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diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html deleted file mode 100644 index 77ff6ce4..00000000 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ /dev/null @@ -1,275 +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>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/3.4.1/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="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, 2013, 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 - (Hellas, 2013, 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="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>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, 2013, 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 - (Hellas, 2013, 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> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div> - </div> - - <div id="format"> - <h2>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><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></div> - <div id="source"> - <h2>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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> -<p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate - and Behaviour</p> -<p>Hellas (2013). 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> - </div> - - <div id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># Model definitions</span></span></span> -<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><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>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A1 <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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> -<span class="r-in"><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="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><span> parent <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">"A1"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A1 <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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> -<span class="r-in"><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="va">sfo_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><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>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A1 <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">"A2"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A2 <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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> -<span class="r-in"><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="va">dfop_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> -<span class="r-in"><span> parent <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">"A1"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A1 <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">"A2"</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> A2 <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></span> -<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> -<span class="r-in"><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="va">d_1_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</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_1_2</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">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="va">f_1_2_tc</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">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</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_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="experimental_data_for_UBA-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># }</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> 2.0.7.</p> -</div> - - </footer></div> - - - - - - - </body></html> - |