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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
commitaf7c6de4db9981ac814362c441fbac22c8faa2d7 (patch)
tree33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/AIC.mmkin.html
parent8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)
Start online docs of the development version
Diffstat (limited to 'docs/dev/reference/AIC.mmkin.html')
-rw-r--r--docs/dev/reference/AIC.mmkin.html275
1 files changed, 114 insertions, 161 deletions
diff --git a/docs/dev/reference/AIC.mmkin.html b/docs/dev/reference/AIC.mmkin.html
index 8c791755..13f870e7 100644
--- a/docs/dev/reference/AIC.mmkin.html
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Calculate the AIC for a column of an mmkin object — AIC.mmkin • mkin</title><!-- jquery --><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/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><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/5.12.1/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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"><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the AIC for a column of an mmkin object — AIC.mmkin"><meta property="og:description" content="Provides a convenient way to compare different kinetic models fitted to the
+same dataset."><meta name="robots" content="noindex"><!-- 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]>
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-<![endif]-->
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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-
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -73,23 +18,21 @@ same dataset." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
</span>
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- <ul class="nav navbar-nav">
- <li>
+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Functions and data</a>
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- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
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- <li>
+ <ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
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<li>
@@ -99,48 +42,50 @@ same dataset." />
<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>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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>
<li>
- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
</li>
- </ul>
-</li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+ </li>
+ </ul></li>
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- <ul class="nav navbar-nav navbar-right">
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- <a href="https://github.com/jranke/mkin/">
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
<span class="fab fa-github fa-lg"></span>
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+ </header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate the AIC for a column of an mmkin object</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/AIC.mmkin.R" class="external-link"><code>R/AIC.mmkin.R</code></a></small>
<div class="hidden name"><code>AIC.mmkin.Rd</code></div>
</div>
@@ -149,102 +94,110 @@ same dataset." />
same dataset.</p>
</div>
- <pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, k <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span>
-
-<span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</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 object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one
-column.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>For compatibility with the generic method</p></td>
- </tr>
- <tr>
- <th>k</th>
- <td><p>As in the generic method</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>As in the generic method (a numeric value for single fits, or a
-dataframe if there are several fits in the column).</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one
+column.</p></dd>
+
+<dt>...</dt>
+<dd><p>For compatibility with the generic method</p></dd>
+
+
+<dt>k</dt>
+<dd><p>As in the generic method</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>As in the generic method (a numeric value for single fits, or a
+dataframe if there are several fits in the column).</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'># skip, as it takes &gt; 10 s on winbuilder</span>
- <span class='va'>f</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='st'>"DFOP"</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>,
- <span class='st'>"FOCUS C"</span> <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='co'># We get a warning because the FOMC model does not converge for the</span>
- <span class='co'># FOCUS A dataset, as it is well described by SFO</span>
-
- <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span>
-</div><div class='output co'>#&gt; [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># or when extracting an mkinfit object</span>
-</div><div class='output co'>#&gt; [1] 55.28197</div><div class='input'>
- <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span>
- <span class='co'># of parameters, the higher (worse) the AIC</span>
- <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; df AIC
-#&gt; SFO 3 55.28197
-#&gt; FOMC 4 57.28222
-#&gt; DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span>
-</div><div class='output co'>#&gt; df AIC
-#&gt; SFO 3 49.28197
-#&gt; FOMC 4 49.28222
-#&gt; DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span>
-</div><div class='output co'>#&gt; df BIC
-#&gt; SFO 3 55.52030
-#&gt; FOMC 4 57.59999
-#&gt; DFOP 5 59.67918</div><div class='input'>
- <span class='co'># For FOCUS C, the more complex models fit better</span>
- <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; df AIC
-#&gt; SFO 3 59.29336
-#&gt; FOMC 4 44.68652
-#&gt; DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; df BIC
-#&gt; SFO 3 59.88504
-#&gt; FOMC 4 45.47542
-#&gt; DFOP 5 30.00984</div><div class='input'>
-
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># skip, as it takes &gt; 10 s on winbuilder</span></span></span>
+<span class="r-in"><span> <span class="va">f</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="st">"DFOP"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
+<span class="r-in"><span> <span class="st">"FOCUS C"</span> <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></span>
+<span class="r-in"><span> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span></span>
+<span class="r-in"><span> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># We get a single number for a single fit</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 55.28197</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="co"># or when extracting an mkinfit object</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 55.28197</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># For FOCUS A, the models fit almost equally well, so the higher the number</span></span></span>
+<span class="r-in"><span> <span class="co"># of parameters, the higher (worse) the AIC</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> df AIC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO 3 55.28197</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC 4 57.28222</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP 5 59.28197</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> df AIC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO 3 49.28197</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC 4 49.28222</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP 5 49.28197</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> df BIC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO 3 55.52030</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC 4 57.59999</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP 5 59.67918</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># For FOCUS C, the more complex models fit better</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> df AIC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO 3 59.29336</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC 4 44.68652</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP 5 29.02372</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> df BIC</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO 3 59.88504</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC 4 45.47542</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP 5 30.00984</span>
+<span class="r-in"><span> </span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
</div>
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