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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
commita77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
treee91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/mkinerrmin.html
parent675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
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+the chi-squared test as defined in the FOCUS kinetics report from 2006." />
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+ <h1>Calculate the minimum error to assume in order to pass the variance test</h1>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small>
+ <div class="hidden name"><code>mkinerrmin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function finds the smallest relative error still resulting in passing
+the chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</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>fit</th>
+ <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>alpha</th>
+ <td><p>The confidence level chosen for the chi-squared test.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A dataframe with the following components:</p>
+<dt>err.min</dt><dd><p>The
+relative error, expressed as a fraction.</p></dd> <dt>n.optim</dt><dd><p>The number of
+optimised parameters attributed to the data series.</p></dd> <dt>df</dt><dd><p>The number of
+remaining degrees of freedom for the chi2 error level calculations. Note
+that mean values are used for the chi2 statistic and therefore every time
+point with observed values in the series only counts one time.</p></dd> The
+dataframe has one row for the total dataset and one further row for each
+observed state variable in the model.
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics, EC
+Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'>
+<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</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='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.0640 4 15
+#&gt; parent 0.0646 2 7
+#&gt; m1 0.0469 2 8</div><div class='input'><span class='co'># \dontrun{</span>
+ <span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.1544 4 13
+#&gt; parent 0.1659 2 7
+#&gt; m1 0.1095 2 6</div><div class='input'># }
+
+</div></pre>
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