diff options
| -rw-r--r-- | tests/testthat/setup_script.R | 7 | ||||
| -rw-r--r-- | tests/testthat/summary_nlmixr_saem_biphasic.txt | 97 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 14 |
3 files changed, 118 insertions, 0 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 4688b7d7..08d899a1 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -201,6 +201,13 @@ 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) +# nlmixr saem +tmp <- capture_output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem", + control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))) +# The FOCEI fit takes too long... +#tmp <- capture_output(nlmixr_focei_biphasic <- nlmixr(mmkin_biphasic, est = "focei", +# control = nlmixr::foceiControl(print = 0))) + # UBA datasets ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")])) diff --git a/tests/testthat/summary_nlmixr_saem_biphasic.txt b/tests/testthat/summary_nlmixr_saem_biphasic.txt new file mode 100644 index 00000000..c5c1fe78 --- /dev/null +++ b/tests/testthat/summary_nlmixr_saem_biphasic.txt @@ -0,0 +1,97 @@ +nlmixr version used for fitting: 2.0.6 +mkin version used for pre-fitting: Dummy 0.0 for testing +R version used for fitting: Dummy R version for testing +Date of fit: Dummy date for testing +Date of summary: Dummy date for testing + +Equations: +d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * parent +d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) + * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * + exp(-k2 * time))) * parent - k_m1 * m1 + +Data: +508 observations of 2 variable(s) grouped in 15 datasets + +Degradation model predictions using RxODE + +Fitted in test time 0 s + +Variance model: Constant variance + +Mean of starting values for individual parameters: + parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 + 100.74 -5.43 -0.05 -2.85 -4.57 + g_qlogis + -0.15 + +Mean of starting values for error model parameters: +sigma_parent sigma_m1 + 3 3 + +Fixed degradation parameter values: +None + +Results: + +Likelihood calculated by gauss3_1.6 + AIC BIC logLik + 2465 2525 -1219 + +Optimised parameters: + est. lower upper +parent_0 100.54 99.7 101.40 +log_k_m1 -5.44 -5.6 -5.24 +f_parent_qlogis -0.06 -0.2 0.05 +log_k1 -2.81 -3.0 -2.65 +log_k2 -4.62 -4.8 -4.41 +g_qlogis -0.14 -0.4 0.17 + +Correlation: + prnt_0 lg_k_1 f_prn_ log_k1 log_k2 +log_k_m1 -0.224 +f_parent_qlogis -0.401 0.335 +log_k1 0.119 0.083 0.019 +log_k2 -0.019 0.237 0.142 0.395 +g_qlogis 0.083 -0.282 -0.218 -0.532 -0.544 + +Random effects (omega): + eta.parent_0 eta.log_k_m1 eta.f_parent_qlogis eta.log_k1 +eta.parent_0 0.05 0.0 0.00 0.00 +eta.log_k_m1 0.00 0.1 0.00 0.00 +eta.f_parent_qlogis 0.00 0.0 0.03 0.00 +eta.log_k1 0.00 0.0 0.00 0.05 +eta.log_k2 0.00 0.0 0.00 0.00 +eta.g_qlogis 0.00 0.0 0.00 0.00 + eta.log_k2 eta.g_qlogis +eta.parent_0 0.00 0.0 +eta.log_k_m1 0.00 0.0 +eta.f_parent_qlogis 0.00 0.0 +eta.log_k1 0.00 0.0 +eta.log_k2 0.08 0.0 +eta.g_qlogis 0.00 0.1 + +Variance model: +sigma_parent sigma_m1 + 4 1 + +Backtransformed parameters: + est. lower upper +parent_0 1e+02 1e+02 1e+02 +k_m1 4e-03 4e-03 5e-03 +f_parent_to_m1 5e-01 5e-01 5e-01 +k1 6e-02 5e-02 7e-02 +k2 1e-02 8e-03 1e-02 +g 5e-01 4e-01 5e-01 + +Resulting formation fractions: + ff +parent_m1 0.5 +parent_sink 0.5 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +parent 27 170 51 12 70 +m1 160 532 NA NA NA diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 130d4596..2e241931 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -72,3 +72,17 @@ test_that("saemix results are reproducible for biphasic fits", { expect_true(all(ci_dfop_sfo_s_d[no_k2, "lower"] < dfop_sfo_pop[no_k2])) expect_true(all(ci_dfop_sfo_s_d[no_k1, "upper"] > dfop_sfo_pop[no_k1])) }) + +test_that("nlmixr results are reproducible for biphasic fits", { + + test_summary <- summary(nlmixr_saem_biphasic) + test_summary$saemixversion <- "Dummy 0.0 for testing" + test_summary$mkinversion <- "Dummy 0.0 for testing" + test_summary$Rversion <- "Dummy R version for testing" + test_summary$date.fit <- "Dummy date for testing" + test_summary$date.summary <- "Dummy date for testing" + test_summary$time <- c(elapsed = "test time 0") + + expect_known_output(print(test_summary, digits = 1), "summary_nlmixr_saem_biphasic.txt") +}) + |