Don't test parhist and llhist on travis, docs

1 files changed, 24 insertions, 7 deletions

diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
index 714cb2fc..83af8dbb 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -112,7 +112,17 @@ mixed-effects models by Duchesne et al (2021).</p>
 <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></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>
+<span></span>
+<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for default</span></span>
+<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for default</span></span>
+<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -149,6 +159,12 @@ for parallel execution.</p></dd>
 
 <p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes
 'multistart.saem.mmkin' and 'multistart'.</p>
+
+
+<p>The object with the highest likelihood</p>
+
+
+<p>The index of the object with the highest likelihood</p>
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -187,11 +203,14 @@ doi: 10.1186/s12859-021-04373-4.</p>
 <span class="r-in"><span><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">f_saem_full</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_full</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="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_full_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-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(log_k2)"</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</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>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</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>
@@ -200,10 +219,8 @@ doi: 10.1186/s12859-021-04373-4.</p>
 <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 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-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>