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diff --git a/docs/PEC_soil.html b/docs/PEC_soil.html deleted file mode 100644 index 9a10757..0000000 --- a/docs/PEC_soil.html +++ /dev/null @@ -1,231 +0,0 @@ -<!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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