Static documentation rebuilt by pkgdown

author: Johannes Ranke <jranke@uni-bremen.de> 2020-05-07 08:59:29 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-05-07 08:59:29 +0200
commit: 8bdb4cd437a9d4663e542f95869e8692aa38dadb (patch)
tree: 2844662f8b143547d9abc8f16264407582367ad9 /docs/reference
parent: 1195dfc8bdbf7c131d6c6ec30fedbbe746af1bee (diff)
14 files changed, 582 insertions, 581 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index eef4f902..46e0cc91 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.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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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
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+<script src="../bootstrap-toc.js"></script>
 
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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@@ -38,7 +42,6 @@
 <meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" />
 <meta property="og:description" content="Function describing decline from a defined starting value using the sum of
 two exponential decline functions." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ two exponential decline functions." />
 
   </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">
@@ -70,7 +73,7 @@ two exponential decline functions." />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -114,7 +117,12 @@ two exponential decline functions." />
 </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 -->
@@ -129,7 +137,7 @@ two exponential decline functions." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Double First-Order in Parallel kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>DFOP.solution.Rd</code></div>
     </div>
 
@@ -138,7 +146,7 @@ two exponential decline functions." />
 two exponential decline functions.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre>
+    <pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,7 +156,7 @@ two exponential decline functions.</p>
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
@@ -175,22 +183,31 @@ kinetic constant.</p></td>
   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
   EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-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="#value">Value</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -201,7 +218,7 @@ kinetic constant.</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index f44ad713..8e2b154e 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -38,7 +42,6 @@
 <meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value, with
 a decreasing rate constant." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ a decreasing rate constant." />
 
   </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">
@@ -70,7 +73,7 @@ a decreasing rate constant." />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -114,7 +117,12 @@ a decreasing rate constant." />
 </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 -->
@@ -129,7 +137,7 @@ a decreasing rate constant." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>First-Order Multi-Compartment kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>FOMC.solution.Rd</code></div>
     </div>
 
@@ -138,7 +146,7 @@ a decreasing rate constant." />
 a decreasing rate constant.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre>
+    <pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,7 +156,7 @@ a decreasing rate constant.</p>
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
@@ -185,23 +193,25 @@ in the original equation.</p>
 <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil:
   A new model based on spatial variability. <em>Environmental Science and
   Technology</em> <b>24</b>, 1032-1038</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-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="#value">Value</a></li>
-      <li><a href="#details">Details</a></li>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -212,7 +222,7 @@ in the original equation.</p>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 82b9324c..ad33d948 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.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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+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
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@@ -38,7 +42,6 @@
 <meta property="og:title" content="Hockey-Stick kinetics — HS.solution" />
 <meta property="og:description" content="Function describing two exponential decline functions with a break point
 between them." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ between them." />
 
   </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">
@@ -70,7 +73,7 @@ between them." />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -114,7 +117,12 @@ between them." />
 </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 -->
@@ -129,7 +137,7 @@ between them." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Hockey-Stick kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>HS.solution.Rd</code></div>
     </div>
 
@@ -138,28 +146,12 @@ between them." />
 between them.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre>
+    <pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre>
 
     <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>
-      <th>t</th>
-      <td><p>Time.</p></td>
-    </tr>
-    <tr>
-      <th>parent.0</th>
-      <td><p>Starting value for the response variable at time zero.</p></td>
-    </tr>
-    <tr>
-      <th>k1</th>
-      <td><p>First kinetic constant.</p></td>
-    </tr>
-    <tr>
-      <th>k2</th>
-      <td><p>Second kinetic constant.</p></td>
-    </tr>
-    <tr>
       <th>tb</th>
       <td><p>Break point. Before this time, exponential decline according to
 <code>k1</code> is calculated, after this time, exponential decline proceeds
@@ -167,31 +159,25 @@ according to <code>k2</code>.</p></td>
     </tr>
     </table>
 
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The value of the response variable at time <code>t</code>.</p>
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
-  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-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="#value">Value</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -202,7 +188,7 @@ according to <code>k2</code>.</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 6af44ab8..677d4b43 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -38,7 +42,6 @@
 <meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value, with
 a concentration dependent rate constant." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ a concentration dependent rate constant." />
 
   </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">
@@ -70,7 +73,7 @@ a concentration dependent rate constant." />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -114,7 +117,12 @@ a concentration dependent rate constant." />
 </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 -->
@@ -129,7 +137,7 @@ a concentration dependent rate constant." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Indeterminate order rate equation kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>IORE.solution.Rd</code></div>
     </div>
 
