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diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html new file mode 100644 index 00000000..bb94fd11 --- /dev/null +++ b/docs/reference/experimental_data_for_UBA.html @@ -0,0 +1,285 @@ +<!-- 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>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin</title> + +<!-- 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="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019" /> + +<meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do 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. +Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below. +Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues. +Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation. +Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16). +Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup. +Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR. +Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81)." /> +<meta name="twitter:card" content="summary" /> + + + +<!-- 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> + <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">0.9.49.5</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> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Experimental datasets used for development and testing of error models</h1> + + <div class="hidden name"><code>experimental_data_for_UBA.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do 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> +<p>Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below.</p> +<p>Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues.</p> +<p>Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation.</p> +<p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16).</p> +<p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup.</p> +<p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR.</p> +<p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81).</p> + + </div> + + <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, + each containing, among others, the following components</p><dl class='dl-horizontal'> + <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> + <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> + </dl> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + + <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>FOCUS (2014) “Generic guidance for Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Version 1.1, 18 December 2014 + <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> +<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate + and Behaviour</p> +<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the + environment</p> +<p>Ranke (2019) Documentation of results obtained for the error model expertise + written for the German Umweltbundesamt.</p> +<p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed + Decision of the United Kingdom made to the European Commission under Regulation (EC) No. + 1141/2010 for renewal of an active substance</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='co'># Model definitions</span> +<span class='no'>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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</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='no'>dfop_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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</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='no'>sfo_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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>A2</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='no'>dfop_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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>A2</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='no'>d_1_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>1</span>:<span class='fl'>2</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_1_2</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Soil"</span>, <span class='fl'>1</span>:<span class='fl'>2</span>) + + +<span class='no'>f_1_2_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"DFOP-SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>dfop_sfo_sfo</span>), <span class='no'>d_1_2</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>) + +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_1_2_tc</span>, <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </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> 1.3.0.</p> +</div> + </footer> + </div> + + + 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