Automatic starting parameters for saem.mmkin

For the case of mkin transformations. This gives faster convergence,
and appears to avoid problems with numeric ODE solutions

2 files changed, 18 insertions, 18 deletions

diff --git a/log/check.log b/log/check.log
index d8225158..3fea2ec6 100644
--- a/log/check.log
+++ b/log/check.log
@@ -57,12 +57,12 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [36s/46s] OK
+* checking examples ... [15s/15s] 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 ... [26s/41s] OK
+* checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK
diff --git a/log/test.log b/log/test.log
index 874d6e24..f20a7f18 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,45 +1,45 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.3s]
+✔ |         5 | Analytical solutions for coupled models [3.2s]
 ✔ |         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 [31.5s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.1s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:98'): 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 [5.0s]
+✔ |        14 | Error model fitting [4.9s]
 ✔ |         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]
 ✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.0s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:74'): 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]
 ✔ |         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 [36.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
-✔ |        16 | Plotting [10.1s]
+✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |         7 | Multistart method for saem.mmkin models [36.7s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ |        16 | Plotting [9.8s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  37 | saemix parent models [71.5s]
+✔ |     1  36 | saemix parent models [66.4s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem
+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 [1.4s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.8s]
+✔ |        10 | Fitting the SFORB model [3.7s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
@@ -47,11 +47,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 216.0 s
+Duration: 211.1 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 268 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 267 ]