Documentation improvements, rebuild static docs

1 files changed, 37 insertions, 36 deletions

diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index 60917ff4..02c44737 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -10,23 +10,27 @@
 
 
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+
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+<script src="../bootstrap-toc.js"></script>
 
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@@ -41,7 +45,6 @@ and returns an object of class nafta that has methods for printing
 and plotting.
 Print nafta objects. The results for the three models are printed in the
 order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -59,7 +62,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
 
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -73,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
       </span>
     </div>
 
@@ -117,7 +120,12 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
 </li>
       </ul>
       <ul class="nav navbar-nav navbar-right">
-        
+        <li>
+  <a href="http://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
       </ul>
       
     </div><!--/.nav-collapse -->
@@ -132,7 +140,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Evaluate parent kinetics using the NAFTA guidance</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small>
     <div class="hidden name"><code>nafta.Rd</code></div>
     </div>
 
@@ -186,20 +194,20 @@ dissipation times.</p></td>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>NAFTA (2011) Guidance for evaluating and calculating degradation
-  kinetics in environmental media. NAFTA Technical Working Group on
-  Pesticides
-  <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
-  accessed 2019-02-22</p>
+kinetics in environmental media. NAFTA Technical Working Group on
+Pesticides
+<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
+accessed 2019-02-22</p>
 <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
-  Calculate Representative Half-life Values and Characterizing Pesticide
-  Degradation
-  <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
+Calculate Representative Half-life Values and Characterizing Pesticide
+Degradation
+<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An list of class <code>nafta</code>. The list element named "mmkin" is the
-  <code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The
-  list element named "title" contains the title of the dataset used. The
-  list element "data" contains the dataset used in the fits.</p>
+<code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The
+list element named "title" contains the title of the dataset used. The
+list element "data" contains the dataset used in the fits.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
@@ -240,20 +248,13 @@ dissipation times.</p></td>
 #&gt; DFOP  429    2380      841
 #&gt; 
 #&gt; Representative half-life:
-#&gt; [1] 841.41</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'>
+#&gt; [1] 841.41</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'>
 </div></pre>
   </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      <li><a href="#source">Source</a></li>
-      <li><a href="#value">Value</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    <p>Johannes Ranke</p>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
@@ -264,7 +265,7 @@ dissipation times.</p></td>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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