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diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 71f1f5d1..2311a67e 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -1,84 +1,71 @@ <!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, shrink-to-fit=no"><meta name="description" content="The datasets were extracted from the active substance evaluation dossier +<!-- 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, shrink-to-fit=no"><title>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018"><meta name="description" content="The datasets were extracted from the active substance evaluation dossier published by EFSA. 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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."><title>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018"><meta property="og:description" content="The datasets were extracted from the active substance evaluation dossier +constrained by data protection regulations."><meta property="og:description" content="The 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> +constrained by data protection regulations."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1> + + <h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/dimethenamid_2018.R" class="external-link"><code>R/dimethenamid_2018.R</code></a></small> <div class="d-none name"><code>dimethenamid_2018.Rd</code></div> </div> @@ -177,11 +164,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># influence of ill-defined rate constants that have</span></span></span> <span class="r-in"><span><span class="co"># extremely small values:</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># If we disregards ill-defined rate constants, the results</span></span></span> <span class="r-in"><span><span class="co"># look more plausible, but the truth is likely to be in</span></span></span> <span class="r-in"><span><span class="co"># between these variants</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># We can also specify a default value for the failing</span></span></span> <span class="r-in"><span><span class="co"># log parameters, to mimic FOCUS guidance</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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> @@ -195,11 +182,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># graphics device used)</span></span></span> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:14:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:14:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:56:10 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:56:10 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -212,7 +199,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 302.335 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 295.43 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -266,9 +253,9 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1264 -0.2186 0.4714</span> <span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1509 -0.2547 0.5565</span> <span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3891 -1.6962 -1.0819</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8231 1.0161</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8307 1.0085</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1205 0.1549</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8167 8.0078</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> @@ -289,7 +276,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8154 8.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.5956 -0.8167 8.0078</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6437 0.2784 1.0091</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 0.9929 0.3719 1.6139</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4530 0.1522 0.7537</span> @@ -300,8 +287,8 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8231 1.0161</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1203 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9196 0.8307 1.0085</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1377 0.1205 0.1549</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> @@ -338,23 +325,23 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - 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