Static documentation rebuilt by pkgdown

7 files changed, 222 insertions, 11 deletions

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 6bb05b3e..0cecdc30 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -33,6 +33,7 @@ reference:
       - "`[.mmkin`"
       - plot.mmkin
       - AIC.mmkin
+      - nlme_function
   - title: Datasets and known results
     contents:
       - FOCUS_2006_A
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 6daabd5e..0e58496e 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -90,7 +90,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-04-02</h4>
+            <h4 class="date">2020-04-04</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -139,9 +139,9 @@
 <a class="sourceLine" id="cb6-15" title="15">  <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a>
 <a class="sourceLine" id="cb6-16" title="16">}</a></code></pre></div>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.239    1.000     3.237        0
-## 1 deSolve, not compiled            3  29.758    9.187    29.739        0
-## 2      Eigenvalue based            3   4.558    1.407     4.554        0
+## 3     deSolve, compiled            3   3.107    1.000     3.105        0
+## 1 deSolve, not compiled            3  28.765    9.258    28.749        0
+## 2      Eigenvalue based            3   4.446    1.431     4.445        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -170,8 +170,8 @@
 <a class="sourceLine" id="cb8-16" title="16">}</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.984    1.000     4.981    0.000
-## 1 deSolve, not compiled            3  55.358   11.107    55.326    0.003
+## 2     deSolve, compiled            3   4.844    1.000     4.842        0
+## 1 deSolve, not compiled            3  53.833   11.113    53.807        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>
diff --git a/docs/news/index.html b/docs/news/index.html
index fc9a0765..cb5e6df3 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,6 +134,7 @@
 <a href="#mkin-0-9-49-10-unreleased" class="anchor"></a>mkin 0.9.49.10 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
+<li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li>
 <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li>
 <li><p>Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset</p></li>
 <li><p>‘plot.mmkin’: Add the argument ‘standardized’ to avoid warnings that occurred when it was passed as part of the additional arguments captured by the dots (…)</p></li>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6ccc9255..a3547e29 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -270,6 +270,12 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> <code><a href="nlme.html">nlme_function()</a></code> </p>
+        </td>
+        <td><p>Estimation of parameter distributions from mmkin row objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index e38c153c..b3be7c2c 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -70,7 +70,7 @@ mkinmod." />
       </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">0.9.49.9</span>
       </span>
     </div>
 
@@ -181,10 +181,11 @@ results on other operating systems or system configurations.</p></td>
 <span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'># Now supplying full names</span>
-<span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>),
-  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'># \dontrun{</span>
+  <span class='co'># Now supplying full names</span>
+  <span class='no'>SFO_SFO.2</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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>),
+    <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'> # }
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
new file mode 100644
index 00000000..b939d1c3
--- /dev/null
+++ b/docs/reference/nlme.html
@@ -0,0 +1,199 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimation of parameter distributions from mmkin row objects — mean_degparms • mkin</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></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" />
+
+<!-- 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>
+
+<!-- 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>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
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+
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+<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — mean_degparms" />
+<meta property="og:description" content="This function sets up and attempts to fit a mixed effects model to
+an mmkin row object. An mmkin row object is essentially a list of mkinfit
+objects that have been obtained by fitting the same model to a list of
+datasets." />
+<meta name="twitter:card" content="summary" />
+
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+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
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+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
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+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
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+        <span class="icon-bar"></span>
+      </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>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
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+  </a>
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+    <li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        
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+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Estimation of parameter distributions from mmkin row objects</h1>
+    
+    <div class="hidden name"><code>nlme.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>This function sets up and attempts to fit a mixed effects model to
+an mmkin row object. An mmkin row object is essentially a list of mkinfit
+objects that have been obtained by fitting the same model to a list of
+datasets.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>mean_degparms</span>(<span class='no'>object</span>)
+
+<span class='fu'>nlme_data</span>(<span class='no'>object</span>)
+
+<span class='fu'>nlme_function</span>(<span class='no'>object</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>object</th>
+      <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A named vector containing mean values of the fitted degradation model parameters</p>
+<p>A groupedData data object</p>
+<p>A function that can be used with nlme</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"></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>
+
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index a8d6dfa4..8ba032de 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -130,6 +130,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/nlme.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html</loc>
   </url>
   <url>