Update vignettes in dev docs

After the post-release fixes to the release version online docs

1 files changed, 45 insertions, 34 deletions

diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
index 0285a193..959f3429 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.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">1.2.4</span>
       </span>
     </div>
 
@@ -135,8 +135,8 @@ residue data on dimethenamid and dimethenamid-P</h1>
                         <h4 data-toc-skip class="author">Johannes
 Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change on 8 January
-2023, last compiled on 16 April 2023</h4>
+            <h4 data-toc-skip class="date">Last change on 20 April 2023,
+last compiled on 20 April 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small>
       <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div>
@@ -156,7 +156,7 @@ can be fitted with the mkin package.</p>
 173340 (Application of nonlinear hierarchical models to the kinetic
 evaluation of chemical degradation data) of the German Environment
 Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.3, which is currently under
+<p>The mkin package is used in version 1.2.4, which is currently under
 development. It contains the test data, and the functions used in 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
@@ -171,10 +171,17 @@ processing, the <code>parallel</code> package is used.</p>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span>
 <span><span class="va">n_cores</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span>
-<span>  <span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span>
-<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
-<span>  <span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># We need to start a new cluster after defining a compiled model that is</span></span>
+<span><span class="co"># saved as a DLL to the user directory, therefore we define a function</span></span>
+<span><span class="co"># This is used again after defining the pathway model</span></span>
+<span><span class="va">start_cluster</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span>
+<span>    <span class="va">ret</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span>
+<span>  <span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
+<span>    <span class="va">ret</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span>
+<span>  <span class="op">}</span></span>
+<span>  <span class="kw"><a href="https://rdrr.io/r/base/function.html" class="external-link">return</a></span><span class="op">(</span><span class="va">ret</span><span class="op">)</span></span>
 <span><span class="op">}</span></span></code></pre></div>
 </div>
 <div class="section level2">
@@ -1441,6 +1448,8 @@ of parent models tested here.</p>
 <span>  unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  quiet <span class="op">=</span> <span class="cn">TRUE</span></span>
 <span><span class="op">)</span></span>
+<span><span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu">start_cluster</span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span>
+<span></span>
 <span><span class="va">deg_mods_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
 <span>  sfo_path_1 <span class="op">=</span> <span class="va">m_sfo_path_1</span>,</span>
 <span>  fomc_path_1 <span class="op">=</span> <span class="va">m_fomc_path_1</span>,</span>
@@ -1883,6 +1892,8 @@ SFORB pathway fit with two-component error, reduced parameter model
 </div>
 <p>Plots of the remaining fits and listings for all successful fits are
 shown in the Appendix.</p>
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a>
@@ -1921,24 +1932,24 @@ Level with Nonlinear Mixed-Effects Models.”</span> <em>Environments</em>
 <div class="section level3">
 <h3 id="plots-of-hierarchical-fits-not-selected-for-refinement">Plots of hierarchical fits not selected for refinement<a class="anchor" aria-label="anchor" href="#plots-of-hierarchical-fits-not-selected-for-refinement"></a>
 </h3>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sfo_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
 <div class="figure" style="text-align: center">
-<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-5-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption">
+<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="SFO pathway fit with two-component error" width="700"><p class="caption">
 SFO pathway fit with two-component error
 </p>
 </div>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"fomc_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
 <div class="figure" style="text-align: center">
-<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption">
+<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="FOMC pathway fit with two-component error" width="700"><p class="caption">
 FOMC pathway fit with two-component error
 </p>
 </div>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">saem_1</span><span class="op">[[</span><span class="st">"sforb_path_1"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
 <div class="figure" style="text-align: center">
-<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption">
+<img src="2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png" alt="HS pathway fit with two-component error" width="700"><p class="caption">
 HS pathway fit with two-component error
 </p>
 </div>
@@ -1961,9 +1972,9 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path
 <div class="section level3">
 <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h3>
-<pre><code>R version 4.2.2 Patched (2022-11-10 r83330)
+<pre><code>R version 4.2.3 (2023-03-15)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux bookworm/sid
+Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
@@ -1982,31 +1993,31 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.41 mkin_1.2.2
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.4
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.34      zoo_1.8-11        tidyselect_1.2.0  xfun_0.35        
- [5] bslib_0.4.2       purrr_1.0.0       lattice_0.20-45   colorspace_2.0-3 
- [9] vctrs_0.5.1       generics_0.1.3    htmltools_0.5.4   yaml_2.3.6       
-[13] pkgbuild_1.4.0    utf8_1.2.2        rlang_1.0.6       pkgdown_2.0.7    
-[17] jquerylib_0.1.4   pillar_1.8.1      glue_1.6.2        DBI_1.1.3        
-[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.1     
-[25] ragg_1.2.4        codetools_0.2-18  memoise_2.0.1     evaluate_0.19    
-[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.0     ps_1.7.2         
-[33] lmtest_0.9-40     fansi_1.0.3       highr_0.9         scales_1.2.1     
-[37] cachem_1.0.6      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
-[41] fs_1.5.2          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.0    
-[45] digest_0.6.31     stringi_1.7.8     processx_3.8.0    dplyr_1.0.10     
-[49] grid_4.2.2        rprojroot_2.0.3   cli_3.5.0         tools_4.2.2      
-[53] magrittr_2.0.3    sass_0.4.4        tibble_3.1.8      crayon_1.5.2     
-[57] pkgconfig_2.0.3   prettyunits_1.1.1 assertthat_0.2.1  rmarkdown_2.19   
-[61] R6_2.5.1          mclust_6.0.0      nlme_3.1-161      compiler_4.2.2   </code></pre>
+ [1] deSolve_1.35      zoo_1.8-12        tidyselect_1.2.0  xfun_0.38        
+ [5] bslib_0.4.2       purrr_1.0.1       lattice_0.21-8    colorspace_2.1-0 
+ [9] vctrs_0.6.1       generics_0.1.3    htmltools_0.5.5   yaml_2.3.7       
+[13] utf8_1.2.3        rlang_1.1.0       pkgbuild_1.4.0    pkgdown_2.0.7    
+[17] jquerylib_0.1.4   pillar_1.9.0      glue_1.6.2        DBI_1.1.3        
+[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.3     
+[25] ragg_1.2.5        codetools_0.2-19  memoise_2.0.1     evaluate_0.20    
+[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.1     ps_1.7.4         
+[33] lmtest_0.9-40     fansi_1.0.4       highr_0.10        scales_1.2.1     
+[37] cachem_1.0.7      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
+[41] fs_1.6.1          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.2    
+[45] digest_0.6.31     stringi_1.7.12    processx_3.8.0    dplyr_1.1.1      
+[49] grid_4.2.3        rprojroot_2.0.3   cli_3.6.1         tools_4.2.3      
+[53] magrittr_2.0.3    sass_0.4.5        tibble_3.2.1      crayon_1.5.2     
+[57] pkgconfig_2.0.3   prettyunits_1.1.1 rmarkdown_2.21    R6_2.5.1         
+[61] mclust_6.0.0      nlme_3.1-162      compiler_4.2.3   </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: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
-<pre><code>MemTotal:       64940452 kB</code></pre>
+<pre><code>MemTotal:       64936316 kB</code></pre>
 </div>
 </div>
   </div>