|
|
<!DOCTYPE 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>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • 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="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014"><meta property="og:description" content="The five datasets were extracted from the active substance evaluation dossier
published by EFSA. Kinetic evaluations shown for these datasets are intended
to illustrate and advance kinetic modelling. The fact that these data and
some results are shown here does not imply a license to use them in the
context of pesticide registrations, as the use of the data may be
constrained by data protection regulations."><!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</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/" 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>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/D24_2014.R" class="external-link"><code>R/D24_2014.R</code></a></small>
<div class="hidden name"><code>D24_2014.Rd</code></div>
</div>
<div class="ref-description">
<p>The five datasets were extracted from the active substance evaluation dossier
published by EFSA. Kinetic evaluations shown for these datasets are intended
to illustrate and advance kinetic modelling. The fact that these data and
some results are shown here does not imply a license to use them in the
context of pesticide registrations, as the use of the data may be
constrained by data protection regulations.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">D24_2014</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
<p>An <a href="mkindsg.html">mkindsg</a> object grouping five datasets</p>
</div>
<div id="source">
<h2>Source</h2>
<p>Hellenic Ministry of Rural Development and Agriculture (2014)
Final addendum to the Renewal Assessment Report - public version - 2,4-D
Volume 3 Annex B.8 Fate and behaviour in the environment
<a href="http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812" class="external-link">http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812</a></p>
</div>
<div id="details">
<h2>Details</h2>
<p>Data for the first dataset are from p. 685. Data for the other four
datasets were used in the preprocessed versions given in the kinetics
section (p. 761ff.), with the exception of residues smaller than 1 for DCP
in the soil from Site I2, where the values given on p. 694 were used.</p>
<p>The R code used to create this data object is installed with this package
in the 'dataset_generation' directory. In the code, page numbers are given for
specific pieces of information in the comments.</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span>
<span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 </span>
<span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span>
<span class="r-out co"><span class="r-pr">#></span> D24 DCP DCA </span>
<span class="r-out co"><span class="r-pr">#></span> 5 4 4 </span>
<span class="r-out co"><span class="r-pr">#></span> Time normalisation factors $f_time_norm:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</span>
<span class="r-out co"><span class="r-pr">#></span> Meta information $meta:</span>
<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span>
<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span>
<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span>
<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span>
<span class="r-in"><span class="co"># \dontrun{</span></span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Mississippi </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: D24 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 1 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> time D24</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 96.8</span>
<span class="r-out co"><span class="r-pr">#></span> 2 2 81.0</span>
<span class="r-out co"><span class="r-pr">#></span> 3 4 81.7</span>
<span class="r-out co"><span class="r-pr">#></span> 4 7 88.2</span>
<span class="r-out co"><span class="r-pr">#></span> 5 15 66.3</span>
<span class="r-out co"><span class="r-pr">#></span> 6 24 72.9</span>
<span class="r-out co"><span class="r-pr">#></span> 7 35 62.6</span>
<span class="r-out co"><span class="r-pr">#></span> 8 56 54.6</span>
<span class="r-out co"><span class="r-pr">#></span> 9 71 35.2</span>
<span class="r-out co"><span class="r-pr">#></span> 10 114 18.0</span>
<span class="r-out co"><span class="r-pr">#></span> 11 183 11.3</span>
<span class="r-out co"><span class="r-pr">#></span> 12 273 9.9</span>
<span class="r-out co"><span class="r-pr">#></span> 13 365 6.3</span>
<span class="r-in"><span class="va">m_D24</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span>
<span class="r-in"> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span>
<span class="r-in"> DCA <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><span class="op">)</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 class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span>
<span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span>
<span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span>
<span class="r-out co"><span class="r-pr">#></span> $D24</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCP; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCP</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCA; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCA</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> Coefficient matrix $coefmat available</span>
<span class="r-out co"><span class="r-pr">#></span> Compiled model $cf available</span>
<span class="r-out co"><span class="r-pr">#></span> Differential equations:</span>
<span class="r-out co"><span class="r-pr">#></span> d_D24/dt = - k_D24 * D24</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCP/dt = + f_D24_to_DCP * k_D24 * D24 - k_DCP * DCP</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span>
<span class="r-in"><span class="va">m_D24_2</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>D24 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"DCP"</span><span class="op">)</span>,</span>
<span class="r-in"> DCP <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"DCA"</span><span class="op">)</span>,</span>
<span class="r-in"> DCA <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><span class="op">)</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 class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24_2</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span>
<span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span>
<span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span>
<span class="r-out co"><span class="r-pr">#></span> $D24</span>
<span class="r-out co"><span class="r-pr">#></span> $type: DFOP; $to: DCP; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCP</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCA; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCA</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> Compiled model $cf available</span>
<span class="r-out co"><span class="r-pr">#></span> Differential equations:</span>
<span class="r-out co"><span class="r-pr">#></span> d_D24/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
<span class="r-out co"><span class="r-pr">#></span> * D24</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *</span>
<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2</span>
<span class="r-out co"><span class="r-pr">#></span> * time))) * D24 - k_DCP * DCP</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span>
<span class="r-in"><span class="co"># }</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> 2.0.2.</p>
</div>
</footer></div>
</body></html>
|
