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| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-09-27 23:00:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-09-27 23:00:48 +0200 |
| commit | 12a31f4c130c551f82232d9ef7dfb608bd52c53f (patch) | |
| tree | 2525ab1ea4102a6edddbd0c2f03f4a851bf2f9c5 /docs/PEC_soil.html | |
| parent | 0d958ab6f84b569b5437f231c56004890c4ae23b (diff) | |
Reorganise repository using standard package layout
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| -rw-r--r-- | docs/PEC_soil.html | 231 |
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diff --git a/docs/PEC_soil.html b/docs/PEC_soil.html new file mode 100644 index 0000000..9a10757 --- /dev/null +++ b/docs/PEC_soil.html @@ -0,0 +1,231 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>PEC_soil. pfm 0.3-8</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" +Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">pfm 0.3-8</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1>Calculate predicted environmental concentrations in soil</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">rate_units</span> <span class="argument">=</span> <span class="string">"g/ha"</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="argument">mixing_depth</span> <span class="argument">=</span> <span class="number">5</span><span class="keyword">,</span> + <span class="argument">PEC_units</span> <span class="argument">=</span> <span class="string">"mg/kg"</span><span class="keyword">,</span> <span class="argument">PEC_pw_units</span> <span class="argument">=</span> <span class="string">"mg/L"</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> + <span class="argument">n_periods</span> <span class="argument">=</span> <span class="number">Inf</span><span class="keyword">,</span> <span class="argument">tillage_depth</span> <span class="argument">=</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">chent</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> + <span class="argument">Koc</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> <span class="argument">Kom</span> <span class="argument">=</span> <span class="symbol">Koc</span><span class="keyword">/</span><span class="number">1.724</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"default"</span><span class="keyword">,</span> + <span class="string">"EFSA_2015"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>rate</dt> + <dd>Application rate in units specified below</dd> + <dt>rate_units</dt> + <dd>Defaults to g/ha</dd> + <dt>interception</dt> + <dd>The fraction of the application rate that does not reach the soil</dd> + <dt>mixing_depth</dt> + <dd>Mixing depth in cm</dd> + <dt>PEC_units</dt> + <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd> + <dt>PEC_pw_units</dt> + <dd>Only mg/L currently supported</dd> + <dt>interval</dt> + <dd>Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days</dd> + <dt>n_periods</dt> + <dd>Number of periods to be considered for long term PEC calculations</dd> + <dt>tillage_depth</dt> + <dd>Periodic (see interval) deeper mixing in cm</dd> + <dt>chent</dt> + <dd>An optional chent object holding substance specific information. Can +also be a name for the substance as a character string</dd> + <dt>DT50</dt> + <dd>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</dd> + <dt>Koc</dt> + <dd>If specified, overrides Koc endpoints from a chent object</dd> + <dt>Kom</dt> + <dd>Calculated from Koc by default, but can explicitly be specified +as Kom here</dd> + <dt>t_avg</dt> + <dd>Averaging times for time weighted average concentrations</dd> + <dt>scenarios</dt> + <dd>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", +the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when +'chents' is specified, the DegT50 with destination 'PECgw' will be used), +and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +model and scenario adjustment factors from the EFSA guidance are used.</dd> + <dt>porewater</dt> + <dd>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 +(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +p. 13).</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> +The predicted concentration in soil +</dl></p> + + </div> + + <div class="Description"> + <h2>Description</h2> + + <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 +the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p> + + </div> + + <div class="Details"> + <h2>Details</h2> + + <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 (PPR panel 2012), only temperature correction using the +Arrhenius equation is performed.</p> + + <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA +guidance (2015, p. 13) can easily be calculated.</p> + + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>If temperature information is available in the selected scenarios, as + 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="References"> + <h2>References</h2> + + <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> + + <p>EFSA (European Food Safety Authority) (2015) 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>13</b>(4) 4093 + doi:10.2903/j.efsa.2015.4093</p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0.25</span><span class="keyword">)</span></div> +<div class='output'> scenario +t_avg default + 0 0.1 +</div> +<div class='input'> +<span class="comment"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> +<span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span></div> +<div class='output'> scenario +t_avg CTN CTC CTS + 0 21.96827 11.53750 9.145259 + 21 21.78517 11.40701 9.017370 +</div> +<div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div> +<div class='output'> scenario +t_avg CLN CLC CLS + 0 0.7589401 0.6674322 0.9147861 + 21 0.7506036 0.6590345 0.8987279 +</div> +<div class='input'> +<span class="comment"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> +<span class="comment"># Metabolite M2</span> +<span class="comment"># Calculate total and porewater soil concentrations for tier 1 scenarios</span> +<span class="comment"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> +<span class="symbol">results_pfm</span> <span class="assignement"><-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span> +<span class="symbol">results_pfm_pw</span> <span class="assignement"><-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>PEC_soil</li> + </ul> + <ul> + + </ul> --> + + + + <h2>Author</h2> + +Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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