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diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html deleted file mode 100644 index 8af0a8e2..00000000 --- a/docs/dev/reference/D24_2014.html +++ /dev/null @@ -1,261 +0,0 @@ -<!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."><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">1.2.3</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</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 class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</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 class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</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> - </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><span class="va">D24_2014</span></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="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</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><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> -<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 $meta:</span> -<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span> -<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span> -<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span> -<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span> -<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span> -<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span> -<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span> -<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span> -<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span> -<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span> -<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span> -<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span> -<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</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> -<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><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> -<span class="r-in"><span> 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> -<span class="r-in"><span> 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> -<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span><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> -<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><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> -<span class="r-in"><span> 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> -<span class="r-in"><span> 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> -<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span><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> -<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><span class="co"># }</span></span></span> -</code></pre></div> - </div> - </div> - <div class="col-md-3 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