diff options
| -rw-r--r-- | print_nlmixr_saem_biphasic.txt | 35 | ||||
| -rw-r--r-- | print_nlmixr_saem_biphasic_tc.txt | 39 | ||||
| -rw-r--r-- | tests/testthat/setup_script.R | 4 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 2 |
4 files changed, 80 insertions, 0 deletions
diff --git a/print_nlmixr_saem_biphasic.txt b/print_nlmixr_saem_biphasic.txt new file mode 100644 index 00000000..5cf80f0f --- /dev/null +++ b/print_nlmixr_saem_biphasic.txt @@ -0,0 +1,35 @@ +Kinetic nonlinear mixed-effects model fit by saem using nlmixr +Structural model: +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: +507 observations of 2 variable(s) grouped in 15 datasets + +Likelihood: + AIC BIC logLik + 2510 2569 -1241 + +Fitted parameters: + Est. SE %RSE Back-transformed(95%CI) BSV(CV% or SD) +parent_0 100 0.444 0.442 100 (99.6, 101) 0.461 +log_k_m1 -5.36 0.0804 1.5 0.00472 (0.00403, 0.00552) 21.5 +f_parent_qlogis -0.0909 0.0868 95.5 0.477 (0.435, 0.52) 0.308 +log_k1 -2.78 0.0977 3.51 0.0618 (0.0511, 0.0749) 30.1 +log_k2 -4.51 0.08 1.77 0.011 (0.00941, 0.0129) 16.6 +g_qlogis -0.121 0.17 141 0.47 (0.388, 0.553) 0.373 +sigma_parent 3.72 3.72 +sigma_m1 1.44 1.44 + Shrink(SD)% +parent_0 69.2%> +log_k_m1 19.6%< +f_parent_qlogis -0.136%> +log_k1 6.71%< +log_k2 23.7%= +g_qlogis 19.5%< +sigma_parent +sigma_m1 diff --git a/print_nlmixr_saem_biphasic_tc.txt b/print_nlmixr_saem_biphasic_tc.txt new file mode 100644 index 00000000..ad59005d --- /dev/null +++ b/print_nlmixr_saem_biphasic_tc.txt @@ -0,0 +1,39 @@ +Kinetic nonlinear mixed-effects model fit by saem using nlmixr +Structural model: +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: +507 observations of 2 variable(s) grouped in 15 datasets + +Likelihood: + AIC BIC logLik + 2400 2468 -1184 + +Fitted parameters: + Est. SE %RSE Back-transformed(95%CI) BSV(CV% or SD) +parent_0 100 0.685 0.682 100 (99, 102) 0.278 +log_k_m1 -5.35 0.0812 1.52 0.00477 (0.00407, 0.00559) 13.7 +f_parent_qlogis -0.091 0.096 106 0.477 (0.431, 0.524) 0.320 +log_k1 -2.76 0.0969 3.5 0.063 (0.0521, 0.0762) 29.9 +log_k2 -4.49 0.0658 1.47 0.0113 (0.00991, 0.0128) 18.6 +g_qlogis -0.167 0.142 85.3 0.458 (0.39, 0.528) 0.339 +sigma_low_parent 1.04 1.04 +rsd_high_parent 0.0531 0.0531 +sigma_low_m1 0.819 0.819 +rsd_high_m1 0.058 0.058 + Shrink(SD)% +parent_0 87.7%> +log_k_m1 44.8%> +f_parent_qlogis -0.375%> +log_k1 6.76%< +log_k2 10.4%< +g_qlogis 20.3%= +sigma_low_parent +rsd_high_parent +sigma_low_m1 +rsd_high_m1 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 08d899a1..bfa70005 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -186,6 +186,8 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { 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_tc <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores, + error_model = "tc") mmkin_biphasic_mixed <- mixed(mmkin_biphasic) # nlme @@ -204,6 +206,8 @@ 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))) +tmp <- capture_output(nlmixr_saem_biphasic_tc <- nlmixr(mmkin_biphasic_tc, 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))) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 2e241931..d30dcaa8 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -83,6 +83,8 @@ test_that("nlmixr results are reproducible for biphasic fits", { test_summary$date.summary <- "Dummy date for testing" test_summary$time <- c(elapsed = "test time 0") + expect_known_output(print(nlmixr_saem_biphasic, digits = 1), "print_nlmixr_saem_biphasic.txt") + expect_known_output(print(nlmixr_saem_biphasic_tc, digits = 1), "print_nlmixr_saem_biphasic_tc.txt") expect_known_output(print(test_summary, digits = 1), "summary_nlmixr_saem_biphasic.txt") }) |