Add test for summary.nlmixr.mmkin

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")
+})
+