@@ -138,7 +146,7 @@ a concentration dependent rate constant." />
 a concentration dependent rate constant.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre>
+    <pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,7 +156,7 @@ a concentration dependent rate constant.</p>
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
@@ -175,37 +183,31 @@ units used.</p></td>
 
     <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance
   for Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='co'># \dontrun{</span>
-    <span class='no'>fit.fomc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-    <span class='no'>fit.iore</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-    <span class='no'>fit.iore.deS</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='co'># \dontrun{</span>
+    <span class='no'>fit.fomc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.002 0 0.002</span></div><div class='input'>    <span class='no'>fit.iore</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k__iore, N) {    parent = (parent_0^(1 - N) - (1 - N) * k__iore * t)^(1/(1 -         N))})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     k__iore = 0.1, N = 1.1): unbenutztes Argument (parent.0 = 85.1)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'>    <span class='no'>fit.iore.deS</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 
     <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='no'>fit.fomc</span>$<span class='no'>par</span>, <span class='no'>fit.iore</span>$<span class='no'>par</span>, <span class='no'>fit.iore.deS</span>$<span class='no'>par</span>,
-                     <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>4</span>)))</div><div class='output co'>#&gt;             fit.fomc.par fit.iore.par fit.iore.deS.par
-#&gt; model par 1  85.87489063    85.874890        85.874890
-#&gt; model par 2   0.05192238    -4.826631        -4.826631
-#&gt; model par 3   0.65096665     1.949403         1.949403
-#&gt; model par 4   1.85744396     1.857444         1.857444</div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>,
-                <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#&gt;              DT50    DT90 DT50back
-#&gt; fomc     1.785233 15.1479 4.559973
-#&gt; iore     1.785233 15.1479 4.559973
-#&gt; iore.deS 1.785233 15.1479 4.559973</div><div class='input'>  # }
+                     <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>4</span>)))</div><div class='output co'>#&gt; <span class='error'>Error in data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, row.names = paste("model par",     1:4)): Objekt 'fit.fomc' nicht gefunden</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>,
+                <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#&gt; <span class='error'>Error in endpoints(fit.fomc): Objekt 'fit.fomc' nicht gefunden</span></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="#value">Value</a></li>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -216,7 +218,7 @@ units used.</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 55fd61a4..93da04eb 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -37,7 +41,6 @@
 
 <meta property="og:title" content="Single First-Order kinetics — SFO.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -55,7 +58,7 @@
 
   </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">
@@ -69,7 +72,7 @@
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -113,7 +116,12 @@
 </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 -->
@@ -128,7 +136,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Single First-Order kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>SFO.solution.Rd</code></div>
     </div>
 
@@ -136,7 +144,7 @@
     <p>Function describing exponential decline from a defined starting value.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre>
+    <pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -146,12 +154,12 @@
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
       <th>k</th>
-      <td><p>Kinetic constant.</p></td>
+      <td><p>Kinetic rate constant.</p></td>
     </tr>
     </table>
 
@@ -164,22 +172,31 @@
   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
   EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-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="#value">Value</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -190,7 +207,7 @@
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index fbf067af..c9f1b471 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -41,7 +45,6 @@ the kinetic model with first-order terms for a two-way transfer from a free
 to a bound fraction, and a first-order degradation term for the free
 fraction.  The initial condition is a defined amount in the free fraction
 and no substance in the bound fraction." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -59,7 +62,7 @@ and no substance in the bound fraction." />
 
   </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 @@ and no substance in the bound fraction." />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -117,7 +120,12 @@ and no substance in the bound fraction." />
 </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 @@ and no substance in the bound fraction." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Single First-Order Reversible Binding kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>SFORB.solution.Rd</code></div>
     </div>
 
@@ -144,20 +152,12 @@ fraction.  The initial condition is a defined amount in the free fraction
 and no substance in the bound fraction.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre>
+    <pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre>
 
     <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>
-      <th>t</th>
-      <td><p>Time.</p></td>
-    </tr>
-    <tr>
-      <th>parent.0</th>
-      <td><p>Starting value for the response variable at time zero.</p></td>
-    </tr>
-    <tr>
       <th>k_12</th>
       <td><p>Kinetic constant describing transfer from free to bound.</p></td>
     </tr>
@@ -176,28 +176,25 @@ fraction.</p></td>
 
     <p>The value of the response variable, which is the sum of free and
   bound fractions at time <code>t</code>.</p>
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
-  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-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="#value">Value</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -208,7 +205,7 @@ fraction.</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e6a373d6..f77881fe 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -53,7 +57,7 @@
 
