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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">1.2.2</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" data-bs-toggle="dropdown" 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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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">Benchmark timings for mkin</a> </li> <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</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/" class="external-link"> <span class="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/HEAD/R/add_err.R" class="external-link"><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> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span> <span> <span class="va">prediction</span>,</span> <span> <span class="va">sdfunc</span>,</span> <span> secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> <span> n <span class="op">=</span> <span class="fl">10</span>,</span> <span> LOD <span class="op">=</span> <span class="fl">0.1</span>,</span> <span> reps <span class="op">=</span> <span class="fl">2</span>,</span> <span> digits <span class="op">=</span> <span class="fl">1</span>,</span> <span> seed <span class="op">=</span> <span class="cn">NA</span></span> <span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>prediction</dt> <dd><p>A prediction from a kinetic model as produced by <code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd> <dt>sdfunc</dt> <dd><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></dd> <dt>secondary</dt> <dd><p>The names of state variables that should have an initial value of zero</p></dd> <dt>n</dt> <dd><p>The number of datasets to be generated.</p></dd> <dt>LOD</dt> <dd><p>The limit of detection (LOD). Values that are below the LOD after adding the random error will be set to NA.</p></dd> <dt>reps</dt> <dd><p>The number of replicates to be generated within the datasets.</p></dd> <dt>digits</dt> <dd><p>The number of digits to which the values will be rounded.</p></dd> <dt>seed</dt> <dd><p>The seed used for the generation of random numbers. If NA, the seed is not set.</p></dd> </dl></div> <div id="value"> <h2>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> </div> <div id="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 https://jrwb.de/posters/piacenza_2015.pdf</p> </div> <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> </div> <div id="ref-examples"> <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The kinetic model</span></span></span> <span class="r-in"><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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.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></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span> <span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span> <span class="r-in"><span><span class="co"># from 2015</span></span></span> <span class="r-in"><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></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</span></span> <span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">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></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span> <span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span> <span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span> <span class="r-in"><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></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">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" class="external-link">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></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span> <span class="r-in"><span><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span></span> <span class="r-in"><span><span class="co"># checks</span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><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" class="external-link">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></span> <span class="r-in"><span> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span> <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span> <span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span> <span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span> <span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span> <span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">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></span></span> <span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> </div> </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></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> </body></html>