More tests

7 files changed, 219 insertions, 172 deletions

diff --git a/tests/testthat/print_mmkin_biphasic_mixed.txt b/tests/testthat/print_mmkin_biphasic_mixed.txt
index 3d92b120..62e485ac 100644
--- a/tests/testthat/print_mmkin_biphasic_mixed.txt
+++ b/tests/testthat/print_mmkin_biphasic_mixed.txt
@@ -21,6 +21,6 @@ OK: No warnings
 
 Mean fitted parameters:
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-        100.700          -6.299          -0.078          -3.094          -3.954 
+   100.70048940     -6.29941397     -0.07845907     -3.09354444     -3.95368996 
        g_qlogis 
-          0.027 
+     0.02729554 
diff --git a/tests/testthat/print_nlme_biphasic.txt b/tests/testthat/print_nlme_biphasic.txt
new file mode 100644
index 00000000..9ea84d44
--- /dev/null
+++ b/tests/testthat/print_nlme_biphasic.txt
@@ -0,0 +1,29 @@
+Kinetic nonlinear mixed-effects model fit by maximum likelihood
+
+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:
+509 observations of 2 variable(s) grouped in 15 datasets
+
+Log-likelihood: -1343
+
+Fixed effects:
+ list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1) 
+       parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
+        100.365          -6.231          -0.078          -3.224          -4.098 
+       g_qlogis 
+         -0.105 
+
+Random effects:
+ Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1)
+ Level: ds
+ Structure: Diagonal
+        parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual
+StdDev:      1.1  0.00017            0.28   0.74   0.82     0.28      2.7
+
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 1bedbf65..e3b56fb3 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -94,7 +94,7 @@ fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TR
 fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE,
   error_model_algorithm = "threestep")
 
