Pass error.init to saemix_model, show in parplot

Due to an oversight, error.init was not really passed to saemix_model in
saem.mmkin. The new initial values were reverted to c(1, 1), in order to
avoid changing the test results. Initial values for error model
parameters are now shown in parplot.multistart.

2 files changed, 20 insertions, 19 deletions

diff --git a/log/build.log b/log/build.log
index a56a64df..c4f9b8a2 100644
--- a/log/build.log
+++ b/log/build.log
@@ -6,3 +6,4 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 * building ‘mkin_1.2.0.tar.gz’
+
diff --git a/log/test.log b/log/test.log
index b305bf58..af8e52fd 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.5s]
+✔ |         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 [1.1s]
-✔ |     1  12 | Dimethenamid data from 2018 [34.5s]
+✔ |        12 | Confidence intervals and p-values [1.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.4s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [5.3s]
+✔ |        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]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [25.6s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.4s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [23.9s]
+✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [0.6s]
+✔ |        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]
-✔ |         9 | Multistart method for saem.mmkin models [40.2s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.6s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [9.5s]
-✔ |        16 | Plotting [10.5s]
+✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |         9 | Multistart method for saem.mmkin models [37.0s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
+✔ |        16 | Plotting [10.1s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [69.8s]
+✔ |     1  36 | saemix parent models [66.0s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [1.6s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.9s]
+✔ |        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) [2.3s]
-✔ |         9 | Hypothesis tests [8.5s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [8.0s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 225.9 s
+Duration: 211.3 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)