Increase test coverage

Also, using mkin analytical solutions for more than one observed
variable is not supported (but could be if out_values would be
reordered).

2 files changed, 22 insertions, 17 deletions

diff --git a/log/check.log b/log/check.log
index b7f6068c..b58119ef 100644
--- a/log/check.log
+++ b/log/check.log
@@ -21,7 +21,8 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking whether package ‘mkin’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
@@ -70,5 +71,9 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: OK
+Status: 1 NOTE
+See
+  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
 
diff --git a/log/test.log b/log/test.log
index fa808f22..cec5e7ed 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,39 +1,39 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [1.6s]
+✔ |         5 | Analytical solutions for coupled models [1.5s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |         7 | Use of precompiled symbols in mkinpredict [3.3s]
+✔ |         6 | Use of precompiled symbols in mkinpredict [3.2s]
 ✔ |        12 | Confidence intervals and p-values [0.4s]
-✔ |     1  12 | Dimethenamid data from 2018 [13.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.5s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:88'): 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 [2.5s]
+✔ |        14 | Error model fitting [2.4s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.3s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.5s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.2s]
 ✔ |         1 | Fitting the logistic model [0.1s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s]
-✔ |     1  11 | Nonlinear mixed-effects models [6.1s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s]
+✔ |     1  17 | Nonlinear mixed-effects models [294.0s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_mixed.R:78'): 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 [0.4s]
+✔ |        10 | Special cases of mkinfit calls [0.3s]
 ✔ |         3 | mkinfit features [0.5s]
 ✔ |         8 | mkinmod model generation and printing
 ✔ |         3 | Model predictions with mkinpredict [0.1s]
-✔ |        12 | Multistart method for saem.mmkin models [21.7s]
+✔ |        12 | Multistart method for saem.mmkin models [23.2s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [3.8s]
-✔ |        15 | Plotting [4.7s]
+✔ |        15 | Plotting [4.8s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [32.0s]
+✔ |     1  36 | saemix parent models [30.7s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
@@ -44,15 +44,15 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         9 | Hypothesis tests [3.0s]
+✔ |         9 | Hypothesis tests [2.9s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 120.2 s
+Duration: 406.1 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 • This still takes almost 2.5 minutes although we do not solve ODEs (1)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 277 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 282 ]