Another attempt to make the test robust

As the last update failed on travis. Now we should be more robust,
as rounding to one digit works better when parameters are
log-transformed (mkin transformations) in the output.

4 files changed, 44 insertions, 20 deletions

diff --git a/log/build.log b/log/build.log
index 5ac21b0d..c4f9b8a2 100644
--- a/log/build.log
+++ b/log/build.log
@@ -5,5 +5,5 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘mkin_1.1.2.tar.gz’
+* building ‘mkin_1.2.0.tar.gz’
 
diff --git a/log/test.log b/log/test.log
index 0e2ca6b2..b4298c40 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,38 +1,38 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.4s]
+✔ |         5 | Analytical solutions for coupled models [3.3s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [63.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.7s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [5.5s]
+✔ |        14 | Error model fitting [5.0s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [28.6s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.6s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s]
+✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [1.1s]
-✔ |         3 | mkinfit features [1.7s]
-✔ |         8 | mkinmod model generation and printing [0.4s]
-✔ |         3 | Model predictions with mkinpredict [0.6s]
-✔ |         7 | Multistart method for saem.mmkin models [93.9s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [7.0s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [13.0s]
-✔ |        16 | Plotting [11.3s]
+✔ |        10 | Special cases of mkinfit calls [0.4s]
+✔ |         3 | mkinfit features [0.7s]
+✔ |         8 | mkinmod model generation and printing [0.2s]
+✔ |         3 | Model predictions with mkinpredict [0.3s]
+✔ |         7 | Multistart method for saem.mmkin models [38.1s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.4s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
+✔ |        16 | Plotting [9.8s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [72.6s]
+✔ |     1  36 | saemix parent models [72.0s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
@@ -43,11 +43,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
-✔ |         9 | Hypothesis tests [8.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ |         9 | Hypothesis tests [8.3s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 324.3 s
+Duration: 208.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/tests/testthat/print_dfop_saemix_1.txt b/tests/testthat/print_dfop_saemix_1.txt
new file mode 100644
index 00000000..f427b3e6
--- /dev/null
+++ b/tests/testthat/print_dfop_saemix_1.txt
@@ -0,0 +1,24 @@
+Kinetic nonlinear mixed-effects model fit by SAEM
+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
+
+Data:
+270 observations of 1 variable(s) grouped in 15 datasets
+
+Likelihood computed by importance sampling
+   AIC  BIC logLik
+  1409 1415   -695
+
+Fitted parameters:
+            estimate lower  upper
+parent_0      100.04 98.89 101.20
+log_k1         -4.12 -4.24  -4.00
+log_k2         -2.67 -2.90  -2.44
+g_qlogis        0.43  0.22   0.64
+a.1             0.92  0.67   1.16
+b.1             0.05  0.04   0.06
+SD.log_k1       0.22  0.14   0.30
+SD.log_k2       0.36  0.21   0.51
+SD.g_qlogis     0.14 -0.11   0.39
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 8e4d668b..646b6110 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -11,7 +11,7 @@ test_that("Print methods work", {
   expect_known_output(print(mixed(mmkin_sfo_1), digits = 2), "print_mmkin_sfo_1_mixed.txt")
   expect_known_output(print(dfop_nlme_1, digits = 1), "print_dfop_nlme_1.txt")
 
-  expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt")
+  expect_known_output(print(dfop_saemix_1, digits = 1), "print_dfop_saemix_1.txt")
 })
 
 test_that("nlme results are reproducible to some degree", {