-# Mixed models data
+# Mixed models data and
 set.seed(123456)
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 n <- n_biphasic <- 15
@@ -153,6 +153,12 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
 # Mixed model fits
 mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc")
 sfo_saemix_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
+
+mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE)
+dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
+dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
+dfop_nlme_1 <- nlme(mmkin_dfop_1)
+
 mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE)
 mmkin_biphasic_mixed <- mixed(mmkin_biphasic)
 nlme_biphasic <- nlme(mmkin_biphasic)
@@ -163,9 +169,9 @@ ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
   function(x) subset(x$data[c("name", "time", "value")]))
 names(ds_uba) <- paste("Dataset", 6:10)
 sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"))
+  A1 = mkinsub("SFO"), quiet = TRUE)
 dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"))
+  A1 = mkinsub("SFO"), quiet = TRUE)
 f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
   ds_uba, quiet = TRUE)
 f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
diff --git a/tests/testthat/summary_nlme_biphasic_s.txt b/tests/testthat/summary_nlme_biphasic_s.txt
new file mode 100644
index 00000000..1e4c3c14
--- /dev/null
+++ b/tests/testthat/summary_nlme_biphasic_s.txt
@@ -0,0 +1,81 @@
+nlme version used for fitting:      Dummy 0.0 for testing 
+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:
+509 observations of 2 variable(s) grouped in 15 datasets
+
+Model predictions using solution type analytical 
+
+Fitted in test time 0 s using 2 iterations
+
+Variance model: Constant variance 
+
+Mean of starting values for individual parameters:
+       parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
+        100.700          -6.299          -0.078          -3.094          -3.954 
+       g_qlogis 
+          0.027 
+
+Fixed degradation parameter values:
+     value  type
+m1_0     0 state
+
+Results:
+
+   AIC  BIC logLik
+  2711 2766  -1343
+
+Optimised, transformed parameters with symmetric confidence intervals:
+                 lower    est.   upper
+parent_0         99.50 100.365 101.229
+log_k_m1         -6.53  -6.231  -5.936
+f_parent_qlogis  -0.24  -0.078   0.084
+log_k1           -3.61  -3.224  -2.839
+log_k2           -4.52  -4.098  -3.677
+g_qlogis         -0.38  -0.105   0.172
+
+Correlation: 
+                prnt_0 lg_k_1 f_prn_ log_k1 log_k2
+log_k_m1        -0.185                            
+f_parent_qlogis -0.161  0.405                     
+log_k1           0.056 -0.014 -0.016              
+log_k2           0.025  0.011 -0.004  0.026       
+g_qlogis        -0.032 -0.046 -0.012 -0.109 -0.103
+
+Random effects:
+ Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1)
+ Level: ds
+ Structure: Diagonal
+        parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual
+StdDev:      1.1  0.00017            0.28   0.74   0.82     0.28      2.7
+
+
+Backtransformed parameters with asymmetric confidence intervals:
+                 lower    est.   upper
+parent_0       1.0e+02 100.365 1.0e+02
+k_m1           1.5e-03   0.002 2.6e-03
+f_parent_to_m1 4.4e-01   0.480 5.2e-01
+k1             2.7e-02   0.040 5.9e-02
+k2             1.1e-02   0.017 2.5e-02
+g              4.1e-01   0.474 5.4e-01
+
+Resulting formation fractions:
+              ff
+parent_m1   0.48
+parent_sink 0.52
+
+Estimated disappearance times:
+       DT50 DT90 DT50back DT50_k1 DT50_k2
+parent   27  105       31      17      42
+m1      352 1171       NA      NA      NA
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 2d69e13e..b9713c6e 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,35 +1,97 @@
-context("Fitting of nonlinear mixed effects models")
-
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-n_biphasic <- 8
-err_1 = list(const = 1, prop = 0.07)
-
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("DFOP", "m1"),
-  m1 = mkinsub("SFO"),
-  quiet = TRUE)
-
-set.seed(123456)
-log_sd <- 0.3
-syn_biphasic_parms <- as.matrix(data.frame(
-  k1 = rlnorm(n_biphasic, log(0.05), log_sd),
-  k2 = rlnorm(n_biphasic, log(0.01), log_sd),
-  g = plogis(rnorm(n_biphasic, 0, log_sd)),
-  f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),
-  k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))
-
-ds_biphasic_mean <- lapply(1:n_biphasic,
-  function(i) {
-    mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],
-      c(parent = 100, m1 = 0), sampling_times)
-  }
-)
-
-set.seed(123456L)
-ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
-  add_err(ds,
-    sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
-    n = 1, secondary = "m1")[[1]]
+context("Nonlinear mixed effects models")
+
+test_that("Parent only models can be fitted using nonlinear mixed effects models", {
+  # Some fits were done in the setup script
+  mmkin_sfo_2 <- mmkin("SFO", ds_sfo, fixed_initials = c(parent = 100), quiet = TRUE)
+
+  sfo_saemix_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
+  sfo_saemix_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
+  s_sfo_s1 <- summary(sfo_saemix_1)
+  s_sfo_s2 <- summary(sfo_saemix_2)
+
+  sfo_nlme_1 <- expect_warning(nlme(mmkin_sfo_1), "not converge")
+  s_sfo_n <- summary(sfo_nlme_1)
+
+  # Compare with input
+  expect_equal(round(s_sfo_s2$confint_ranef["SD.log_k_parent", "est."], 1), 0.3)
+  # k_parent is a bit different from input 0.03 here
+  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), 0.035)
+  expect_equal(round(s_sfo_s2$confint_back["k_parent", "est."], 3), 0.035)
+
+  # But the result is pretty unanimous between methods
+  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
+    round(s_sfo_s2$confint_back["k_parent", "est."], 3))
+  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
+    round(s_sfo_n$confint_back["k_parent", "est."], 3))
+
+  s_dfop_s1 <- summary(dfop_saemix_1)
+  s_dfop_s2 <- summary(dfop_saemix_2)
+  s_dfop_n <- summary(dfop_nlme_1)
+
+  dfop_pop <- as.numeric(dfop_pop)
+  expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop))
+  expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop))
+  expect_true(all(s_dfop_s2$confint_back[, "lower"] < dfop_pop))
+  expect_true(all(s_dfop_s2$confint_back[, "upper"] > dfop_pop))
+
+
+  # We get < 20% deviations with transformations made in mkin
+  rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop
+  expect_true(all(rel_diff_1 < 0.2))
+
+  # We get < 8% deviations with transformations made in saemix
+  rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
+  expect_true(all(rel_diff_2 < 0.08))
+})
+
+test_that("Print methods work", {
+  expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
+  expect_known_output(print(nlme_biphasic, digits = 2), "print_nlme_biphasic.txt")
+  expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt")
+})
+
+test_that("nlme results are reproducible", {
+
+  test_summary <- summary(nlme_biphasic)
+  test_summary$nlmeversion <- "Dummy 0.0 for testing"
+  test_summary$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 = 2), "summary_nlme_biphasic_s.txt")
+
+  dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
+  ci_dfop_sfo_n <- summary(nlme_biphasic)$confint_back
+  # expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop)) # k2 is overestimated
+  expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop))
+})
+
+test_that("saem results are reproducible for biphasic fits", {
+
+  test_summary <- summary(saem_biphasic_s)
+  test_summary$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$time <- c(elapsed = "test time 0")
+
+  expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
+
+  dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
+  ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
+  expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
+  expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
+
+  # The following does not work, as k1 and k2 are not fitted well
+  ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
+  # expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop))
+  # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
+
+  # Somehow this does not work at the moment. But it took forever (~ 10 min) anyways...
+  #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
+
 })
 
-f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE)
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index db44c850..ae2841c0 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,6 +35,9 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
+  plot_biphasic_nlme <- function() plot(dfop_nlme_1)
+  vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
+
   plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem)
   vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s)
 
@@ -46,7 +49,6 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
   #plot_biphasic_saem_s <- function() plot(saem_biphasic_s)
   plot_biphasic_saem_m <- function() plot(saem_biphasic_m)
 
