<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> <!-- bootstrap-toc --> <link rel="stylesheet" href="../bootstrap-toc.css"> <script src="../bootstrap-toc.js"></script> <!-- Font Awesome icons --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> <!-- headroom.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../pkgdown.js"></script> <meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> <meta property="og:description" content="Normally distributed errors are added to data predicted for a specific degradation model using mkinpredict. The variance of the error may depend on the predicted value and is specified as a standard deviation." /> <meta name="robots" content="noindex"> <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> <li> <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> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> </ul> </li> <li> <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Add normally distributed errors to simulated kinetic degradation data</h1> <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/add_err.R'><code>R/add_err.R</code></a></small> <div class="hidden name"><code>add_err.Rd</code></div> </div> <div class="ref-description"> <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> <pre class="usage"><span class='fu'>add_err</span><span class='op'>(</span> <span class='va'>prediction</span>, <span class='va'>sdfunc</span>, secondary <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, n <span class='op'>=</span> <span class='fl'>10</span>, LOD <span class='op'>=</span> <span class='fl'>0.1</span>, reps <span class='op'>=</span> <span class='fl'>2</span>, digits <span class='op'>=</span> <span class='fl'>1</span>, seed <span class='op'>=</span> <span class='cn'>NA</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>prediction</th> <td><p>A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> </tr> <tr> <th>sdfunc</th> <td><p>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.</p></td> </tr> <tr> <th>secondary</th> <td><p>The names of state variables that should have an initial value of zero</p></td> </tr> <tr> <th>n</th> <td><p>The number of datasets to be generated.</p></td> </tr> <tr> <th>LOD</th> <td><p>The limit of detection (LOD). Values that are below the LOD after adding the random error will be set to NA.</p></td> </tr> <tr> <th>reps</th> <td><p>The number of replicates to be generated within the datasets.</p></td> </tr> <tr> <th>digits</th> <td><p>The number of digits to which the values will be rounded.</p></td> </tr> <tr> <th>seed</th> <td><p>The seed used for the generation of random numbers. If NA, the seed is not set.</p></td> </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>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>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 https://jrwb.de/posters/piacenza_2015.pdf</p> <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> <p>Johannes Ranke</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># The kinetic model</span> <span class='va'>m_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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, M1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.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'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># Generate a prediction for a specific set of parameters</span> <span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</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='op'>)</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='va'>d_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>/</span><span class='fl'>1000</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</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='va'>d_SFO_SFO_err</span> <span class='op'><-</span> <span class='fu'>add_err</span><span class='op'>(</span><span class='va'>d_SFO_SFO</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fl'>10</span>, n <span class='op'>=</span> <span class='fl'>3</span>, seed <span class='op'>=</span> <span class='fl'>123456789</span> <span class='op'>)</span> <span class='co'># Name the datasets for nicer plotting</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_SFO_SFO_err</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> <span class='co'># Name the model in the list of models (with only one member in this case) for</span> <span class='co'># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span> <span class='co'># checks</span> <span class='co'># \dontrun{</span> <span class='va'>f_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_SFO_SFO</span><span class='op'>)</span>, <span class='va'>d_SFO_SFO_err</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>)</span> </div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><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'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><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'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span> </div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> <h2 data-toc-skip>Contents</h2> </nav> </div> </div> <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> </div> </body> </html>