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-index">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -111,7 +115,12 @@
 </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 -->
@@ -143,6 +152,11 @@
           <p class="section-desc"><p>Essential functionality</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -176,6 +190,11 @@ more datasets</p></td>
           <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -251,6 +270,11 @@ with mkinfit</p></td>
           <p class="section-desc"><p>Functions working with aggregated results</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -278,6 +302,11 @@ of an mmkin object</p></td>
           <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -310,6 +339,11 @@ of an mmkin object</p></td>
           <p class="section-desc"></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -402,6 +436,11 @@ of an mmkin object</p></td>
           <p class="section-desc"></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -422,6 +461,11 @@ of an mmkin object</p></td>
           <p class="section-desc"></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -521,6 +565,11 @@ kinetic models fitted with mkinfit</p></td>
           <p class="section-desc"><p>Parent only model solutions</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -560,7 +609,7 @@ kinetic models fitted with mkinfit</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
+          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> <code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
         </td>
         <td><p>Logistic kinetics</p></td>
       </tr>
@@ -571,6 +620,11 @@ kinetic models fitted with mkinfit</p></td>
           <p class="section-desc"></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -585,6 +639,11 @@ kinetic models fitted with mkinfit</p></td>
           <p class="section-desc"><p>Functions that have been superseded</p></p>
         </th>
       </tr>
+      
+      
+    </tbody><tbody>
+      
+      
       <tr>
         
         <td>
@@ -596,20 +655,10 @@ kinetic models fitted with mkinfit</p></td>
     </table>
   </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="#section-main-functions">Main functions</a></li>
-      <li><a href="#section-show-results">Show results</a></li>
-      <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
-      <li><a href="#section-mixed-models">Mixed models</a></li>
-      <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
-      <li><a href="#section-nafta-guidance">NAFTA guidance</a></li>
-      <li><a href="#section-helper-functions-mainly-used-internally">Helper functions mainly used internally</a></li>
-      <li><a href="#section-analytical-solutions">Analytical solutions</a></li>
-      <li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li>
-      <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
-    </ul>
+  <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>
 
@@ -620,7 +669,7 @@ kinetic models fitted with mkinfit</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png
index b9fb891c..fd11d0c0 100644
--- a/docs/reference/logistic.solution-1.png
+++ b/docs/reference/logistic.solution-1.png
diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png
index 78a31f93..fd11d0c0 100644
--- a/docs/reference/logistic.solution-2.png
+++ b/docs/reference/logistic.solution-2.png
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index b2f24d45..3e87b90d 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
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@@ -37,8 +41,9 @@
 
 <meta property="og:title" content="Logistic kinetics — logistic.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth
+Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth" />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +61,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
 
   </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">
@@ -70,7 +75,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       </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">0.9.49.11</span>
       </span>
     </div>
 
@@ -114,7 +119,12 @@ an increasing rate constant, supposedly caused by microbial growth" />
 </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 -->
@@ -129,16 +139,20 @@ an increasing rate constant, supposedly caused by microbial growth" />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Logistic kinetics</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logistic.solution.R'><code>R/logistic.solution.R</code></a>, <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>logistic.solution.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth</p>
+<p>Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth</p>
     </div>
 
-    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
+    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)
+
+<span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,7 +162,7 @@ an increasing rate constant, supposedly caused by microbial growth</p>
       <td><p>Time.</p></td>
     </tr>
     <tr>
-      <th>parent.0</th>
+      <th>parent_0</th>
       <td><p>Starting value for the response variable at time zero.</p></td>
     </tr>
     <tr>
@@ -163,6 +177,10 @@ an increasing rate constant, supposedly caused by microbial growth</p>
       <th>r</th>
       <td><p>Growth rate of the increase in the rate constant.</p></td>
     </tr>
+    <tr>
+      <th>parent.0</th>
+      <td><p>Starting value for the response variable at time zero.</p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -172,6 +190,8 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 
     <p>The solution of the logistic model reduces to the
   <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
+<p>The solution of the logistic model reduces to the
+  <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
@@ -179,16 +199,25 @@ an increasing rate constant, supposedly caused by microbial growth</p>
   EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   Version 1.1, 18 December 2014
   <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <div class='dont-index'><p>Other parent solutions: 
+<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>,
+<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>,
+<code><a href='HS.solution.html'>HS.solution</a>()</code>,
+<code><a href='IORE.solution.html'>IORE.solution</a>()</code>,
+<code><a href='SFO.solution.html'>SFO.solution</a>()</code>,
+<code><a href='SFORB.solution.html'>SFORB.solution</a>()</code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
   <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
        <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
-       <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
        <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
          <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
                          <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
@@ -205,32 +234,38 @@ an increasing rate constant, supposedly caused by microbial growth</p>
     <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
     <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
 
