Deal with covariates in summary for saem.mmkin objects

2 files changed, 21 insertions, 16 deletions

diff --git a/log/check.log b/log/check.log
index 9f05935f..cb313bc0 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
@@ -58,7 +59,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking sizes of PDF files under ‘inst/doc’ ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [11s/11s] OK
+* checking examples ... [10s/11s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... 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 de28f836..54aa3c73 100644
--- a/log/test.log
+++ b/log/test.log
@@ -4,50 +4,50 @@
 ✔ |         5 | Analytical solutions for coupled models [1.6s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |        12 | Confidence intervals and p-values [0.4s]
-✔ |     1  12 | Dimethenamid data from 2018 [12.0s]
+✔ |        12 | Confidence intervals and p-values [0.3s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.5s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:99'): 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 [2.3s]
+✔ |        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) [0.4s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.5s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.2s]
 ✔ |         1 | Fitting the logistic model [0.1s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s]
-✔ |     1  11 | Nonlinear mixed-effects models [5.9s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.5s]
+✔ |     1  11 | Nonlinear mixed-effects models [5.7s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [0.5s]
+✔ |        10 | Special cases of mkinfit calls [0.4s]
 ✔ |         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 [21.2s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [3.7s]
-✔ |        15 | Plotting [4.9s]
+✔ |        15 | Plotting [4.4s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [32.6s]
+✔ |     1  36 | saemix parent models [30.8s]
 ────────────────────────────────────────────────────────────────────────────────
 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
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [1.7s]
+✔ |        10 | Fitting the SFORB model [1.6s]
 ✔ |         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: 114.8 s
+Duration: 112.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)