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diff --git a/docs/add_err.html b/docs/add_err.html deleted file mode 100644 index 78c69d3e..00000000 --- a/docs/add_err.html +++ /dev/null @@ -1,201 +0,0 @@ -<!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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