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diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
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+ <ul class="nav navbar-nav"><li>
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@@ -98,6 +41,9 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
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+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
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<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
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@@ -112,34 +58,27 @@
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<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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<h1>Subsetting method for mmkin objects</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small>
<div class="hidden name"><code>Extract.mmkin.Rd</code></div>
</div>
@@ -147,122 +86,116 @@
<p>Subsetting method for mmkin objects</p>
</div>
- <pre class="usage"># S3 method for mmkin
-[(x, i, j, ..., drop = FALSE)</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>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td>
- </tr>
- <tr>
- <th>i</th>
- <td><p>Row index selecting the fits for specific models</p></td>
- </tr>
- <tr>
- <th>j</th>
- <td><p>Column index selecting the fits to specific datasets</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Not used, only there to satisfy the generic method definition</p></td>
- </tr>
- <tr>
- <th>drop</th>
- <td><p>If FALSE, the method always returns an mmkin object, otherwise
-either a list of mkinfit objects or a single mkinfit object.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre><code># S3 method for mmkin
+[(x, i, j, ..., drop = FALSE)</code></pre></div>
+ </div>
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>x</dt>
+<dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd>
+<dt>i</dt>
+<dd><p>Row index selecting the fits for specific models</p></dd>
+<dt>j</dt>
+<dd><p>Column index selecting the fits to specific datasets</p></dd>
+<dt>...</dt>
+<dd><p>Not used, only there to satisfy the generic method definition</p></dd>
+<dt>drop</dt>
+<dd><p>If FALSE, the method always returns an mmkin object, otherwise
+either a list of mkinfit objects or a single mkinfit object.</p></dd>
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+ <p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p>
+ </div>
+ <div id="author">
+ <h2>Author</h2>
<p>Johannes Ranke</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
- <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
- <span class='va'>fits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>,
- cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
- <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>
-</div><div class='output co'>#&gt; &lt;mmkin&gt; object
-#&gt; Status of individual fits:
-#&gt;
-#&gt; dataset
-#&gt; model B C
-#&gt; FOMC OK OK
-#&gt;
-#&gt; OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span>
-</div><div class='output co'>#&gt; &lt;mmkin&gt; object
-#&gt; Status of individual fits:
-#&gt;
-#&gt; dataset
-#&gt; model B
-#&gt; SFO OK
-#&gt; FOMC OK
-#&gt;
-#&gt; OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span>
-</div><div class='output co'>#&gt; &lt;mmkin&gt; object
-#&gt; Status of individual fits:
-#&gt;
-#&gt; dataset
-#&gt; model B
-#&gt; SFO OK
-#&gt;
-#&gt; OK: No warnings</div><div class='input'>
- <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span>
- <span class='co'># This extracts an mkinfit object with lots of components</span>
- <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span>
- <span class='op'>)</span>
-</div><div class='output co'>#&gt; $par
-#&gt; parent_0 log_alpha log_beta sigma
-#&gt; 99.666192 2.549850 5.050586 1.890202
-#&gt;
-#&gt; $objective
-#&gt; [1] 28.58291
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 21
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 25 78
-#&gt;
-#&gt; $message
-#&gt; [1] "both X-convergence and relative convergence (5)"
-#&gt; </div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
+<span class="r-in"> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span>
+<span class="r-in"> <span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><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="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span>
+<span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model B C </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC OK OK</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-in"> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model B </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO OK</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC OK</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-in"> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model B </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO OK</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-in"></span>
+<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span>
+<span class="r-in"> <span class="co"># This extracts an mkinfit object with lots of components</span></span>
+<span class="r-in"> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span>
+<span class="r-in"> <span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $par</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 log_alpha log_beta sigma </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 99.666192 2.549850 5.050586 1.890202 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $objective</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 28.58291</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $convergence</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $evaluations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> function gradient </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 25 78 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $message</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "both X-convergence and relative convergence (5)"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+</code></pre></div>
+ </div>
</div>
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- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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