Facilitate centering covariates

The motivation for this is to obtain confidence intervals for
covariate dependent parameters that are valid for a median/mean
value of the covariate.

Implementation by adding an argument to the 'saem' function, and
adapting the relevant functions working with 'saem' objects.

Vignettes, the template and tests were updated to use the new functionality.

3 files changed, 20 insertions, 20 deletions

diff --git a/log/build.log b/log/build.log
index b2206986..37262b29 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_1.2.10.tar.gz’
+* building ‘mkin_1.2.11.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index d036724d..94fd8095 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,15 +1,15 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.5.0 (2025-04-11)
+* using R version 4.5.1 (2025-06-13)
 * using platform: x86_64-pc-linux-gnu
 * R was compiled by
-    gcc (Debian 12.2.0-14) 12.2.0
-    GNU Fortran (Debian 12.2.0-14) 12.2.0
-* running under: Debian GNU/Linux 12 (bookworm)
+    gcc (Debian 12.2.0-14+deb12u1) 12.2.0
+    GNU Fortran (Debian 12.2.0-14+deb12u1) 12.2.0
+* running under: Debian GNU/Linux 13 (trixie)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.10’
+* this is package ‘mkin’ version ‘1.2.11’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... OK
 * checking package namespace information ... OK
@@ -60,12 +60,12 @@
 * 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 ... [13s/13s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
-* checking re-building of vignette outputs ... [13s/11s] OK
+* checking re-building of vignette outputs ... [15s/11s] 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 7bf36295..1b7f5c00 100644
--- a/log/test.log
+++ b/log/test.log
@@ -4,29 +4,29 @@
 ✔ |          5 | Analytical solutions for coupled models [1.6s]
 ✔ |          5 | Calculation of Akaike weights
 ✔ |          3 | Export dataset for reading into CAKE
-✔ |          6 | Use of precompiled symbols in mkinpredict [3.4s]
+✔ |          6 | Use of precompiled symbols in mkinpredict [3.6s]
 ✔ |         12 | Confidence intervals and p-values
 ✔ |          1 | Solutions with deSolve
-✔ |      1  12 | Dimethenamid data from 2018 [13.1s]
-✔ |         14 | Error model fitting [2.6s]
+✔ |      1  12 | Dimethenamid data from 2018 [14.1s]
+✔ |         14 | Error model fitting [2.8s]
 ✔ |          5 | Time step normalisation
 ✔ |          4 | Calculation of FOCUS chi2 error levels
 ✔ |         14 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
 ✔ |          4 | Test fitting the decline of metabolites from their maximum
 ✔ |          1 | Fitting the logistic model
-✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [19.9s]
-✔ |      2  16 | Nonlinear mixed-effects models [145.2s]
+✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [20.5s]
+✔ |      2  20 | Nonlinear mixed-effects models [144.7s]
 ✔ |          3 | Test dataset classes mkinds and mkindsg
 ✔ |         10 | Special cases of mkinfit calls
 ✔ |          3 | mkinfit features
 ✔ |          8 | mkinmod model generation and printing
 ✔ |          4 | Model predictions with mkinpredict
-✔ |         12 | Multistart method for saem.mmkin models [23.4s]
+✔ |         12 | Multistart method for saem.mmkin models [23.7s]
 ✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |          9 | Nonlinear mixed-effects models with nlme [4.0s]
-✔ |         15 | Plotting [4.7s]
+✔ |          9 | Nonlinear mixed-effects models with nlme [4.3s]
+✔ |         15 | Plotting [4.8s]
 ✔ |          4 | Residuals extracted from mkinfit models
-✔ |      1  38 | saemix parent models [36.0s]
+✔ |      1  38 | saemix parent models [35.6s]
 ✔ |          2 | Complex test case from Schaefer et al. (2007) Piacenza paper
 ✔ |         11 | Processing of residue series
 ✔ |         10 | Fitting the SFORB model [1.7s]
@@ -38,15 +38,15 @@
 ✔ |          2 | water-sediment
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 265.4 s
+Duration: 267.4 s
 
 ── Skipped tests (4) ───────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 5 minutes on my new system
   (1): 'test_dmta.R:88:3'
 • Fitting with saemix takes around 10 minutes when using deSolve (1):
   'test_mixed.R:80:3'
-• This is seldom used, so save some time (1): 'test_mixed.R:135:3'
+• This is seldom used, so save some time (1): 'test_mixed.R:155:3'
 • This still takes almost 2.5 minutes although we do not solve ODEs (1):
   'test_saemix_parent.R:143:3'
 
-[ FAIL 0 | WARN 0 | SKIP 4 | PASS 287 ]
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 291 ]