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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
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tree33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/mkinerrmin.html
parent8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)
Start online docs of the development version
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index 94c575cb..2c9f0b13 100644
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@@ -73,23 +18,21 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
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- <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>
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@@ -99,48 +42,50 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
<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>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
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- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
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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='https://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrmin.R" class="external-link"><code>R/mkinerrmin.R</code></a></small>
<div class="hidden name"><code>mkinerrmin.Rd</code></div>
</div>
@@ -149,89 +94,100 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
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='op'>(</span><span class='va'>fit</span>, alpha <span class='op'>=</span> <span class='fl'>0.05</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>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
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>fit</dt>
+<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
+
+
+<dt>alpha</dt>
+<dd><p>The confidence level chosen for the chi-squared test.</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>A dataframe with the following components:</p>
+<dl><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
+point with observed values in the series only counts one time.</p></dd>
+</dl><p>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
+observed state variable in the model.</p>
+ </div>
+ <div id="details">
+ <h2>Details</h2>
+ <p>This function is used internally by <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>.</p>
+ </div>
+ <div id="references">
+ <h2>References</h2>
+ <p>FOCUS (2006) “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
+Registration” 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='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
- use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='va'>fit_FOCUS_D</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</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='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_D</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</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='va'>fit_FOCUS_E</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_E</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
- <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_E</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</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'><span class='co'># }</span>
-
-</div></pre>
+<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+ </div>
+
+ <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="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</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></span>
+<span class="r-in"><span><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</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="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.0640 4 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 0.0646 2 7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> m1 0.0469 2 8</span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.1544 4 13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 0.1659 2 7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> m1 0.1095 2 6</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
</div>
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