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authorJohannes Ranke <jranke@uni-bremen.de>2022-02-28 20:46:39 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-02-28 20:46:39 +0100
commit931ca24a70995c78958140b1d53dfd52e0e9bc4d (patch)
treedce6df944e07cb427043c851d9addf4a545cf1fb /tests/testthat
parent9110b14f3cb40dbacbf78b8f7b3d9d212de6985b (diff)
Add test for summary.nlmixr.mmkin
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/setup_script.R7
-rw-r--r--tests/testthat/summary_nlmixr_saem_biphasic.txt97
-rw-r--r--tests/testthat/test_mixed.R14
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")
+})
+

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