diff options
Diffstat (limited to 'docs/dev/reference/add_err.html')
| -rw-r--r-- | docs/dev/reference/add_err.html | 287 |
1 files changed, 287 insertions, 0 deletions
diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html new file mode 100644 index 00000000..a4317cd7 --- /dev/null +++ b/docs/dev/reference/add_err.html @@ -0,0 +1,287 @@ +<!-- 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-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</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="http://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='http://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='no'>prediction</span>, + <span class='no'>sdfunc</span>, + <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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 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="examples"><a class="anchor" href="#examples"></a>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'><-</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='st'>"M1"</span>), + <span class='kw'>M1</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'>#> <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='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><-</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'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></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) 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='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</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/base/plot.html'>plot</a></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><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/base/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'># } + +</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> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |