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<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> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><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="d-none name"><code>D24_2014.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <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 @@ -119,24 +79,27 @@ 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="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <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> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <a href="mkindsg.html">mkindsg</a> object grouping five datasets</p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></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 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p> </div> - <div id="details"> - <h2>Details</h2> - <p>Data for the first dataset are from p. 685. Data for the other four + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>The acronyms used for the 2,4-D transformation products are DCP for +2,4-dichlorophenol and DCA for 2,4-dichloroanisole.</p> +<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> @@ -145,8 +108,8 @@ 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="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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 $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 </span> @@ -232,30 +195,73 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2</span> <span class="r-out co"><span class="r-pr">#></span> * time))) * D24 - k_DCP * DCP</span> <span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span> +<span class="r-in"><span><span class="va">D24_2014_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</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">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">D24_2014_data</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</span><span class="va">ds</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">title</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_D24_2014_const</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> models <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></span> +<span class="r-in"><span> <span class="st">"SFO-SFO-SFO"</span> <span class="op">=</span> <span class="va">m_D24</span>, </span></span> +<span class="r-in"><span> <span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">m_D24_2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">D24_2014_data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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">f_D24_2014_const</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model Mississippi Fayette RefSol 03-G Site E1 Site I2</span> +<span class="r-out co"><span class="r-pr">#></span> SFO-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Z: Observations with value of zero were removed from the data</span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</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_D24_2014_const</span><span class="op">[</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="D24_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">f_D24_2014_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_D24_2014_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</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">f_D24_2014_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model Mississippi Fayette RefSol 03-G Site E1 Site I2</span> +<span class="r-out co"><span class="r-pr">#></span> SFO-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> DFOP-SFO-SFO OK Z Z Z Z </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Z: Observations with value of zero were removed from the data</span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</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_D24_2014_tc</span><span class="op">[</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="D24_2014-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># For dataset 3, the best fit is obtained using constant </span></span></span> +<span class="r-in"><span><span class="co"># variance and the DFOP-SFO-SFO model</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_const</span><span class="op">[[</span><span class="st">"SFO-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>, </span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_const</span><span class="op">[[</span><span class="st">"DFOP-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>, </span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_tc</span><span class="op">[[</span><span class="st">"SFO-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="va">f_D24_2014_tc</span><span class="op">[[</span><span class="st">"DFOP-SFO-SFO"</span>, <span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_const[["SFO-SFO-SFO", 3]] 7 220.4991</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_const[["DFOP-SFO-SFO", 3]] 9 179.8933</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_tc[["SFO-SFO-SFO", 3]] 8 200.7663</span> +<span class="r-out co"><span class="r-pr">#></span> f_D24_2014_tc[["DFOP-SFO-SFO", 3]] 10 181.8933</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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div 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