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<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/HEAD/R/AIC.mmkin.R" class="external-link"><code>R/AIC.mmkin.R</code></a></small>
<div class="d-none name"><code>AIC.mmkin.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Provides a convenient way to compare different kinetic models fitted to the
same dataset.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class '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 class '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 class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one
column.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>For compatibility with the generic method</p></dd>
<dt id="arg-k">k<a class="anchor" aria-label="anchor" href="#arg-k"></a></dt>
<dd><p>As in the generic method</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p>Johannes Ranke</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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 > 10 s on winbuilder</span></span></span>
<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</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-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</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">#></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">#></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">#></span> df AIC</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28198</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> df AIC</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28198</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> df BIC</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59974</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> df AIC</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.29336</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC 4 44.68652</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> df BIC</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.88504</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC 4 45.47542</span>
<span class="r-out co"><span class="r-pr">#></span> DFOP 5 30.00984</span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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