-  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
-#&gt; kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
-#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
-#&gt; r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
-#&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
-#&gt;                Upper
-#&gt; parent_0 109.9341588
-#&gt; kmax       0.1041853
-#&gt; k0         0.4448750
-#&gt; r          1.1821121
-#&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.854  10.83349</div><div class='input'>
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></div><div class='input'>
+
+  <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
+       <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
+       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
+         <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
+                         <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
+         <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='co'># Fit with synthetic data</span>
+  <span class='no'>logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"logistic"</span>))
+
+  <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
+  <span class='no'>parms_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
+  <span class='no'>d_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>,
+    <span class='no'>parms_logistic</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+    <span class='no'>sampling_times</span>)
+  <span class='no'>d_2_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>,
+    <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
+    <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
+
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></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="#value">Value</a></li>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#references">References</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -241,7 +276,7 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 4f5d9f67..778c5132 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.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>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -40,7 +44,6 @@
 mkinfit does not take mkinds datasets as argument, but works with dataframes
 such as the on contained in the data field of mkinds objects. Some datasets
 provided by this package come as mkinds objects nevertheless." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -58,7 +61,7 @@ provided by this package come as mkinds objects nevertheless." />
 
   </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">
@@ -116,7 +119,12 @@ provided by this package come as mkinds objects nevertheless." />
 </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 -->
@@ -131,7 +139,7 @@ provided by this package come as mkinds objects nevertheless." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>A dataset class for mkin</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small>
     <div class="hidden name"><code>mkinds.Rd</code></div>
     </div>
 
@@ -149,7 +157,7 @@ provided by this package come as mkinds objects nevertheless.</p>
     <div class='dont-index'><p>The S3 printing method <code><a href='print.mkinds.html'>print.mkinds</a></code></p></div>
     <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    <p><div class="r6-fields"></p><dl class='dl-horizontal'>
+    <p><div class="r6-fields"></p><dl'>
 <dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd>
 
 <dt><code>sampling_times</code></dt><dd><p>The sampling times</p></dd>
@@ -178,10 +186,10 @@ and value in order to be compatible with mkinfit</p></dd>
 <p><hr>
 <a id="method-new"></a></p><h3>Method <code>new()</code></h3>
 <p>Create a new mkinds object</p><h3>Usage</h3>
-<p><div class="r"></p><pre>mkinds$new(title = "", data, time_unit = NA, unit = NA)</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='no'>data</span>, <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>unit</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre><p></div></p>
 
 <h3>Arguments</h3>
-<p><div class="arguments"></p><dl class='dl-horizontal'>
+<p><div class="arguments"></p><dl'>
 <dt><code>title</code></dt><dd><p>The dataset title</p></dd>
 
 <dt><code>data</code></dt><dd><p>The data</p></dd>
@@ -194,10 +202,10 @@ and value in order to be compatible with mkinfit</p></dd>
 <p><hr>
 <a id="method-clone"></a></p><h3>Method <code>clone()</code></h3>
 <p>The objects of this class are cloneable with this method.</p><h3>Usage</h3>
-<p><div class="r"></p><pre>mkinds$clone(deep = FALSE)</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>mkinds</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
 <h3>Arguments</h3>
-<p><div class="arguments"></p><dl class='dl-horizontal'>
+<p><div class="arguments"></p><dl'>
 <dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
 
 </dl><p></div></p>
@@ -213,15 +221,10 @@ and value in order to be compatible with mkinfit</p></dd>
 #&gt; With a maximum of  1  replicates</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="#see-also">See also</a></li>
-      <li><a href="#public-fields">Public fields</a></li>
-      <li><a href="#methods">Methods</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <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>
 
@@ -232,7 +235,7 @@ and value in order to be compatible with mkinfit</p></dd>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 09837505..62823c58 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.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>
 <!-- Bootstrap -->
 
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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@@ -43,7 +47,6 @@ kinetic model is solved using the function mkinpredict. The
 parameters of the selected error model are fitted simultaneously with the
 degradation model parameters, as both of them are arguments of the
 likelihood function." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -61,7 +64,7 @@ likelihood function." />
 
   </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">
@@ -119,7 +122,12 @@ likelihood function." />
 </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 -->
@@ -134,7 +142,7 @@ likelihood function." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Fit a kinetic model to data with one or more state variables</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinfit.R'><code>R/mkinfit.R</code></a></small>
     <div class="hidden name"><code>mkinfit.Rd</code></div>
     </div>
 
