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authorJohannes Ranke <jranke@uni-bremen.de>2024-08-26 17:11:43 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2024-08-26 17:11:43 +0200
commit913c383880da2a5f4bdb71c8a82107afbad6ef13 (patch)
tree1c5a988748fc49fde4c279a96650deb26039b711 /docs/reference/PEC_soil.html
parent9e62ed638e530a5cebebf491de055caca49a56ef (diff)
parent396ba6c42252426a132be56b9f417786a1f276e3 (diff)
Merge branch 'main' into crop_group
Diffstat (limited to 'docs/reference/PEC_soil.html')
-rw-r--r--docs/reference/PEC_soil.html101
1 files changed, 46 insertions, 55 deletions
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 @@
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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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/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
+and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><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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+and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."></head><body>
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- <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>
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- <p></p><p>Developed by Johannes Ranke.</p>
+ <p>Developed by Johannes Ranke.</p>
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+ <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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