Update vignette and static docs

5 files changed, 44 insertions, 19 deletions

diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index f9b27a0c..8d26e55a 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -109,7 +109,7 @@
       <h1 data-toc-skip>Short demo of the multistart method</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 19 September 2022 (rebuilt 2022-09-19)</h4>
+            <h4 data-toc-skip class="date">Last change 19 September 2022 (rebuilt 2022-09-28)</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/pkgdown.yml b/docs/dev/pkgdown.yml
index 144a7f80..ee93ec22 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
-last_built: 2022-09-19T10:47Z
+last_built: 2022-09-28T14:45Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index b7a5de92..cbd44762 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -237,7 +237,7 @@ degradation models and one or more error models</p></td>
         </td>
         <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
       </tr><tr><td>
-          <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> <code><a href="multistart.html">parms(<i>&lt;multistart&gt;</i>)</a></code> </p>
+          <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> </p>
         </td>
         <td><p>Perform a hierarchical model fit with multiple starting values</p></td>
       </tr><tr><td>
diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
index c85e6d1e..714cb2fc 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -100,16 +100,19 @@ mixed-effects models by Duchesne et al (2021).</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">50</span>,</span>
+<span>  cores <span class="op">=</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="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</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>  cluster <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for saem.mmkin</span></span>
-<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, cluster <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for multistart</span></span>
-<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="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># S3 method for multistart</span></span>
-<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<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="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -124,7 +127,12 @@ used?</p></dd>
 
 
 <dt>cores</dt>
-<dd><p>How many fits should be run in parallel?</p></dd>
+<dd><p>How many fits should be run in parallel (only on posix platforms)?</p></dd>
+
+
+<dt>cluster</dt>
+<dd><p>A cluster as returned by <a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">parallel::makeCluster</a> to be used
+for parallel execution.</p></dd>
 
 
 <dt>...</dt>
@@ -144,9 +152,7 @@ used?</p></dd>
     </div>
     <div id="details">
     <h2>Details</h2>
-    <p>Currently, parallel execution of the fits is only supported using
-<a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply</a>, i.e. not available on Windows.</p>
-<p>In case the online version of this help page contains error messages
+    <p>In case the online version of this help page contains error messages
 in the example code and no plots, this is due to the multistart method
 not working when called by pkgdown. Please refer to the
 <a href="https://pkgdown.jrwb.de/mkin/dev/articles/web_only/multistart.html">online vignette</a>
@@ -186,10 +192,18 @@ doi: 10.1186/s12859-021-04373-4.</p>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in UseMethod("parms", object):</span> no applicable method for 'parms' applied to an object of class "try-error"</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>all scheduled cores encountered errors in user code</span>
+<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span>
+<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span>
+<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span>
+<span class="r-in"><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="r-in"><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="fl">12</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterExport</a></span><span class="op">(</span><span class="va">cl</span>, <span class="st">"f_mmkin"</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in get(name, envir = envir):</span> object 'f_mmkin' not found</span>
+<span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in checkForRemoteErrors(val):</span> 12 nodes produced errors; first error: object 'f_mmkin' not found</span>
 <span class="r-in"><span><span class="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in UseMethod("parms", object):</span> no applicable method for 'parms' applied to an object of class "try-error"</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in parhist(f_saem_reduced_multi, lpos = "bottomright"):</span> object 'f_saem_reduced_multi' not found</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>calling par(new=TRUE) with no plot</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html
index ded4567a..949bb2f9 100644
--- a/docs/dev/reference/parms.html
+++ b/docs/dev/reference/parms.html
@@ -46,12 +46,15 @@ without considering the error structure that was assumed for the fit."><meta nam
       <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
@@ -80,7 +83,7 @@ without considering the error structure that was assumed for the fit."><meta nam
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Extract model parameters</h1>
-    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.mkinfit.R" class="external-link"><code>R/parms.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.R" class="external-link"><code>R/parms.R</code></a></small>
     <div class="hidden name"><code>parms.Rd</code></div>
     </div>
 
@@ -97,7 +100,10 @@ without considering the error structure that was assumed for the fit.</p>
 <span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for mmkin</span></span>
-<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for multistart</span></span>
+<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, exclude_failed <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -119,6 +125,11 @@ during the optimisation?</p></dd>
 <dd><p>Should the error model parameters be returned
 in addition to the degradation parameters?</p></dd>
 
+
+<dt>exclude_failed</dt>
+<dd><p>For <a href="multistart.html">multistart</a> objects, should rows for failed fits
+be removed from the returned parameter matrix?</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>