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diff --git a/docs/add_err.html b/docs/add_err.html new file mode 100644 index 00000000..78c69d3e --- /dev/null +++ b/docs/add_err.html @@ -0,0 +1,201 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>add_err. mkin 0.9.44.9000</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" + Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">mkin 0.9.44.9000</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1> + Add normally distributed errors to simulated kinetic degradation data +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="functioncall"><a href='add_err.html'>add_err</a></span><span class="keyword">(</span><span class="symbol">prediction</span><span class="keyword">,</span> <span class="symbol">sdfunc</span><span class="keyword">,</span> + <span class="argument">n</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">LOD</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">,</span> <span class="argument">reps</span> <span class="argument">=</span> <span class="number">2</span><span class="keyword">,</span> + <span class="argument">digits</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">,</span> <span class="argument">seed</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>prediction</dt> + <dd> + A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></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="Description"> + <h2>Description</h2> + + <p>Normally distributed errors are added to data predicted for a specific + degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error + may depend on the predicted value and is specified as a standard deviation.</p> + + </div> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> + A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. + the components of the list are datasets compatible with + <code><a href='mkinfit.html'>mkinfit</a></code>. +</dl></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="comment"># The kinetic model</span> +<span class="symbol">m_SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"M1"</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">M1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">use_of_ff</span> <span class="argument">=</span> <span class="string">"max"</span><span class="keyword">)</span></div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'> +<span class="comment"># Generate a prediction for a specific set of parameters</span> +<span class="symbol">sampling_times</span> <span class="assignement">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">,</span> <span class="number">7</span><span class="keyword">,</span> <span class="number">14</span><span class="keyword">,</span> <span class="number">28</span><span class="keyword">,</span> <span class="number">60</span><span class="keyword">,</span> <span class="number">90</span><span class="keyword">,</span> <span class="number">120</span><span class="keyword">)</span> + +<span class="comment"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> +<span class="comment"># from 2015</span> +<span class="symbol">d_SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">m_SFO_SFO</span><span class="keyword">,</span> + <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_parent</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">,</span> <span class="argument">f_parent_to_M1</span> <span class="argument">=</span> <span class="number">0.5</span><span class="keyword">,</span> + <span class="argument">k_M1</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/Log'>log</a></span><span class="keyword">(</span><span class="number">2</span><span class="keyword">)</span><span class="keyword">/</span><span class="number">1000</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">M1</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="symbol">sampling_times</span><span class="keyword">)</span> + +<span class="comment"># Add an error term with a constant (independent of the value) standard deviation</span> +<span class="comment"># of 10, and generate three datasets</span> +<span class="symbol">d_SFO_SFO_err</span> <span class="assignement"><-</span> <span class="functioncall"><a href='add_err.html'>add_err</a></span><span class="keyword">(</span><span class="symbol">d_SFO_SFO</span><span class="keyword">,</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">x</span><span class="keyword">)</span> <span class="number">10</span><span class="keyword">,</span> <span class="argument">n</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">seed</span> <span class="argument">=</span> <span class="number">123456789</span> <span class="keyword">)</span> + +<span class="comment"># Name the datasets for nicer plotting</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">d_SFO_SFO_err</span><span class="keyword">)</span> <span class="assignement"><-</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span><span class="keyword">(</span><span class="string">"Dataset"</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">:</span><span class="number">3</span><span class="keyword">)</span> + +<span class="comment"># Name the model in the list of models (with only one member in this case)</span> +<span class="comment"># for nicer plotting later on.</span> +<span class="comment"># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span> +<span class="comment"># are easy and examples are run often. Use only one core not to offend CRAN</span> +<span class="comment"># checks</span> +<span class="symbol">f_SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mmkin.html'>mmkin</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="string">"SFO-SFO"</span> <span class="argument">=</span> <span class="symbol">m_SFO_SFO</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="symbol">d_SFO_SFO_err</span><span class="keyword">,</span> <span class="argument">cores</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">,</span> + <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">method.modFit</span> <span class="argument">=</span> <span class="string">"Marq"</span><span class="keyword">)</span> + +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">f_SFO_SFO</span><span class="keyword">)</span></div> +<p><img src='add_err-4.png' alt='' width='540' height='400' /></p> +<div class='input'> +<span class="comment"># We would like to inspect the fit for dataset 3 more closely</span> +<span class="comment"># Using double brackets makes the returned object an mkinfit object</span> +<span class="comment"># instead of a list of mkinfit objects, so plot.mkinfit is used</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">f_SFO_SFO</span><span class="keyword">[[</span><span class="number">3</span><span class="keyword">]</span><span class="keyword">]</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div> +<p><img src='add_err-6.png' alt='' width='540' height='400' /></p> +<div class='input'> +<span class="comment"># If we use single brackets, we should give two indices (model and dataset),</span> +<span class="comment"># and plot.mmkin is used</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">f_SFO_SFO</span><span class="keyword">[</span><span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">]</span><span class="keyword">)</span></div> +<p><img src='add_err-8.png' alt='' width='540' height='400' /></p> +<div class='input'></div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>add_err</li> + </ul> + <ul> + <li> manip </li> + </ul> --> + + + + <h2>Author</h2> + + Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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