@@ -168,8 +176,8 @@ likelihood function.</p>
   <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
   <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
   <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>),
-  <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>,
-    <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>),
+  <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>,
+    <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>),
   <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
   <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>,
   <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
@@ -414,82 +422,7 @@ estimators.</p>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
 <span class='co'># Use shorthand notation for parent only degradation</span>
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.11 
-#&gt; R version used for fitting:       3.6.3 
-#&gt; Date of fit:     Mon Apr 20 18:52:22 2020 
-#&gt; Date of summary: Mon Apr 20 18:52:22 2020 
-#&gt; 
-#&gt; Equations:
-#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-#&gt; 
-#&gt; Model predictions using solution type analytical 
-#&gt; 
-#&gt; Fitted using 222 model solutions performed in 0.473 s
-#&gt; 
-#&gt; Error model: Constant variance 
-#&gt; 
-#&gt; Error model algorithm: OLS 
-#&gt; 
-#&gt; Starting values for parameters to be optimised:
-#&gt;          value   type
-#&gt; parent_0  85.1  state
-#&gt; alpha      1.0 deparm
-#&gt; beta      10.0 deparm
-#&gt; 
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt;               value lower upper
-#&gt; parent_0  85.100000  -Inf   Inf
-#&gt; log_alpha  0.000000  -Inf   Inf
-#&gt; log_beta   2.302585  -Inf   Inf
-#&gt; 
-#&gt; Fixed parameter values:
-#&gt; None
-#&gt; 
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt;           Estimate Std. Error    Lower   Upper
-#&gt; parent_0  85.87000     1.8070 81.23000 90.5200
-#&gt; log_alpha  0.05192     0.1353 -0.29580  0.3996
-#&gt; log_beta   0.65100     0.2287  0.06315  1.2390
-#&gt; sigma      1.85700     0.4378  0.73200  2.9830
-#&gt; 
-#&gt; Parameter correlation:
-#&gt;             parent_0  log_alpha   log_beta     sigma
-#&gt; parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
-#&gt; log_alpha -1.565e-01  1.000e+00  9.564e-01 1.007e-07
-#&gt; log_beta  -3.142e-01  9.564e-01  1.000e+00 8.568e-08
-#&gt; sigma      4.758e-08  1.007e-07  8.568e-08 1.000e+00
-#&gt; 
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt;          Estimate t value    Pr(&gt;t)   Lower  Upper
-#&gt; parent_0   85.870  47.530 3.893e-08 81.2300 90.520
-#&gt; alpha       1.053   7.393 3.562e-04  0.7439  1.491
-#&gt; beta        1.917   4.373 3.601e-03  1.0650  3.451
-#&gt; sigma       1.857   4.243 4.074e-03  0.7320  2.983
-#&gt; 
-#&gt; FOCUS Chi2 error levels in percent:
-#&gt;          err.min n.optim df
-#&gt; All data   6.657       3  6
-#&gt; parent     6.657       3  6
-#&gt; 
-#&gt; Estimated disappearance times:
-#&gt;         DT50  DT90 DT50back
-#&gt; parent 1.785 15.15     4.56
-#&gt; 
-#&gt; Data:
-#&gt;  time variable observed predicted residual
-#&gt;     0   parent     85.1    85.875  -0.7749
-#&gt;     1   parent     57.9    55.191   2.7091
-#&gt;     3   parent     29.9    31.845  -1.9452
-#&gt;     7   parent     14.6    17.012  -2.4124
-#&gt;    14   parent      9.7     9.241   0.4590
-#&gt;    28   parent      6.6     4.754   1.8460
-#&gt;    63   parent      4.0     2.102   1.8977
-#&gt;    91   parent      3.9     1.441   2.4590
-#&gt;   119   parent      0.6     1.092  -0.4919</div><div class='input'>
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'>
 <span class='co'># One parent compound, one metabolite, both single first order.</span>
 <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span>
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
@@ -497,7 +430,8 @@ estimators.</p>
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
                            <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       1.465       0.003       1.474 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.526       0.000       1.526 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink   k_parent_m1     k_m1_sink         sigma 
+#&gt;  99.598483069   0.047920122   0.050777612   0.005260651   3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -567,7 +501,8 @@ estimators.</p>
 #&gt; Sum of squared residuals at call 126: 371.2134
 #&gt; Sum of squared residuals at call 135: 371.2134
 #&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       1.052       0.000       1.068 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.084       0.000       1.085 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink   k_parent_m1     k_m1_sink         sigma 
+#&gt;  99.598483072   0.047920122   0.050777612   0.005260651   3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -583,25 +518,23 @@ estimators.</p>
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span>
-<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
+<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent = 100.75), alpha = 1,     beta = 10): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): Objekt 'fit.FOMC' nicht gefunden</span></div><div class='input'>
 <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
 <span class='no'>SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
                                  <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
-<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># }</span>
+<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k_12, k_21, k_1output) {    sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 *         k_21 - (k_12 + k_1output) * k_21)    b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp    b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp    parent = parent_0 * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 *         t) + ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent_free = 100.75), k_1output = 0.1,     k_12 = 0.1, k_21 = 0.02): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode,     quiet = TRUE): Objekt 'fit.SFORB' nicht gefunden</span></div><div class='input'><span class='co'># }</span>
 
