Release date, update pkgdown development docs

7 files changed, 192 insertions, 61 deletions

diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 979cf2c6..917a6865 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 16 January 2018
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index 9feecfce..e4e457fc 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -136,7 +136,7 @@ to the US EPA SOP for the NAFTA guidance</h1>
 Ranke</h4>
             
             <h4 data-toc-skip class="date">26 February 2019 (rebuilt
-2023-04-16)</h4>
+2023-05-19)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
       <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 87bdd55f..b3c12f66 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -423,8 +423,24 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
 <td align="left">Ryzen 9 7950X</td>
 <td align="left">4.2.3</td>
 <td align="left">1.2.3</td>
-<td align="right">1.404</td>
-<td align="right">1.933</td>
+<td align="right">1.406</td>
+<td align="right">1.948</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">1.386</td>
+<td align="right">1.960</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">1.400</td>
+<td align="right">1.936</td>
 </tr>
 </tbody>
 </table>
@@ -649,9 +665,27 @@ for each test.</p>
 <td align="left">Ryzen 9 7950X</td>
 <td align="left">4.2.3</td>
 <td align="left">1.2.3</td>
-<td align="right">0.797</td>
-<td align="right">2.124</td>
-<td align="right">1.182</td>
+<td align="right">0.793</td>
+<td align="right">2.109</td>
+<td align="right">1.178</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">0.779</td>
+<td align="right">2.080</td>
+<td align="right">1.106</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">0.800</td>
+<td align="right">2.118</td>
+<td align="right">1.172</td>
 </tr>
 </tbody>
 </table>
@@ -958,11 +992,35 @@ dataset, i.e. one fit for each test.</p>
 <td align="left">4.2.3</td>
 <td align="left">1.2.3</td>
 <td align="right">0.432</td>
-<td align="right">0.551</td>
-<td align="right">0.616</td>
-<td align="right">1.039</td>
-<td align="right">0.734</td>
-<td align="right">0.981</td>
+<td align="right">0.549</td>
+<td align="right">0.609</td>
+<td align="right">1.052</td>
+<td align="right">0.743</td>
+<td align="right">0.989</td>
+</tr>
+<tr class="even">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.4</td>
+<td align="right">0.410</td>
+<td align="right">0.526</td>
+<td align="right">0.553</td>
+<td align="right">1.249</td>
+<td align="right">0.712</td>
+<td align="right">0.948</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">4.3.0</td>
+<td align="left">1.2.5</td>
+<td align="right">0.433</td>
+<td align="right">0.558</td>
+<td align="right">0.618</td>
+<td align="right">1.053</td>
+<td align="right">0.745</td>
+<td align="right">0.986</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index e7905860..a0b34dda 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@ definitions in mkin</h1>
                         <h4 data-toc-skip class="author">Johannes
 Ranke</h4>
             
-            <h4 data-toc-skip class="date">2023-04-16</h4>
+            <h4 data-toc-skip class="date">2023-05-19</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
       <div class="hidden name"><code>compiled_models.rmd</code></div>
@@ -214,10 +214,10 @@ solution is also implemented, which is included in the tests below.</p>
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span>
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 4            analytical            1    1.000   0.105</span></span>
-<span><span class="co">## 3     deSolve, compiled            1    1.276   0.134</span></span>
-<span><span class="co">## 2      Eigenvalue based            1    1.762   0.185</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1   21.914   2.301</span></span></code></pre>
+<span><span class="co">## 4            analytical            1    1.000   0.108</span></span>
+<span><span class="co">## 3     deSolve, compiled            1    1.259   0.136</span></span>
+<span><span class="co">## 2      Eigenvalue based            1    1.704   0.184</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   21.574   2.330</span></span></code></pre>
 <p>We see that using the compiled model is by more than a factor of 10
 faster than using deSolve without compiled code.</p>
 </div>
@@ -248,12 +248,12 @@ compiled code is available.</p>
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 2     deSolve, compiled            1    1.000   0.176</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1   23.938   4.213</span></span></code></pre>
+<span><span class="co">## 2     deSolve, compiled            1    1.000   0.178</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   23.708   4.220</span></span></code></pre>
 <p>Here we get a performance benefit of a factor of 24 using the version
 of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 1.2.3 on</p>
-<pre><code><span><span class="co">## R version 4.2.3 (2023-03-15)</span></span>
+<p>This vignette was built with mkin 1.2.5 on</p>
+<pre><code><span><span class="co">## R version 4.3.0 (2023-04-21)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
 <span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre>
 <pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre>
diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html
index eb4a11a5..60e65367 100644
--- a/docs/dev/articles/web_only/dimethenamid_2018.html
+++ b/docs/dev/articles/web_only/dimethenamid_2018.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -136,7 +136,7 @@ from 2018</h1>
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 1 July 2022,
-built on 16 Apr 2023</h4>
+built on 19 May 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small>
       <div class="hidden name"><code>dimethenamid_2018.rmd</code></div>
@@ -615,13 +615,13 @@ satisfactory precision.</p>
 </h2>
 <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code>R version 4.2.3 (2023-03-15)
+<pre><code>R version 4.3.0 (2023-04-21)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -631,27 +631,30 @@ locale:
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-162 mkin_1.2.3   knitr_1.42  
+[1] saemix_3.2   npde_3.3     nlme_3.1-162 mkin_1.2.5   knitr_1.42  
 
