nls <- nls(value ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = subset(DFOP_par_c, name == "parent")) -f_2_anova <- lm(value ~ as.factor(time), data = subset(DFOP_par_c, name == "parent")) -# Two metabolites +# mkinfit with two metabolites m_synth_SFO_lin <- mkinmod( parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), @@ -137,7 +123,7 @@ set.seed(123456) ds_dfop <- lapply(1:n, function(i) { ds_mean <- mkinpredict(DFOP, dfop_parms[i, ], c(parent = dfop_pop$parent_0), sampling_times) - add_err(ds_mean, const, n = 1)[[1]] + add_err(ds_mean, tc, n = 1)[[1]] }) set.seed(123456) @@ -184,20 +170,22 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { # Mixed model fits 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_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores, + error_model = "tc") + mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores, control = list(eval.max = 500, iter.max = 400), error_model = "tc") # nlme -dfop_nlme_1 <- nlme(mmkin_dfop_1) +dfop_nlme_1 <- suppressWarnings(nlme(mmkin_dfop_1)) nlme_biphasic <- suppressWarnings(nlme(mmkin_biphasic)) # saemix 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") +sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0") +dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", + no_random_effect = "parent_0") saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) |