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diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 75b8fe9..2fc946e 100644
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@@ -1,64 +1,12 @@
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -69,35 +17,21 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">pfm</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span>
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+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Reference</a>
</li>
- </ul>
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-
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+ </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
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+ </header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plot time series of decline data</h1>
@@ -109,97 +43,101 @@
<p>Plot time series of decline data</p>
</div>
- <pre class="usage"><span class='co'># S3 method for one_box</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(
- <span class='no'>x</span>,
- <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</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='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</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>,
- <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>],
- <span class='no'>...</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>x</th>
- <td><p>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</p></td>
- </tr>
- <tr>
- <th>xlim</th>
- <td><p>Limits for the x axis</p></td>
- </tr>
- <tr>
- <th>ylim</th>
- <td><p>Limits for the y axis</p></td>
- </tr>
- <tr>
- <th>xlab</th>
- <td><p>Label for the x axis</p></td>
- </tr>
- <tr>
- <th>ylab</th>
- <td><p>Label for the y axis</p></td>
- </tr>
- <tr>
- <th>max_twa</th>
- <td><p>If a numeric value is given, the maximum time weighted
-average concentration(s) is/are shown in the graph.</p></td>
- </tr>
- <tr>
- <th>max_twa_var</th>
- <td><p>Variable for which the maximum time weighted average should
-be shown if max_twa is not NULL.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Further arguments passed to methods</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
- <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</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='no'>dfop_pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</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'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>))
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># Use a fitted mkinfit model</span>
-<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='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></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='plot.one_box-3.png' alt='' width='700' height='433' /></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="#see-also">See also</a></li>
- <li><a href="#examples">Examples</a></li>
- </ul>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span>
+<span> <span class="va">x</span>,</span>
+<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
+<span> ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
+<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
+<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span>
+<span> max_twa <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> max_twa_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>x</dt>
+<dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd>
+
+
+<dt>xlim</dt>
+<dd><p>Limits for the x axis</p></dd>
+
+
+<dt>ylim</dt>
+<dd><p>Limits for the y axis</p></dd>
+
+
+<dt>xlab</dt>
+<dd><p>Label for the x axis</p></dd>
+
+<dt>ylab</dt>
+<dd><p>Label for the y axis</p></dd>
+
+
+<dt>max_twa</dt>
+<dd><p>If a numeric value is given, the maximum time weighted
+average concentration(s) is/are shown in the graph.</p></dd>
+
+
+<dt>max_twa_var</dt>
+<dd><p>Variable for which the maximum time weighted average should
+be shown if max_twa is not NULL.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments passed to methods</p></dd>
+
+</dl></div>
+ <div id="see-also">
+ <h2>See also</h2>
+ <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op">&lt;-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pred</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span>
+<span class="r-in"><span><span class="va">m_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span><span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span><span class="va">pred_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op">&lt;-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span>
+</code></pre></div>
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