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diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index e73b989a..488ca302 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -1,18 +1,18 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <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>Introduction to mkin • mkin</title> -<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> +<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> <script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> <meta property="og:description" content=""> <meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- 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]--> @@ -22,14 +22,15 @@ <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"> + <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.47.6</span> </span> </div> @@ -84,7 +85,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-11-26</h4> + <h4 class="date">2019-01-31</h4> <div class="hidden name"><code>mkin.Rmd</code></div> @@ -98,7 +99,7 @@ <h1 class="hasAnchor"> <a href="#abstract" class="anchor"></a>Abstract</h1> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> <span class="citation">(Ranke 2016)</span> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># Define the kinetic model</span></a> <a class="sourceLine" id="cb1-3" data-line-number="3">m_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> <a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">M1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> @@ -107,12 +108,12 @@ <a class="sourceLine" id="cb1-7" data-line-number="7"></a> <a class="sourceLine" id="cb1-8" data-line-number="8"></a> <a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co"># Produce model predictions using some arbitrary parameters</span></a> -<a class="sourceLine" id="cb1-10" data-line-number="10">sampling_times =<span class="st"> </span><span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</a> +<a class="sourceLine" id="cb1-10" data-line-number="10">sampling_times =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</a> <a class="sourceLine" id="cb1-11" data-line-number="11">d_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(m_SFO_SFO_SFO,</a> -<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="kw">c</span>(<span class="dt">k_parent =</span> <span class="fl">0.03</span>,</a> -<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="dt">k_M1 =</span> <span class="kw">log</span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">100</span>,</a> -<a class="sourceLine" id="cb1-14" data-line-number="14"> <span class="dt">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="dt">k_M2 =</span> <span class="kw">log</span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">50</span>),</a> -<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="kw">c</span>(<span class="dt">parent =</span> <span class="dv">100</span>, <span class="dt">M1 =</span> <span class="dv">0</span>, <span class="dt">M2 =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k_parent =</span> <span class="fl">0.03</span>,</a> +<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="dt">k_M1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">100</span>,</a> +<a class="sourceLine" id="cb1-14" data-line-number="14"> <span class="dt">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="dt">k_M2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">50</span>),</a> +<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">parent =</span> <span class="dv">100</span>, <span class="dt">M1 =</span> <span class="dv">0</span>, <span class="dt">M2 =</span> <span class="dv">0</span>),</a> <a class="sourceLine" id="cb1-16" data-line-number="16"> sampling_times)</a> <a class="sourceLine" id="cb1-17" data-line-number="17"></a> <a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co"># Generate a dataset by adding normally distributed errors with</span></a> @@ -125,7 +126,7 @@ <a class="sourceLine" id="cb1-25" data-line-number="25">f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb1-26" data-line-number="26"></a> <a class="sourceLine" id="cb1-27" data-line-number="27"><span class="co"># Plot the results separately for parent and metabolites</span></a> -<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> @@ -246,9 +247,8 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a 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