 loaded via a namespace (and not attached):
- [1] highr_0.10        pillar_1.9.0      bslib_0.4.2       compiler_4.2.3   
- [5] jquerylib_0.1.4   tools_4.2.3       mclust_6.0.0      digest_0.6.31    
- [9] tibble_3.2.1      jsonlite_1.8.4    evaluate_0.20     memoise_2.0.1    
-[13] lifecycle_1.0.3   gtable_0.3.3      lattice_0.21-8    pkgconfig_2.0.3  
-[17] rlang_1.1.0       DBI_1.1.3         cli_3.6.1         yaml_2.3.7       
-[21] parallel_4.2.3    pkgdown_2.0.7     xfun_0.38         fastmap_1.1.1    
-[25] gridExtra_2.3     dplyr_1.1.1       stringr_1.5.0     generics_0.1.3   
-[29] desc_1.4.2        fs_1.6.1          vctrs_0.6.1       sass_0.4.5       
-[33] systemfonts_1.0.4 tidyselect_1.2.0  rprojroot_2.0.3   lmtest_0.9-40    
-[37] grid_4.2.3        glue_1.6.2        R6_2.5.1          textshaping_0.3.6
-[41] fansi_1.0.4       rmarkdown_2.21    purrr_1.0.1       ggplot2_3.4.2    
-[45] magrittr_2.0.3    codetools_0.2-19  scales_1.2.1      htmltools_0.5.5  
-[49] colorspace_2.1-0  ragg_1.2.5        utf8_1.2.3        stringi_1.7.12   
-[53] munsell_0.5.0     cachem_1.0.7      zoo_1.8-12       </code></pre>
+ [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
+ [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
+ [9] grid_4.3.0        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.4   
+[13] DBI_1.1.3         mclust_6.0.0      gridExtra_2.3     purrr_1.0.1      
+[17] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
+[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
+[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.0       parallel_4.3.0   
+[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          ragg_1.2.5        pkgconfig_2.0.3  
+[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
+[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 highr_0.10       
+[49] xfun_0.39         tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0 
+[53] htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.0   </code></pre>
 </div>
 <div class="section level2">
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index 2de5059c..7855f177 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 20 April 2023
-(rebuilt 2023-04-20)</h4>
+(rebuilt 2023-05-19)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small>
       <div class="hidden name"><code>multistart.rmd</code></div>
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 66740a11..22acf655 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
       </span>
     </div>
 
@@ -135,7 +135,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 17 February 2023
-(rebuilt 2023-04-16)</h4>
+(rebuilt 2023-05-19)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -398,10 +398,30 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="left">Linux</td>
 <td align="left">1.2.3</td>
 <td align="left">3.2</td>
-<td align="right">1.389</td>
-<td align="right">2.300</td>
-<td align="right">1.880</td>
-<td align="right">2.355</td>
+<td align="right">1.419</td>
+<td align="right">2.374</td>
+<td align="right">1.926</td>
+<td align="right">2.398</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">0.972</td>
+<td align="right">2.550</td>
+<td align="right">1.987</td>
+<td align="right">2.055</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">0.994</td>
+<td align="right">2.546</td>
+<td align="right">1.999</td>
+<td align="right">2.070</td>
 </tr>
 </tbody>
 </table>
@@ -473,10 +493,30 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="left">Linux</td>
 <td align="left">1.2.3</td>
 <td align="left">3.2</td>
-<td align="right">2.300</td>
-<td align="right">3.075</td>
-<td align="right">3.206</td>
-<td align="right">3.471</td>
+<td align="right">2.348</td>
+<td align="right">3.134</td>
+<td align="right">3.253</td>
+<td align="right">3.530</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">2.127</td>
+<td align="right">3.587</td>
+<td align="right">3.433</td>
+<td align="right">3.595</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">2.152</td>
+<td align="right">3.316</td>
+<td align="right">3.309</td>
+<td align="right">3.337</td>
 </tr>
 </tbody>
 </table>
@@ -540,8 +580,24 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="left">Linux</td>
 <td align="left">1.2.3</td>
 <td align="left">3.2</td>
-<td align="right">12.951</td>
-<td align="right">294.082</td>
+<td align="right">12.841</td>
+<td align="right">292.688</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">12.160</td>
+<td align="right">265.934</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">11.249</td>
+<td align="right">290.918</td>
 </tr>
 </tbody>
 </table>
@@ -599,7 +655,21 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="left">Linux</td>
 <td align="left">1.2.3</td>
 <td align="left">3.2</td>
-<td align="right">477.297</td>
+<td align="right">483.027</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">456.252</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.5</td>
+<td align="left">3.2</td>
+<td align="right">479.637</td>
 </tr>
 </tbody>
 </table>