Update static docs and build logv1.2.6

9 files changed, 37 insertions, 30 deletions

diff --git a/docs/404.html b/docs/404.html
index adab3ba6..eadf13f5 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index c4b4e788..f6ad43c2 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
diff --git a/docs/articles/prebuilt/2023_mesotrione_parent.html b/docs/articles/prebuilt/2023_mesotrione_parent.html
index 2b81cec4..8f166a73 100644
--- a/docs/articles/prebuilt/2023_mesotrione_parent.html
+++ b/docs/articles/prebuilt/2023_mesotrione_parent.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
@@ -138,7 +138,7 @@ parent degradation kinetics with residue data on mesotrione</h1>
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change on 4 August 2023,
-last compiled on 10 August 2023</h4>
+last compiled on 13 Oktober 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2023_mesotrione_parent.rmd" class="external-link"><code>vignettes/prebuilt/2023_mesotrione_parent.rmd</code></a></small>
       <div class="hidden name"><code>2023_mesotrione_parent.rmd</code></div>
@@ -158,7 +158,7 @@ parameters. Because in some other case studies, the SFORB
 parameterisation of biexponential decline has shown some advantages over
 the DFOP parameterisation, SFORB was included in the list of tested
 models as well.</p>
-<p>The mkin package is used in version 1.2.5, which is contains the
+<p>The mkin package is used in version 1.2.6, which is contains the
 functions that were used for the evaluations. The <code>saemix</code>
 package is used as a backend for fitting the NLHM, but is also loaded to
 make the convergence plot function available.</p>
@@ -2504,28 +2504,30 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.43 mkin_1.2.5
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.6
 
 loaded via a namespace (and not attached):
  [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
- [5] lattice_0.20-45   digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
- [9] grid_4.3.1        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.5   
-[13] mclust_6.0.0      gridExtra_2.3     purrr_1.0.1       fansi_1.0.4      
-[17] scales_1.2.1      textshaping_0.3.6 jquerylib_0.1.4   cli_3.6.1        
-[21] rlang_1.1.1       munsell_0.5.0     cachem_1.0.8      yaml_2.3.7       
-[25] tools_4.3.1       memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0 
-[29] ggplot2_3.4.2     vctrs_0.6.2       R6_2.5.1          zoo_1.8-12       
-[33] lifecycle_1.0.3   stringr_1.5.0     fs_1.6.2          ragg_1.2.5       
-[37] pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2      
-[41] pillar_1.9.0      gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4
-[45] xfun_0.39         tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0 
-[49] htmltools_0.5.5   nlme_3.1-162      rmarkdown_2.22    compiler_4.3.1   </code></pre>
+ [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
+ [9] grid_4.3.1        fastmap_1.1.1     cellranger_1.1.0  rprojroot_2.0.3  
+[13] jsonlite_1.8.4    DBI_1.1.3         mclust_6.0.0      gridExtra_2.3    
+[17] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      codetools_0.2-19 
+[21] textshaping_0.3.6 jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1      
+[25] munsell_0.5.0     cachem_1.0.8      yaml_2.3.7        tools_4.3.1      
+[29] memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2    
+[33] vctrs_0.6.2       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3  
+[37] stringr_1.5.0     fs_1.6.2          MASS_7.3-60       ragg_1.2.5       
+[41] pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2      
+[45] pillar_1.9.0      gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4
+[49] highr_0.10        xfun_0.39         tibble_3.2.1      lmtest_0.9-40    
+[53] tidyselect_1.2.0  htmltools_0.5.5   nlme_3.1-162      rmarkdown_2.21   
+[57] compiler_4.3.1    readxl_1.4.2     </code></pre>
 </div>
 <div class="section level3">
 <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
 </h3>
-<pre><code>CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre>
-<pre><code>MemTotal:       12165632 kB</code></pre>
+<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
+<pre><code>MemTotal:       64928100 kB</code></pre>
 </div>
 </div>
   </div>
diff --git a/docs/authors.html b/docs/authors.html
index 3e717fb9..2e97a0dc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
@@ -135,13 +135,13 @@
 
     <p>Ranke J (2023).
 <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>.
-R package version 1.2.5, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
+R package version 1.2.6, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
 </p>
     <pre>@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2023},
-  note = {R package version 1.2.5},
+  note = {R package version 1.2.6},
   url = {https://pkgdown.jrwb.de/mkin/},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index e13f573e..79dadd3b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index ab791e4e..01185d99 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
@@ -108,13 +108,17 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.2.5" id="mkin-125">mkin 1.2.5<a class="anchor" aria-label="anchor" href="#mkin-125"></a></h2>
+<h2 class="page-header" data-toc-text="1.2.6" id="mkin-126">mkin 1.2.6<a class="anchor" aria-label="anchor" href="#mkin-126"></a></h2>
+<ul><li>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Fix an erroneous call to the ‘endpoints()’ function</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.2.5" id="mkin-125-2023-08-09">mkin 1.2.5 (2023-08-09)<a class="anchor" aria-label="anchor" href="#mkin-125-2023-08-09"></a></h2>
 <ul><li><p>‘vignettes/mesotrione_parent_2023.rnw’: Prebuilt vignette showing how covariate modelling can be done for all relevant parent degradation models.</p></li>
 <li><p>‘inst/testdata/mesotrione_soil_efsa_2016}.xlsx’: Another example spreadsheets for use with ‘read_spreadsheet()’, featuring pH dependent degradation</p></li>
 <li><p>R/illparms.R: Fix the detection of ill-defined slope or error model parameters for the case that the estimate is negative</p></li>
 </ul></div>
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124">mkin 1.2.4<a class="anchor" aria-label="anchor" href="#mkin-124"></a></h2>
+<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124-2023-05-19">mkin 1.2.4 (2023-05-19)<a class="anchor" aria-label="anchor" href="#mkin-124-2023-05-19"></a></h2>
 <ul><li>R/endpoints.R: Fix the calculation of endpoints for user specified covariate values</li>
 </ul></div>
     <div class="section level2">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f86c9fe4..e4473e98 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -17,7 +17,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2023-08-10T05:26Z
+last_built: 2023-10-13T14:33Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 0ba00cdc..a7f02199 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span>
       </span>
     </div>
 
diff --git a/log/build.log b/log/build.log
index 717128fd..6f7ac8ab 100644
--- a/log/build.log
+++ b/log/build.log
@@ -5,6 +5,7 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
+Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’
 Removed empty directory ‘mkin/vignettes/web_only’
-* building ‘mkin_1.2.5.tar.gz’
+* building ‘mkin_1.2.6.tar.gz’