 <span class='co'># \dontrun{</span>
 <span class='co'># Weighted fits, including IRLS</span>
 <span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
                       <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.11 
-#&gt; R version used for fitting:       3.6.3 
-#&gt; Date of fit:     Mon Apr 20 18:52:37 2020 
-#&gt; Date of summary: Mon Apr 20 18:52:37 2020 
+#&gt; R version used for fitting:       4.0.0 
+#&gt; Date of fit:     Thu May  7 08:59:03 2020 
+#&gt; Date of summary: Thu May  7 08:59:03 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -609,7 +542,7 @@ estimators.</p>
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 422 model solutions performed in 1.087 s
+#&gt; Fitted using 422 model solutions performed in 1.106 s
 #&gt; 
 #&gt; Error model: Constant variance 
 #&gt; 
@@ -716,9 +649,9 @@ estimators.</p>
 #&gt;   100       m1    33.13  31.98163  1.148e+00
 #&gt;   120       m1    25.15  28.78984 -3.640e+00
 #&gt;   120       m1    33.31  28.78984  4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.11 
-#&gt; R version used for fitting:       3.6.3 
-#&gt; Date of fit:     Mon Apr 20 18:52:40 2020 
-#&gt; Date of summary: Mon Apr 20 18:52:40 2020 
+#&gt; R version used for fitting:       4.0.0 
+#&gt; Date of fit:     Thu May  7 08:59:06 2020 
+#&gt; Date of summary: Thu May  7 08:59:06 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -726,7 +659,7 @@ estimators.</p>
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 979 model solutions performed in 2.518 s
+#&gt; Fitted using 979 model solutions performed in 2.604 s
 #&gt; 
 #&gt; Error model: Variance unique to each observed variable 
 #&gt; 
@@ -848,9 +781,9 @@ estimators.</p>
 #&gt;   100       m1    33.13  31.98773  1.142e+00
 #&gt;   120       m1    25.15  28.80429 -3.654e+00
 #&gt;   120       m1    33.31  28.80429  4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.11 
-#&gt; R version used for fitting:       3.6.3 
-#&gt; Date of fit:     Mon Apr 20 18:52:50 2020 
-#&gt; Date of summary: Mon Apr 20 18:52:50 2020 
+#&gt; R version used for fitting:       4.0.0 
+#&gt; Date of fit:     Thu May  7 08:59:16 2020 
+#&gt; Date of summary: Thu May  7 08:59:16 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -858,7 +791,7 @@ estimators.</p>
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 2552 model solutions performed in 10.186 s
+#&gt; Fitted using 2552 model solutions performed in 10.544 s
 #&gt; 
 #&gt; Error model: Two-component variance function 
 #&gt; 
@@ -977,20 +910,10 @@ estimators.</p>
 
 </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="#details">Details</a></li>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#see-also">See also</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>
 
@@ -1001,7 +924,7 @@ estimators.</p>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index b25f2da3..d1204e2e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -10,23 +10,27 @@
 
 
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+<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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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -40,7 +44,6 @@
 name to a list, specifying the kinetic model type and reaction or transfer
 to other observed compartments. Instead of specifying several expressions, a
 list of lists can be given in the speclist argument." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -58,7 +61,7 @@ list of lists can be given in the speclist argument." />
 
   </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">
@@ -72,7 +75,7 @@ list of lists can be given in the speclist argument." />
       </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">0.9.49.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
       </span>
     </div>
 
@@ -116,7 +119,12 @@ list of lists can be given in the speclist argument." />
 </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 -->
@@ -131,7 +139,7 @@ list of lists can be given in the speclist argument." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Function to set up a kinetic model with one or more state variables</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small>
     <div class="hidden name"><code>mkinmod.Rd</code></div>
     </div>
 
