Rebuild docs with pkgdown 1.1.0

1 files changed, 31 insertions, 8 deletions

diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 1c2aabe..dc068c3 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -21,12 +21,15 @@
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+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
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 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" />
 
 <meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS
@@ -37,6 +40,9 @@ maintained on github is supported. In such installations, FOCUS PELMO is
 installed into the package installation directory of PELMO.installeR
 and run using wine." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -59,8 +65,12 @@ and run using wine." />
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">pfm</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">pfm</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -75,8 +85,14 @@ and run using wine." />
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
-        
+        <li>
+  <a href="https://github.com/jranke/pfm">
+    <span class="fa fa-github fa-lg"></span>
+     
+  </a>
+</li>
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -84,12 +100,15 @@ and run using wine." />
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Set up runs for FOCUS PELMO</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small>
+    <div class="hidden name"><code>PELMO_runs.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>Per default, the runs are not only set up but also executed with FOCUS
 PELMO, the results are processed and returned. Currently, only FOCUS PELMO
@@ -99,6 +118,7 @@ maintained on github is supported. In such installations, FOCUS PELMO is
 installed into the package installation directory of <code>PELMO.installeR</code>
 and run using <code>wine</code>.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
   <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@@ -109,7 +129,7 @@ and run using <code>wine</code>.</p>
 
 <span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre>
     
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
@@ -209,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
 #&gt; 
 #&gt; </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span>
 <span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;     220.760       1.509      30.234 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) {
+#&gt;       0.388       0.088      30.344 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) {
   <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]]))
 }</div><div class='output co'>#&gt; CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'>
 <span class='co'># Demonstrate some results with metabolites.</span>
@@ -255,5 +275,8 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
       </footer>
    </div>
 
+  
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 </html>
+