-  vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
   vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m)
 
   # different results when working with eigenvalues
diff --git a/tests/testthat/test_saem.R b/tests/testthat/test_saem.R
deleted file mode 100644
index aa32d0b5..00000000
--- a/tests/testthat/test_saem.R
+++ /dev/null
@@ -1,133 +0,0 @@
-context("Nonlinear mixed effects models fitted with SAEM from saemix")
-
-set.seed(123456)
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-n <- n_biphasic <- 15
-log_sd <- 0.3
-err_1 = list(const = 1, prop = 0.05)
-tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop)
-const <- function(value) 2
-
-SFO <- mkinmod(parent = mkinsub("SFO"))
-k_parent = rlnorm(n, log(0.03), log_sd)
-ds_sfo <- lapply(1:n, function(i) {
-  ds_mean <- mkinpredict(SFO, c(k_parent = k_parent[i]),
-    c(parent = 100), sampling_times)
-  add_err(ds_mean, tc, n = 1)[[1]]
-})
-
-DFOP <- mkinmod(parent = mkinsub("DFOP"))
-dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)
-dfop_parms <- as.matrix(data.frame(
-  k1 = rlnorm(n, log(dfop_pop$k1), log_sd),
-  k2 = rlnorm(n, log(dfop_pop$k2), log_sd),
-  g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))
-ds_dfop <- lapply(1:n, function(i) {
-  ds_mean <- mkinpredict(DFOP, dfop_parms[i, ],
-    c(parent = dfop_pop$parent_0), sampling_times)
-  add_err(ds_mean, const, n = 1)[[1]]
-})
-
-set.seed(123456)
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("DFOP", "m1"),
-  m1 = mkinsub("SFO"),
-  quiet = TRUE)
-syn_biphasic_parms <- as.matrix(data.frame(
-  k1 = rlnorm(n_biphasic, log(0.05), log_sd),
-  k2 = rlnorm(n_biphasic, log(0.01), log_sd),
-  g = plogis(rnorm(n_biphasic, 0, log_sd)),
-  f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),
-  k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))
-ds_biphasic_mean <- lapply(1:n_biphasic,
-  function(i) {
-    mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],
-      c(parent = 100, m1 = 0), sampling_times)
-  }
-)
-ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
-  add_err(ds,
-    sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
-    n = 1, secondary = "m1")[[1]]
-})
-
-test_that("Parent only models can be fitted with saemix", {
-  # Some fits were done in the setup script
-  mmkin_sfo_2 <- mmkin("SFO", ds_sfo, fixed_initials = c(parent = 100), quiet = TRUE)
-
-  sfo_saemix_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
-  sfo_saemix_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
-  s_sfo_s1 <- summary(sfo_saemix_1)
-  s_sfo_s2 <- summary(sfo_saemix_2)
-
-  sfo_nlme_1 <- expect_warning(nlme(mmkin_sfo_1), "not converge")
-  s_sfo_n <- summary(sfo_nlme_1)
-
-  # Compare with input
-  expect_equal(round(s_sfo_s2$confint_ranef["SD.log_k_parent", "est."], 1), 0.3)
-  # k_parent is a bit different from input 0.03 here
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), 0.035)
-  expect_equal(round(s_sfo_s2$confint_back["k_parent", "est."], 3), 0.035)
-
-  # But the result is pretty unanimous between methods
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
-    round(s_sfo_s2$confint_back["k_parent", "est."], 3))
-  expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
-    round(s_sfo_n$confint_back["k_parent", "est."], 3))
-
-  mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE)
-
-  dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
-  dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
-  dfop_nlme_1 <- nlme(mmkin_dfop_1)
-  s_dfop_s1 <- summary(dfop_saemix_1)
-  s_dfop_s2 <- summary(dfop_saemix_2)
-  s_dfop_n <- summary(dfop_nlme_1)
-
-  dfop_pop <- as.numeric(dfop_pop)
-  expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop))
-  expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop))
-  expect_true(all(s_dfop_s2$confint_back[, "lower"] < dfop_pop))
-  expect_true(all(s_dfop_s2$confint_back[, "upper"] > dfop_pop))
-
-
-  # We get < 20% deviations with transformations made in mkin
-  rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop
-  expect_true(all(rel_diff_1 < 0.2))
-
-  # We get < 8% deviations with transformations made in saemix
-  rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
-  expect_true(all(rel_diff_2 < 0.08))
-})
-
-test_that("Print methods work", {
-  expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt")
-  expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
-})
-
-test_that("Saemix results are reproducible", {
-
-  test_summary <- summary(saem_biphasic_s)
-  test_summary$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$time <- c(elapsed = "test time 0")
-
-  expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
-
-  dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
-  ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
-  expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
-  expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
-
-  # The following does not work, as k1 and k2 are not fitted well
-  ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
-  # expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop))
-  # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
-
-  # Somehow this does not work at the moment. But it took forever (~ 10 min) anyways...
-  #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)
-
-})