Improve docs and update pkgdown

3 files changed, 46 insertions, 46 deletions

diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 610d1bdd..43ed0f69 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -106,7 +106,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-08-10)</h4>
+            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-09-16)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -134,15 +134,15 @@
 <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:18 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:18 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:35 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:35 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 133 model solutions performed in 0.031 s</span></span>
+<span><span class="co">## Fitted using 133 model solutions performed in 0.032 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -240,15 +240,15 @@
 <span><span class="co">## doubtful</span></span></code></pre>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:18 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:18 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 369 model solutions performed in 0.082 s</span></span>
+<span><span class="co">## Fitted using 369 model solutions performed in 0.081 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -352,15 +352,15 @@
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:19 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:19 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span>
+<span><span class="co">## Fitted using 239 model solutions performed in 0.049 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -433,8 +433,8 @@
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:19 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:19 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:37 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -539,8 +539,8 @@
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:20 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:20 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -652,8 +652,8 @@
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:21 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:21 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
@@ -717,8 +717,8 @@
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
 <span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Wed Aug 10 15:28:21 2022 </span></span>
-<span><span class="co">## Date of summary: Wed Aug 10 15:28:21 2022 </span></span>
+<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
+<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 3dbf2881..e5bc5a21 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -106,7 +106,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-08-10)</h4>
+            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-09-16)</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>
@@ -337,8 +337,8 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.2</td>
-<td align="right">1.940</td>
-<td align="right">3.619</td>
+<td align="right">1.957</td>
+<td align="right">3.633</td>
 </tr>
 </tbody>
 </table>
@@ -507,9 +507,9 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.2</td>
-<td align="right">1.490</td>
-<td align="right">6.035</td>
-<td align="right">2.799</td>
+<td align="right">1.503</td>
+<td align="right">6.147</td>
+<td align="right">2.803</td>
 </tr>
 </tbody>
 </table>
@@ -729,12 +729,12 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.2</td>
-<td align="right">0.857</td>
+<td align="right">0.861</td>
 <td align="right">1.295</td>
-<td align="right">1.483</td>
-<td align="right">2.989</td>
-<td align="right">1.919</td>
-<td align="right">2.766</td>
+<td align="right">1.507</td>
+<td align="right">3.102</td>
+<td align="right">1.961</td>
+<td align="right">2.852</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html
index 81b15cb9..60f1ab5a 100644
--- a/docs/dev/articles/web_only/dimethenamid_2018.html
+++ b/docs/dev/articles/web_only/dimethenamid_2018.html
@@ -106,7 +106,7 @@
       <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 1 July 2022, built on 10 Aug 2022</h4>
+            <h4 data-toc-skip class="date">Last change 1 July 2022, built on 16 Sep 2022</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>
@@ -457,24 +457,24 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.1   npde_3.2     nlme_3.1-158 mkin_1.1.2   knitr_1.39  
+[1] nlme_3.1-158 mkin_1.1.2   knitr_1.39  
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.33      zoo_1.8-10        tidyselect_1.1.2  xfun_0.31        
- [5] bslib_0.4.0       purrr_0.3.4       lattice_0.20-45   colorspace_2.0-3 
- [9] vctrs_0.4.1       generics_0.1.3    htmltools_0.5.3   yaml_2.3.5       
-[13] utf8_1.2.2        rlang_1.0.4       pkgdown_2.0.6     jquerylib_0.1.4  
-[17] pillar_1.8.0      glue_1.6.2        DBI_1.1.3         lifecycle_1.0.1  
-[21] stringr_1.4.0     munsell_0.5.0     gtable_0.3.0      ragg_1.2.2       
-[25] codetools_0.2-18  memoise_2.0.1     evaluate_0.15     fastmap_1.1.0    
-[29] lmtest_0.9-40     parallel_4.2.1    fansi_1.0.3       highr_0.9        
-[33] scales_1.2.0      cachem_1.0.6      desc_1.4.1        jsonlite_1.8.0   
-[37] systemfonts_1.0.4 fs_1.5.2          textshaping_0.3.6 gridExtra_2.3    
-[41] ggplot2_3.3.6     digest_0.6.29     stringi_1.7.8     dplyr_1.0.9      
-[45] grid_4.2.1        rprojroot_2.0.3   cli_3.3.0         tools_4.2.1      
-[49] magrittr_2.0.3    sass_0.4.2        tibble_3.1.8      pkgconfig_2.0.3  
-[53] assertthat_0.2.1  rmarkdown_2.14.3  R6_2.5.1          mclust_5.4.10    
-[57] compiler_4.2.1   </code></pre>
+ [1] deSolve_1.33       zoo_1.8-10         tidyselect_1.1.2   xfun_0.31         
+ [5] bslib_0.4.0        purrr_0.3.4        lattice_0.20-45    colorspace_2.0-3  
+ [9] vctrs_0.4.1        generics_0.1.3     htmltools_0.5.3    yaml_2.3.5        
+[13] utf8_1.2.2         rlang_1.0.4        pkgdown_2.0.6      saemix_3.1        
+[17] jquerylib_0.1.4    pillar_1.8.0       glue_1.6.2         DBI_1.1.3         
+[21] lifecycle_1.0.1    stringr_1.4.0      munsell_0.5.0      gtable_0.3.0      
+[25] ragg_1.2.2         memoise_2.0.1      evaluate_0.15      npde_3.2          
+[29] fastmap_1.1.0      lmtest_0.9-40      parallel_4.2.1     fansi_1.0.3       
+[33] highr_0.9          KernSmooth_2.23-20 scales_1.2.0       cachem_1.0.6      
+[37] desc_1.4.1         jsonlite_1.8.0     systemfonts_1.0.4  fs_1.5.2          
+[41] textshaping_0.3.6  gridExtra_2.3      ggplot2_3.3.6      digest_0.6.29     
+[45] stringi_1.7.8      dplyr_1.0.9        grid_4.2.1         rprojroot_2.0.3   
+[49] cli_3.3.0          tools_4.2.1        magrittr_2.0.3     sass_0.4.2        
+[53] tibble_3.1.8       pkgconfig_2.0.3    assertthat_0.2.1   rmarkdown_2.14.3  
+[57] mclust_5.4.10      R6_2.5.1           compiler_4.2.1    </code></pre>
 </div>
 <div class="section level2">
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>