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<h1>Calculate predicted environmental concentrations in soil</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_soil.R'><code>R/PEC_soil.R</code></a></small>
<div class="hidden name"><code>PEC_soil.Rd</code></div>
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<div class="ref-description">
<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>
<pre class="usage"><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>,
<span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
<span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
<span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>,
<span class='st'>"EFSA_2015"</span>), <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>rate</th>
<td><p>Application rate in units specified below</p></td>
</tr>
<tr>
<th>rate_units</th>
<td><p>Defaults to g/ha</p></td>
</tr>
<tr>
<th>interception</th>
<td><p>The fraction of the application rate that does not reach the soil</p></td>
</tr>
<tr>
<th>mixing_depth</th>
<td><p>Mixing depth in cm</p></td>
</tr>
<tr>
<th>PEC_units</th>
<td><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></td>
</tr>
<tr>
<th>PEC_pw_units</th>
<td><p>Only mg/L currently supported</p></td>
</tr>
<tr>
<th>interval</th>
<td><p>Period of the deeper mixing, defaults to 365, which is a year if
rate units are in days</p></td>
</tr>
<tr>
<th>n_periods</th>
<td><p>Number of periods to be considered for long term PEC calculations</p></td>
</tr>
<tr>
<th>tillage_depth</th>
<td><p>Periodic (see interval) deeper mixing in cm</p></td>
</tr>
<tr>
<th>chent</th>
<td><p>An optional chent object holding substance specific information. Can
also be a name for the substance as a character string</p></td>
</tr>
<tr>
<th>DT50</th>
<td><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></td>
</tr>
<tr>
<th>Koc</th>
<td><p>If specified, overrides Koc endpoints from a chent object</p></td>
</tr>
<tr>
<th>Kom</th>
<td><p>Calculated from Koc by default, but can explicitly be specified
as Kom here</p></td>
</tr>
<tr>
<th>t_avg</th>
<td><p>Averaging times for time weighted average concentrations</p></td>
</tr>
<tr>
<th>scenarios</th>
<td><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",
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.</p></td>
</tr>
<tr>
<th>porewater</th>
<td><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
(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015,
p. 13).</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The predicted concentration in soil</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>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>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>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>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> scenario
#> t_avg default
#> 0 0.1</div><div class='input'>
<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span>
<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#> 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='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> 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='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span>
<span class='co'># Metabolite M2</span>
<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span>
<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span>
<span class='no'>results_pfm</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)
<span class='no'>results_pfm_pw</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
Johannes Ranke
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