Mesotrione data and vignette

The vignette illustrates pH dependent degradation (covariate modelling)
with some detail for the parent compound.

Also, a bug in the saem method of the illparms function was fixed, which
prevented to find ill-defined parameters in cases where e.g. slopes of
covariate models have a negative estimate.

3 files changed, 41 insertions, 36 deletions

diff --git a/log/build.log b/log/build.log
index 30c5e432..717128fd 100644
--- a/log/build.log
+++ b/log/build.log
@@ -6,5 +6,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/vignettes/web_only’
-* building ‘mkin_1.2.4.tar.gz’
+* building ‘mkin_1.2.5.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 970fbc7a..fedb0bd9 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,5 +1,5 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.3.0 Patched (2023-05-18 r84448)
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Debian 12.2.0-14) 12.2.0
@@ -9,9 +9,9 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.4’
+* this is package ‘mkin’ version ‘1.2.5’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... [2s/10s] Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... [3s/12s] Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -45,7 +45,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... [15s/15s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -62,17 +62,22 @@ 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 ... OK
+* checking examples ... [18s/18s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
-* checking re-building of vignette outputs ... OK
+* checking re-building of vignette outputs ... [17s/17s] OK
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... OK
+* checking HTML version of manual ... NOTE
+Skipping checking math rendering: package 'V8' unavailable
 * checking for non-standard things in the check directory ... OK
 * 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 b1b4ae31..2f1b6949 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,24 +1,24 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [1.5s]
+✔ |         5 | Analytical solutions for coupled models [2.9s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |         6 | Use of precompiled symbols in mkinpredict [3.1s]
-✔ |        12 | Confidence intervals and p-values [0.4s]
-✔ |     1  12 | Dimethenamid data from 2018 [12.5s]
+✔ |         6 | Use of precompiled symbols in mkinpredict [5.7s]
+✔ |        12 | Confidence intervals and p-values [1.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [33.1s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:88:3'): 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 [2.3s]
+✔ |        14 | Error model fitting [7.5s]
 ✔ |         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]
-✔ |         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 [18.9s]
-✔ |     2  16 | Nonlinear mixed-effects models [148.4s]
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ |         1 | Fitting the logistic model [0.2s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [43.6s]
+✔ |     2  16 | Nonlinear mixed-effects models [364.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
@@ -27,31 +27,31 @@ Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work
 Reason: This is seldom used, so save some time
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        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 [23.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [3.5s]
-✔ |        15 | Plotting [4.5s]
+✔ |        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]
+✔ |        12 | Multistart method for saem.mmkin models [80.2s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.0s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [9.1s]
+✔ |        15 | Plotting [10.9s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [30.7s]
+✔ |     1  36 | saemix parent models [77.0s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_saemix_parent.R:143:3'): 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]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.2s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [1.7s]
+✔ |        10 | Fitting the SFORB model [3.5s]
 ✔ |         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 [2.9s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
+✔ |         5 | Summary [0.2s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.8s]
+✔ |         9 | Hypothesis tests [6.7s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 259.6 s
+Duration: 656.7 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)