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diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 46c92f4..e86dd6d 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,51 +1,42 @@ <!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="This is a basic calculation of a contaminant concentration in bulk soil +<!-- 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>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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil"><meta name="description" content="This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. 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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]> -<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> +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."></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"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><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="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</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"> <span class="navbar-toggler-icon"></span> </button> <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> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></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> + + <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> @@ -88,99 +79,101 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>rate</dt> + + +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>Application rate in units specified below</p></dd> -<dt>rate_units</dt> +<dt id="arg-rate-units">rate_units<a class="anchor" aria-label="anchor" href="#arg-rate-units"></a></dt> <dd><p>Defaults to g/ha</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>The fraction of the application rate that does not reach the soil</p></dd> -<dt>mixing_depth</dt> +<dt id="arg-mixing-depth">mixing_depth<a class="anchor" aria-label="anchor" href="#arg-mixing-depth"></a></dt> <dd><p>Mixing depth in cm</p></dd> -<dt>PEC_units</dt> +<dt id="arg-pec-units">PEC_units<a class="anchor" aria-label="anchor" href="#arg-pec-units"></a></dt> <dd><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></dd> -<dt>PEC_pw_units</dt> +<dt id="arg-pec-pw-units">PEC_pw_units<a class="anchor" aria-label="anchor" href="#arg-pec-pw-units"></a></dt> <dd><p>Only mg/L currently supported</p></dd> -<dt>interval</dt> +<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a></dt> <dd><p>Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation units are in days</p></dd> -<dt>n_periods</dt> +<dt id="arg-n-periods">n_periods<a class="anchor" aria-label="anchor" href="#arg-n-periods"></a></dt> <dd><p>Number of periods to be considered for long term PEC calculations</p></dd> -<dt>tillage_depth</dt> +<dt id="arg-tillage-depth">tillage_depth<a class="anchor" aria-label="anchor" href="#arg-tillage-depth"></a></dt> <dd><p>Periodic (see interval) deeper mixing in cm</p></dd> -<dt>leaching_depth</dt> +<dt id="arg-leaching-depth">leaching_depth<a class="anchor" aria-label="anchor" href="#arg-leaching-depth"></a></dt> <dd><p>EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage depth are taken into account in this implementation.</p></dd> -<dt>crop</dt> +<dt id="arg-crop">crop<a class="anchor" aria-label="anchor" href="#arg-crop"></a></dt> <dd><p>Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping cycle per year are currently supported.</p></dd> -<dt>cultivation</dt> +<dt id="arg-cultivation">cultivation<a class="anchor" aria-label="anchor" href="#arg-cultivation"></a></dt> <dd><p>Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios other than EFSA_2017</p></dd> -<dt>chent</dt> +<dt id="arg-chent">chent<a class="anchor" aria-label="anchor" href="#arg-chent"></a></dt> <dd><p>An optional chent object holding substance specific information. Can also be a name for the substance as a character string</p></dd> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero degradation is assumed</p></dd> -<dt>FOMC</dt> +<dt id="arg-fomc">FOMC<a class="anchor" aria-label="anchor" href="#arg-fomc"></a></dt> <dd><p>If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC is calculated using these parameters without temperature correction</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>If specified, overrides Koc endpoints from a chent object</p></dd> -<dt>Kom</dt> +<dt id="arg-kom">Kom<a class="anchor" aria-label="anchor" href="#arg-kom"></a></dt> <dd><p>Calculated from Koc by default, but can explicitly be specified as Kom here</p></dd> -<dt>t_avg</dt> +<dt id="arg-t-avg">t_avg<a class="anchor" aria-label="anchor" href="#arg-t-avg"></a></dt> <dd><p>Averaging times for time weighted average concentrations</p></dd> -<dt>t_act</dt> +<dt id="arg-t-act">t_act<a class="anchor" aria-label="anchor" href="#arg-t-act"></a></dt> <dd><p>Time series for actual concentrations</p></dd> -<dt>scenarios</dt> +<dt id="arg-scenarios">scenarios<a class="anchor" aria-label="anchor" href="#arg-scenarios"></a></dt> <dd><p>If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", @@ -190,12 +183,12 @@ and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also model and scenario adjustment factors from the EFSA guidance are used.</p></dd> -<dt>leaching</dt> +<dt id="arg-leaching">leaching<a class="anchor" aria-label="anchor" href="#arg-leaching"></a></dt> <dd><p>Should leaching be taken into account? The default is FALSE, except when the EFSA_2017 scenarios are used.</p></dd> -<dt>porewater</dt> +<dt id="arg-porewater">porewater<a class="anchor" aria-label="anchor" href="#arg-porewater"></a></dt> <dd><p>Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion @@ -205,9 +198,7 @@ p. 13).</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The predicted concentration in soil</p> + <p>The predicted concentration in soil</p> </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> @@ -305,23 +296,23 @@ doi:10.2903/j.efsa.2015.4093</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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </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="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</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> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> |