Static documentation rebuilt by pkgdown::build_site()

author: Johannes Ranke <jranke@uni-bremen.de> 2016-10-06 09:19:21 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2016-10-06 09:19:21 +0200
commit: 38f9e15f0c972c1516ae737a2bca8d7789581bbd (patch)
tree: 724c9dc19901f24f427757ac81001f07bf298024 /docs/reference/add_err.html
parent: ec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (diff)
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+        <li>
+  <a href="../index.html">Home</a>
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+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/jranke/mkin">
+    <span class="fa fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
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+      
+      </header>
+
+      <div class="page-header">
+  <h1>
+</h1>
+</div>
+
+<div class="row">
+  <div class="col-md-9">
+    
+    <p>Normally distributed errors are added to data predicted for a specific
+  degradation model using <code>mkinpredict</code>. The variance of the error
+  may depend on the predicted value and is specified as a standard deviation.</p>
+    
+
+    <pre><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>,
+          <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+          <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+    
+    <h2>Arguments</h2>
+    <dl class="dl-horizontal">
+      <dt>prediction</dt>
+      <dd>
+    A prediction from a kinetic model as produced by <code>mkinpredict</code>.
+  </dd>
+      <dt>sdfunc</dt>
+      <dd>
+    A function taking the predicted value as its only argument and returning
+    a standard deviation that should be used for generating the random error
+    terms for this value.
+  </dd>
+      <dt>n</dt>
+      <dd>
+    The number of datasets to be generated.
+  </dd>
+      <dt>LOD</dt>
+      <dd>
+    The limit of detection (LOD). Values that are below the LOD after adding
+    the random error will be set to NA.
+  </dd>
+      <dt>reps</dt>
+      <dd>
+    The number of replicates to be generated within the datasets.
+  </dd>
+      <dt>digits</dt>
+      <dd>
+    The number of digits to which the values will be rounded.
+  </dd>
+      <dt>seed</dt>
+      <dd>
+    The seed used for the generation of random numbers. If NA, the seed 
+    is not set.
+  </dd>
+    </dl>
+    
+    <div class="Value">
+      <h2>Value</h2>
+
+      <p>A list of datasets compatible with <code>mmkin</code>, i.e.
+  the components of the list are datasets compatible with 
+  <code>mkinfit</code>.</p>
+    </div>
+
+    <div class="References">
+      <h2>References</h2>
+
+      <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy
+  http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p>
+    </div>
+    
+    <h2 id="examples">Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'># The kinetic model</span>
+<span class='no'>m_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>),
+                     <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
+<span class='co'># Generate a prediction for a specific set of parameters</span>
+<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
+
+<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span>
+<span class='co'># from 2015</span>
+<span class='no'>d_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinpredict</span>(<span class='no'>m_SFO_SFO</span>,
+                         <span class='fu'>c</span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
+                           <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>),
+                         <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+                         <span class='no'>sampling_times</span>)
+
+<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span>
+<span class='co'># of 10, and generate three datasets</span>
+<span class='no'>d_SFO_SFO_err</span> <span class='kw'>&lt;-</span> <span class='fu'>add_err</span>(<span class='no'>d_SFO_SFO</span>, <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fl'>10</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456789</span> )
+
+<span class='co'># Name the datasets for nicer plotting</span>
+<span class='fu'>names</span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'>&lt;-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
+
+<span class='co'># Name the model in the list of models (with only one member in this case)</span>
+<span class='co'># for nicer plotting later on.</span>
+<span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span>
+<span class='co'># are easy and examples are run often. Use only one core not to offend CRAN</span>
+<span class='co'># checks</span>
+<span class='no'>f_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>),
+                   <span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+                   <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
+
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'>
+<span class='co'># We would like to inspect the fit for dataset 3 more closely</span>
+<span class='co'># Using double brackets makes the returned object an mkinfit object</span>
+<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span>
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-6.png' alt='' width='540' height='400' /><div class='input'>
+<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span>
+<span class='co'># and plot.mmkin is used</span>
+<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><img src='unknown-8.png' alt='' width='540' height='400' /><div class='input'>
+</div></pre>
+  </div>
+  <div class="col-md-3">
+    <h2>Author</h2>
+    
+  Johannes Ranke
+
+  </div>
+</div>
+
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author	Johannes Ranke <jranke@uni-bremen.de>	2016-10-06 09:19:21 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2016-10-06 09:19:21 +0200
commit	38f9e15f0c972c1516ae737a2bca8d7789581bbd (patch)
tree	724c9dc19901f24f427757ac81001f07bf298024 /docs/reference/add_err.html
parent	ec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (diff)