Some more tests for nlmixr.mmkin

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")
 })