@@ -205,7 +213,7 @@ applicable to give detailed information about the C function being built.</p></t
   <dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
   <dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be
     represented by one.</p></dd>
-  <dt>ll</dt><dd><p>The likelihood function, taking the parameter vector as the first argument.</p></dd>
+  <dt>cf</dt><dd><p>If generated, the compiled function as returned by cfunction.</p></dd>
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -244,7 +252,7 @@ in the FOCUS and NAFTA guidance documents are used.</p>
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt;  /usr/lib/R/bin/R CMD SHLIB file414965c335f6.c 2&gt; file414965c335f6.c.err.txt 
+#&gt;  /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2&gt; file66a9718e919b.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
@@ -277,19 +285,10 @@ in the FOCUS and NAFTA guidance documents are used.</p>
                           <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='co'># }</span></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="#value">Value</a></li>
-      <li><a href="#details">Details</a></li>
-      <li><a href="#note">Note</a></li>
-      <li><a href="#references">References</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>
 
@@ -300,7 +299,7 @@ in the FOCUS and NAFTA guidance documents are used.</p>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index fe5bc975..689fb7c7 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.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>
 <!-- Bootstrap -->
 
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -39,7 +43,6 @@
 <meta property="og:description" content="This function produces a time series for all the observed variables in a
 kinetic model as specified by mkinmod, using a specific set of
 kinetic parameters and initial values for the state variables." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -57,7 +60,7 @@ kinetic parameters and initial values for the state variables." />
 
   </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">
@@ -71,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
       </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">0.9.49.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
       </span>
     </div>
 
@@ -115,7 +118,12 @@ kinetic parameters and initial values for the state variables." />
 </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 -->
@@ -130,7 +138,7 @@ kinetic parameters and initial values for the state variables." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Produce predictions from a kinetic model using specific parameters</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinpredict.R'><code>R/mkinpredict.R</code></a></small>
     <div class="hidden name"><code>mkinpredict.Rd</code></div>
     </div>
 
