Complete documentation and fix a bug

The bug was introduced by the changes in summary.saem.mmkin.R and
surfaced in the tests when using saemix transformations.

2 files changed, 19 insertions, 13 deletions

diff --git a/log/check.log b/log/check.log
index 8fce3fd1..c2b4aa50 100644
--- a/log/check.log
+++ b/log/check.log
@@ -7,8 +7,10 @@
 * checking extension type ... Package
 * this is package ‘mkin’ version ‘1.1.2’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
+
+The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -69,5 +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 d7d623d7..b6ec2084 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,11 +1,11 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.2s]
+✔ |         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 [31.3s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.6s]
 ────────────────────────────────────────────────────────────────────────────────
 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
@@ -16,7 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ✔ |        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]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s]
+✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.3s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
@@ -29,20 +29,20 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         3 | Model predictions with mkinpredict [0.4s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.8s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
-✔ |        16 | Plotting [9.7s]
+✔ |        16 | Plotting [9.9s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        37 | saemix parent models [208.2s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
+✔ |        37 | saemix parent models [208.7s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3s]
 ✔ |        11 | Processing of residue series
-✔ |         7 | Fitting the SFORB model [3.6s]
+✔ |         7 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [7.6s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [7.8s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 304.2 s
+Duration: 305.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)