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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:36:50 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:36:50 +0100
commitc951aa74553ac1be9ffc4930322b703453abce82 (patch)
tree1ef30d64314cebc5c28fa74c93cb811007d46979 /docs/reference/PEC_soil.html
parent7dd316f2ebc3edc321431419a02ccbd6ea47fef3 (diff)
parent4079a2c496aa4e8c6dc2a93afedcbedbf7a852b5 (diff)
Merge remote-tracking branch 'refs/remotes/origin/main'
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diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index f7e1da5..447e01d 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -1,4 +1,5 @@
<!DOCTYPE html>
+<<<<<<< HEAD
<!-- 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>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</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="Calculate predicted environmental concentrations in soil — PEC_soil"><meta property="og:description" content="This is a basic calculation of a contaminant concentration in bulk soil
based on complete, instantaneous mixing. If an interval is given, an
attempt is made at calculating a long term maximum concentration using
@@ -39,11 +40,60 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- math
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate predicted environmental concentrations in soil</h1>
+=======
+<!-- 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="This is a basic calculation of a contaminant concentration in bulk soil
+based on complete, instantaneous mixing. If an interval is given, an
+attempt is made at calculating a long term maximum concentration using
+the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012
+and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</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="Calculate predicted environmental concentrations in soil — PEC_soil"><meta property="og:description" content="This is a basic calculation of a contaminant concentration in bulk soil
+based on complete, instantaneous mixing. If an interval is given, an
+attempt is made at calculating a long term maximum concentration using
+the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012
+and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- 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]>
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+<![endif]--></head><body>
+ <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+ <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+
+ <a class="navbar-brand me-2" href="../index.html">pfm</a>
+
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small>
+
+
+ <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+
+ <div id="navbar" class="collapse navbar-collapse ms-3">
+ <ul class="navbar-nav me-auto"><li class="active nav-item">
+ <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+ </ul><form class="form-inline my-2 my-lg-0" role="search">
+ <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div>
+
+>>>>>>> refs/remotes/origin/main
- <div class="hidden name"><code>PEC_soil.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">
+ <img src="" class="logo" alt=""><h1>Calculate predicted environmental concentrations in soil</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_soil.R" class="external-link"><code>R/PEC_soil.R</code></a></small>
+ <div class="d-none name"><code>PEC_soil.Rd</code></div>
</div>
- <div class="ref-description">
+ <div class="ref-description section level2">
<p>This is a basic calculation of a contaminant concentration in bulk soil
based on complete, instantaneous mixing. If an interval is given, an
attempt is made at calculating a long term maximum concentration using
@@ -51,7 +101,12 @@ the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012
and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p>
</div>
+<<<<<<< HEAD
<div id="ref-usage">
+=======
+ <div class="section level2">
+ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+>>>>>>> refs/remotes/origin/main
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil</span><span class="op">(</span></span>
<span> <span class="va">rate</span>,</span>
<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span>
@@ -78,8 +133,13 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p>
<span><span class="op">)</span></span></code></pre></div>
</div>
+<<<<<<< HEAD
<div id="arguments">
<h2>Arguments</h2>
+=======
+ <div class="section level2">
+ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+>>>>>>> refs/remotes/origin/main
<dl><dt>rate</dt>
<dd><p>Application rate in units specified below</p></dd>
@@ -195,14 +255,24 @@ soil concentrations? Based on equation (7) given in the PPR panel opinion
p. 13).</p></dd>
</dl></div>
+<<<<<<< HEAD
<div id="value">
<h2>Value</h2>
+=======
+ <div class="section level2">
+ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>The predicted concentration in soil</p>
</div>
+<<<<<<< HEAD
<div id="details">
<h2>Details</h2>
+=======
+ <div class="section level2">
+ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>This assumes that the complete load to soil during the time specified by
'interval' (typically 365 days) is dosed at once. As in the PPR panel
opinion cited below (EFSA PPR panel 2012), only temperature correction using the
@@ -210,36 +280,51 @@ Arrhenius equation is performed.</p>
<p>Total soil and porewater PEC values for the scenarios as defined in the EFSA
guidance (2017, p. 14/15) can easily be calculated.</p>
</div>
+<<<<<<< HEAD
<div id="note">
<h2>Note</h2>
+=======
+ <div class="section level2">
+ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>While time weighted average (TWA) concentrations given in the examples
from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not
true for the TWA concentrations given for the same example in the EFSA guidance
from 2017 (p. 92).</p>
<p>According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be
- taken into account for the EFSA 2017 scenarios, using the evaluation depth
- (here mixing depth) as the depth of the layer from which leaching takes
- place. However, as the amount leaching below the evaluation depth
- (often 5 cm) will partly be mixed back during tillage, the default in this function
- is to use the tillage depth for the calculation of the leaching rate.</p>
+taken into account for the EFSA 2017 scenarios, using the evaluation depth
+(here mixing depth) as the depth of the layer from which leaching takes
+place. However, as the amount leaching below the evaluation depth
+(often 5 cm) will partly be mixed back during tillage, the default in this function
+is to use the tillage depth for the calculation of the leaching rate.</p>
<p>If temperature information is available in the selected scenarios, as
+<<<<<<< HEAD
e.g. in the EFSA scenarios, the DT50 for groundwater modelling
(destination 'PECgw') is taken from the chent object, otherwise the DT50
with destination 'PECsoil'.</p>
</div>
<div id="references">
<h2>References</h2>
+=======
+e.g. in the EFSA scenarios, the DT50 for groundwater modelling
+(destination 'PECgw') is taken from the chent object, otherwise the DT50
+with destination 'PECsoil'.</p>
+ </div>
+ <div class="section level2">
+ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>EFSA Panel on Plant Protection Products and their Residues (2012)
- Scientific Opinion on the science behind the guidance for scenario
- selection and scenario parameterisation for predicting environmental
- concentrations of plant protection products in soil. <em>EFSA Journal</em>
- <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p>
+Scientific Opinion on the science behind the guidance for scenario
+selection and scenario parameterisation for predicting environmental
+concentrations of plant protection products in soil. <em>EFSA Journal</em>
+<b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p>
<p>EFSA (European Food Safety Authority) 2017) EFSA guidance document for
- predicting environmental concentrations of active substances of plant
- protection products and transformation products of these active substances
- in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982
- doi:10.2903/j.efsa.2017.4982</p>
+predicting environmental concentrations of active substances of plant
+protection products and transformation products of these active substances
+in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982
+doi:10.2903/j.efsa.2017.4982</p>
<p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for
+<<<<<<< HEAD
predicting environmental concentrations of active substances of plant
protection products and transformation products of these active substances
in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
@@ -252,6 +337,20 @@ from 2017 (p. 92).</p>
<div id="ref-examples">
<h2>Examples</h2>
+=======
+predicting environmental concentrations of active substances of plant
+protection products and transformation products of these active substances
+in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
+doi:10.2903/j.efsa.2015.4093</p>
+ </div>
+ <div class="section level2">
+ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+ <p>Johannes Ranke</p>
+ </div>
+
+ <div class="section level2">
+ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+>>>>>>> refs/remotes/origin/main
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> scenario</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> t_avg default</span>
@@ -297,6 +396,7 @@ from 2017 (p. 92).</p>
<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
</code></pre></div>
</div>
+<<<<<<< HEAD
</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>
@@ -313,11 +413,30 @@ from 2017 (p. 92).</p>
</div>
</footer></div>
+=======
+ </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+ </nav></aside></div>
+
+
+ <footer><div class="pkgdown-footer-left">
+ <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+ <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>
+>>>>>>> refs/remotes/origin/main
+
+<<<<<<< HEAD
+=======
+>>>>>>> refs/remotes/origin/main
</body></html>

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