@@ -258,32 +266,11 @@ solver is used.</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-  <span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
-  <span class='co'># Compare solution types</span>
-  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt;    time  degradinol
-#&gt; 1     0 100.0000000
-#&gt; 2     1  74.0818221
-#&gt; 3     2  54.8811636
-#&gt; 4     3  40.6569660
-#&gt; 5     4  30.1194212
-#&gt; 6     5  22.3130160
-#&gt; 7     6  16.5298888
-#&gt; 8     7  12.2456428
-#&gt; 9     8   9.0717953
-#&gt; 10    9   6.7205513
-#&gt; 11   10   4.9787068
-#&gt; 12   11   3.6883167
-#&gt; 13   12   2.7323722
-#&gt; 14   13   2.0241911
-#&gt; 15   14   1.4995577
-#&gt; 16   15   1.1108997
-#&gt; 17   16   0.8229747
-#&gt; 18   17   0.6096747
-#&gt; 19   18   0.4516581
-#&gt; 20   19   0.3345965
-#&gt; 21   20   0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt;    time  degradinol
+<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
+<span class='co'># Compare solution types</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
 #&gt; 3     2  54.8811636
@@ -304,8 +291,8 @@ solver is used.</p></td>
 #&gt; 18   17   0.6096747
 #&gt; 19   18   0.4516581
 #&gt; 20   19   0.3345965
-#&gt; 21   20   0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt;    time  degradinol
+#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
 #&gt; 3     2  54.8811636
@@ -326,8 +313,8 @@ solver is used.</p></td>
 #&gt; 18   17   0.6096747
 #&gt; 19   18   0.4516581
 #&gt; 20   19   0.3345965
-#&gt; 21   20   0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt;    time  degradinol
+#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
 #&gt; 3     2  54.8811636
@@ -349,92 +336,68 @@ solver is used.</p></td>
 #&gt; 19   18   0.4516581
 #&gt; 20   19   0.3345965
 #&gt; 21   20   0.2478752</div><div class='input'>
-
-  <span class='co'># Compare integration methods to analytical solution</span>
-  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-        <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2480043</div><div class='input'> <span class='co'># rk4 is not as precise here</span>
-
-  <span class='co'># The number of output times used to make a lot of difference until the</span>
-  <span class='co'># default for atol was adjusted</span>
-  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
-        <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt;     time degradinol
-#&gt; 201   20  0.2478752</div><div class='input'>  <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
-        <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt;      time degradinol
+<span class='co'># Compare integration methods to analytical solution</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
+#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
+#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
+#&gt; 21   20  0.2480043</div><div class='input'><span class='co'># rk4 is not as precise here</span>
+
+<span class='co'># The number of output times used to make a lot of difference until the</span>
+<span class='co'># default for atol was adjusted</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+      <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt;     time degradinol
+#&gt; 201   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+      <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt;      time degradinol
 #&gt; 2001   20  0.2478752</div><div class='input'>
-  <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
-  <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
-                    <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
-    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
-                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
-                <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
-#&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.003       0.000       0.003 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
-    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
-                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
-                <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
-#&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.002       0.000       0.002 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
-    <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
-                <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
-                <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
-#&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.021       0.000       0.021 </div><div class='input'>
-  <span class='co'># \dontrun{</span>
-    <span class='co'># Predict from a fitted model</span>
-    <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
-#&gt; Sum of squared residuals at call 3: 552.5739
-#&gt; Sum of squared residuals at call 4: 552.5739
-#&gt; Sum of squared residuals at call 6: 279.9345
-#&gt; Sum of squared residuals at call 7: 279.9344
-#&gt; Sum of squared residuals at call 8: 279.9294
-#&gt; Sum of squared residuals at call 9: 279.9294
-#&gt; Sum of squared residuals at call 12: 200.3629
-#&gt; Sum of squared residuals at call 13: 200.3629
-#&gt; Sum of squared residuals at call 18: 197.904
-#&gt; Sum of squared residuals at call 22: 197.904
-#&gt; Sum of squared residuals at call 25: 196.6753
-#&gt; Sum of squared residuals at call 27: 196.6753
-#&gt; Sum of squared residuals at call 32: 196.5742
-#&gt; Sum of squared residuals at call 33: 196.5742
-#&gt; Sum of squared residuals at call 34: 196.5742
-#&gt; Sum of squared residuals at call 38: 196.5361
-#&gt; Sum of squared residuals at call 40: 196.5361
-#&gt; Sum of squared residuals at call 44: 196.5336
-#&gt; Sum of squared residuals at call 45: 196.5336
-#&gt; Sum of squared residuals at call 50: 196.5334
-#&gt; Sum of squared residuals at call 51: 196.5334
-#&gt; Sum of squared residuals at call 52: 196.5334
-#&gt; Sum of squared residuals at call 56: 196.5334
-#&gt; Sum of squared residuals at call 58: 196.5334
-#&gt; Sum of squared residuals at call 59: 196.5334
-#&gt; Sum of squared residuals at call 65: 196.5334
-#&gt; Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt;   time   parent       m1
+<span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
+<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+                  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+  <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
+    <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+      <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,],
+    <span class='kw'>deSolve_compiled</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+      <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+      <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,],
+    <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+     <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+     <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,],
+    <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>)
+}</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt;               test replications elapsed relative user.self sys.self user.child
+#&gt; 3          deSolve           10   0.229   28.625     0.229        0          0
+#&gt; 2 deSolve_compiled           10   0.008    1.000     0.008        0          0
+#&gt; 1            eigen           10   0.025    3.125     0.026        0          0
+#&gt;   sys.child
+#&gt; 3         0
+#&gt; 2         0
+#&gt; 1         0</div><div class='input'>
+<span class='co'># Since mkin 0.9.49.11 we also have analytical solutions for some models, including SFO-SFO</span>
+<span class='co'>#    deSolve = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),</span>
+<span class='co'>#     c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</span>
+<span class='co'>#     solution_type = "analytical", use_compiled = FALSE)[201,],</span>
+
+<span class='co'># \dontrun{</span>
+  <span class='co'># Predict from a fitted model</span>
+  <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt;   time   parent       m1
 #&gt; 1  0.0 82.49216 0.000000
 #&gt; 2  0.1 80.00563 1.179963
 #&gt; 3  0.2 77.59404 2.312596
 #&gt; 4  0.3 75.25515 3.399443
 #&gt; 5  0.4 72.98675 4.442000
-#&gt; 6  0.5 70.78673 5.441717</div><div class='input'>  # }
+#&gt; 6  0.5 70.78673 5.441717</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="#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>
 
@@ -445,7 +408,7 @@ solver is used.</p></td>
 </div>
 
 <div class="pkgdown">
-  <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>
 </div>
 
       </footer>
author	Johannes Ranke <jranke@uni-bremen.de>	2020-05-07 08:59:29 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-05-07 08:59:29 +0200
commit	8bdb4cd437a9d4663e542f95869e8692aa38dadb (patch)
tree	2844662f8b143547d9abc8f16264407582367ad9 /docs/reference
parent	1195dfc8bdbf7c131d6c6ec30fedbbe746af1bee (diff)