Update docs, use R6 support of roxygen

5 files changed, 120 insertions, 79 deletions

diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 9f9e3c3..16dc5db 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -40,8 +40,11 @@
 
 
 <meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
-<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
-Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
+<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data
+and some associated statistics.  like maximum moving window average
+concentrations, and dataframes holding the events exceeding specified
+thresholds.  Usually, an instance of this class will be generated
+by read.TOXSWA_cwa." />
 
 
 
@@ -110,8 +113,11 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
     </div>
 
     <div class="ref-description">
-    <p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
-Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
+    <p>An R6 class for holding TOXSWA water concentration (cwa) data
+and some associated statistics.  like maximum moving window average
+concentrations, and dataframes holding the events exceeding specified
+thresholds.  Usually, an instance of this class will be generated
+by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
     </div>
 
 
@@ -119,30 +125,19 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
     <p>An <code>R6Class</code> generator object.</p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
-
-    
-
-<dl'>
-  <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value
-        in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
-        adsorbed to suspended matter will be used. The resulting dataframe is stored in the
-        <code>events</code> field of the object.</p></dd>
-  <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above.
-        Again, if <code>total = TRUE</code>, the total concentration including the amount
-        adsorbed to suspended matter will be used.</p></dd>
-
-</dl>
-
     <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
     <p><div class="r6-fields"></p><dl'>
-<dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd>
+<dt><code>filename</code></dt><dd><p>Length one character vector holding the filename.</p></dd>
 
-<dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd>
+<dt><code>basedir</code></dt><dd><p>Length one character vector holding the directory where the file came from.</p></dd>
+
+<dt><code>zipfile</code></dt><dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd>
 
 <dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd>
 
+<dt><code>substance</code></dt><dd><p>The TOXSWA name of the substance.</p></dd>
+
 <dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd>
 
 <dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd>
@@ -166,8 +161,7 @@ for the requested moving window sizes in days.</p></dd>
 </ul>
 <p><hr>
 <a id="method-new"></a></p><h3>Method <code>new()</code></h3>
-
-<h3>Usage</h3>
+<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3>
 <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>(
   <span class='no'>filename</span>,
   <span class='no'>basedir</span>,
@@ -177,22 +171,52 @@ for the requested moving window sizes in days.</p></dd>
   <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
 )</pre><p></div></p>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl'>
+<dt><code>filename</code></dt><dd><p>The filename</p></dd>
+
+<dt><code>basedir</code></dt><dd><p>The directory to look in</p></dd>
+
+<dt><code>zipfile</code></dt><dd><p>Optional path to a zipfile holding the file</p></dd>
+
+<dt><code>segment</code></dt><dd><p>Either "last" or the number of the segment for which to read the data</p></dd>
+
+<dt><code>substance</code></dt><dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd>
+
+<dt><code>total</code></dt><dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd>
+
+</dl><p></div></p>
 <p><hr>
 <a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3>
-
-<h3>Usage</h3>
+<p>Add to the `windows` field described above.</p><h3>Usage</h3>
 <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl'>
+<dt><code>windows</code></dt><dd><p>Window sizes in days</p></dd>
+
+<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to
+suspended matter will be used.</p></dd>
+
+</dl><p></div></p>
 <p><hr>
 <a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3>
-
-<h3>Usage</h3>
+<p>Populate a datataframe with event information for the specified
+threshold value.  The resulting dataframe is stored in the `events`
+field of the object.</p><h3>Usage</h3>
 <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl'>
+<dt><code>thresholds</code></dt><dd><p>Threshold values in µg/L.</p></dd>
+
+<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to
+suspended matter will be used.</p></dd>
+
+</dl><p></div></p>
 <p><hr>
 <a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
-
-<h3>Usage</h3>
+<p>Print a `TOXSWA_cwa` object</p><h3>Usage</h3>
 <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p>
 
 <p><hr>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 944f1f2..186390e 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -393,6 +393,25 @@ water concentrations</p></td>
     </tbody><tbody>
       <tr>
         <th colspan="2">
+          <h2 id="section-work-with-chent-objects-containing-relevant-information" class="hasAnchor"><a href="#section-work-with-chent-objects-containing-relevant-information" class="anchor"></a>Work with chent objects containing relevant information</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      
+      
+    </tbody><tbody>
+      
+      
+      <tr>
+        
+        <td>
+          <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p>
+        </td>
+        <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
           <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2>
           <p class="section-desc"></p>
         </th>
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index d2e62f6..8d06107 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.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/2.0.6/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">
@@ -37,7 +41,6 @@
 
 <meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" />
 <meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" />
-<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">
@@ -112,7 +115,7 @@
     <pre class="usage"><span class='fu'>pfm_degradation</span>(
   <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>,
   <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
-  <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>),
+  <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>),
   <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>,
   <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>,
   <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>)
@@ -152,22 +155,17 @@ is calculated (SFO model).</p></td>
 
     <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/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt;   time    parent
-#&gt; 1    0 1.0000000
-#&gt; 2    1 0.9330330
-#&gt; 3    2 0.8705506
-#&gt; 4    3 0.8122524
-#&gt; 5    4 0.7578583
-#&gt; 6    5 0.7071068</div></pre>
+#&gt; 0    0 1.0000000
+#&gt; 1    1 0.9330330
+#&gt; 2    2 0.8705506
+#&gt; 3    3 0.8122524
+#&gt; 4    4 0.7578583
+#&gt; 5    5 0.7071068</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="#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>
 
@@ -178,7 +176,7 @@ is calculated (SFO model).</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/sawtooth-2.png b/docs/reference/sawtooth-2.png
index ad93165..87da954 100644
--- a/docs/reference/sawtooth-2.png
+++ b/docs/reference/sawtooth-2.png
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index 7720afc..fea24d4 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.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" />
 
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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/0.11.0/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">
@@ -36,9 +40,8 @@
 
 
 <meta property="og:title" content="Create decline time series for multiple applications — sawtooth" />
-<meta property="og:description" content="If the application pattern is specified in applications, 
+<meta property="og:description" content="If the application pattern is specified in applications,
 n and i are disregarded." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ n and i are disregarded." />
 
   </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">
@@ -107,7 +110,7 @@ n and i are disregarded." />
     </div>
 
     <div class="ref-description">
-    <p>If the application pattern is specified in <code>applications</code>, 
+    <p>If the application pattern is specified in <code>applications</code>,
 <code>n</code> and <code>i</code> are disregarded.</p>
     </div>
 
@@ -145,10 +148,10 @@ the corresponding amounts applied in the second column.</p></td>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>))
 <span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>)
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</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='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</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'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</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='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</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='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0165</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
 <span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.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='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'>
 <span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
 #&gt;    parent        m1 
 #&gt; 0.7834480 0.8617048 
@@ -162,13 +165,10 @@ the corresponding amounts applied in the second column.</p></td>
 #&gt;  21.00  47.85 
 #&gt; </div></pre>
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-      <li><a href="#arguments">Arguments</a></li>
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@@ -179,7 +179,7 @@ the corresponding amounts applied in the second column.</p></td>
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