Additional algorithm "d_c", more tests, docs

The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
author: Johannes Ranke <jranke@uni-bremen.de> 2019-06-04 15:09:28 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2019-06-04 15:09:28 +0200
commit: 95178837d3f91e84837628446b5fd468179af2b9 (patch)
tree: 8b162d5a22b28b59ca9c6bb27bf8f9dfbeaefbae /docs/reference/experimental_data_for_UBA.html
parent: 9a96391589fef9f80f9c6c4881cc48a509cb75f2 (diff)
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+ by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate
+ and advance error model specifications. The fact that these data and some
+ results are shown here do not imply a license to use them in the context of
+ pesticide registrations, as the use of the data may be constrained by
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+    <div class="page-header">
+    <h1>Experimental datasets used for development and testing of error models</h1>
+    
+    <div class="hidden name"><code>experimental_data_for_UBA.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>The 12 datasets were extracted from active substance evaluation dossiers published
+ by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate
+ and advance error model specifications. The fact that these data and some
+ results are shown here do not imply a license to use them in the context of
+ pesticide registrations, as the use of the data may be constrained by
+ data protection regulations.</p>
+    
+    </div>
+
+    <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>,
+  each containing, among others, the following components</p><dl class='dl-horizontal'>
+    <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd>
+    <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
+  </dl>
+    
+    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+    <p>Ranke (2019) Documentation of results obtained for the error model expertise
+  written for the German Umweltbundesamt.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>
+<span class='co'># Model definitions</span>
+<span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</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'>"A1"</span>),
+  <span class='kw'>A1</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'>dfop_sfo</span> <span class='kw'>&lt;-</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
+  <span class='kw'>A1</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'>sfo_sfo_sfo</span> <span class='kw'>&lt;-</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'>"A1"</span>),
+  <span class='kw'>A1</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'>"A2"</span>),
+  <span class='kw'>A2</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'>dfop_sfo_sfo</span> <span class='kw'>&lt;-</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>),
+  <span class='kw'>A1</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'>"A2"</span>),
+  <span class='kw'>A2</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'>d_1_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>1</span>:<span class='fl'>2</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_1_2</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Soil"</span>, <span class='fl'>1</span>:<span class='fl'>2</span>)
+
+
+<span class='no'>f_1_2_tc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"DFOP-SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>dfop_sfo_sfo</span>), <span class='no'>d_1_2</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
+
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_1_2_tc</span>, <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      
+      <li><a href="#format">Format</a></li>
+
+      <li><a href="#source">Source</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
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+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
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+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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author	Johannes Ranke <jranke@uni-bremen.de>	2019-06-04 15:09:28 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2019-06-04 15:09:28 +0200
commit	95178837d3f91e84837628446b5fd468179af2b9 (patch)
tree	8b162d5a22b28b59ca9c6bb27bf8f9dfbeaefbae /docs/reference/experimental_data_for_UBA.html
parent	9a96391589fef9f80f9c6c4881cc48a509cb75f2 (diff)