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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:36:50 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 13:36:50 +0100
commitc951aa74553ac1be9ffc4930322b703453abce82 (patch)
tree1ef30d64314cebc5c28fa74c93cb811007d46979 /docs/reference/PEC_sw_focus.html
parent7dd316f2ebc3edc321431419a02ccbd6ea47fef3 (diff)
parent4079a2c496aa4e8c6dc2a93afedcbedbf7a852b5 (diff)
Merge remote-tracking branch 'refs/remotes/origin/main'
Diffstat (limited to 'docs/reference/PEC_sw_focus.html')
-rw-r--r--docs/reference/PEC_sw_focus.html149
1 files changed, 140 insertions, 9 deletions
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 605d2cc..c5efeb9 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -1,9 +1,14 @@
<!DOCTYPE html>
+<<<<<<< HEAD
<!-- 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=1.0"><title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.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"><!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus"><meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+=======
+<!-- 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 reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+>>>>>>> refs/remotes/origin/main
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
single application. At current, this is not done automatically in
this implementation. Only Step 1 PECs are calculated. However,
+<<<<<<< HEAD
input files can be generated that are suitable as input for
the FOCUS calculator."><!-- 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>
@@ -41,11 +46,59 @@ the FOCUS calculator."><!-- mathjax --><script src="https://cdnjs.cloudflare.com
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate PEC surface water at FOCUS Step 1</h1>
+=======
+input files are generated that are suitable as input also for Step 2
+to be used with the FOCUS calculator."><title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • 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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/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 PEC surface water at FOCUS Step 1 — PEC_sw_focus"><meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+authored by Michael Klein, in R. Note that results for multiple
+applications should be compared to the corresponding results for a
+single application. At current, this is not done automatically in
+this implementation. Only Step 1 PECs are calculated. However,
+input files are generated that are suitable as input also for Step 2
+to be used with the FOCUS calculator."><!-- 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>
+ <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">
- <div class="hidden name"><code>PEC_sw_focus.Rd</code></div>
+ <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="">0.6.0</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></div>
+
+>>>>>>> refs/remotes/origin/main
+
+ </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 PEC surface water at FOCUS Step 1</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_focus.R" class="external-link"><code>R/PEC_sw_focus.R</code></a></small>
+ <div class="d-none name"><code>PEC_sw_focus.Rd</code></div>
</div>
- <div class="ref-description">
+ <div class="ref-description section level2">
<p>This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
@@ -55,7 +108,12 @@ input files can be generated that are suitable as input for
the FOCUS calculator.</p>
</div>
+<<<<<<< HEAD
<div id="ref-usage">
+=======
+ <div class="section level2">
+ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+>>>>>>> refs/remotes/origin/main
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_focus</span><span class="op">(</span></span>
<span> <span class="va">parent</span>,</span>
<span> <span class="va">rate</span>,</span>
@@ -73,6 +131,7 @@ the FOCUS calculator.</p>
<span> met_form_water <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> txt_file <span class="op">=</span> <span class="st">"pesticide.txt"</span>,</span>
<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<<<<<<< HEAD
<span> append <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
@@ -82,6 +141,17 @@ the FOCUS calculator.</p>
<dl><dt>parent</dt>
<dd><p>A list containing substance specific parameters, e.g.
conveniently generated by [chent_focus_sw].</p></dd>
+=======
+<span> append <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div class="section level2">
+ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+ <dl><dt>parent</dt>
+<dd><p>A list containing substance specific parameters, e.g.
+conveniently generated by <a href="chent_focus_sw.html">chent_focus_sw</a>.</p></dd>
+>>>>>>> refs/remotes/origin/main
<dt>rate</dt>
@@ -103,7 +173,11 @@ applications are given explicitly</p></dd>
<dt>met</dt>
<dd><p>A list containing metabolite specific parameters. e.g.
+<<<<<<< HEAD
conveniently generated by [chent_focus_sw]. If not NULL,
+=======
+conveniently generated by <a href="chent_focus_sw.html">chent_focus_sw</a>. If not NULL,
+>>>>>>> refs/remotes/origin/main
the PEC is calculated for this compound, not the parent.</p></dd>
@@ -111,18 +185,30 @@ the PEC is calculated for this compound, not the parent.</p></dd>
<dd><p>The fraction of the application rate reaching the waterbody
via drift. If NA, this is derived from the scenario name and the number
of applications via the drift data defined by the
+<<<<<<< HEAD
[FOCUS_Step_12_scenarios]</p></dd>
+=======
+<a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd>
+>>>>>>> refs/remotes/origin/main
<dt>f_rd</dt>
<dd><p>The fraction of the amount applied reaching the waterbody via
+<<<<<<< HEAD
runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the -->
+=======
+runoff/drainage. At Step 1, it is assumed to be 10%, be it the
+>>>>>>> refs/remotes/origin/main
parent or a metabolite</p></dd>
<dt>scenario</dt>
<dd><p>The name of the scenario. Must be one of the scenario
+<<<<<<< HEAD
names given in [FOCUS_Step_12_scenarios]</p></dd>
+=======
+names given in <a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd>
+>>>>>>> refs/remotes/origin/main
<dt>region</dt>
@@ -158,25 +244,39 @@ should be written</p></dd>
<dt>append</dt>
+<<<<<<< HEAD
<dd><p>Should the input text file be appended, if it exists?</p></dd>
</dl></div>
<div id="note">
<h2>Note</h2>
+=======
+<dd><p>Should the input text file be appended?</p></dd>
+
+</dl></div>
+ <div class="section level2">
+ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>The formulas for input to the waterbody via runoff/drainage of the
- parent and subsequent formation of the metabolite in water is not
- documented in the model description coming with the calculator. As one would
- expect, this appears to be (as we get the same results) calculated by
- multiplying the application rate with the molar weight
- correction and the formation fraction in water/sediment systems.</p>
+parent and subsequent formation of the metabolite in water is not
+documented in the model description coming with the calculator. As one would
+expect, this appears to be (as we get the same results) calculated by
+multiplying the application rate with the molar weight
+correction and the formation fraction in water/sediment systems.</p>
<p>Step 2 is not implemented.</p>
</div>
+<<<<<<< HEAD
<div id="references">
<h2>References</h2>
+=======
+ <div class="section level2">
+ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+>>>>>>> refs/remotes/origin/main
<p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
- FOrum for the Co-ordination of pesticde fate models and their USe.
- http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p>
+FOrum for the Co-ordination of pesticde fate models and their USe.
+http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf</p>
<p>Website of the Steps 1 and 2 calculator at the Joint Research
+<<<<<<< HEAD
Center of the European Union:
http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
</div>
@@ -186,6 +286,17 @@ should be written</p></dd>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span>
<span class="r-in"><span><span class="va">dummy_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></span>
+=======
+Center of the European Union:
+http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
+ </div>
+
+ <div class="section level2">
+ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span>
+<span class="r-in"><span><span class="va">dummy_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, append <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+>>>>>>> refs/remotes/origin/main
<span class="r-out co"><span class="r-pr">#&gt;</span> $f_drift</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -284,6 +395,7 @@ should be written</p></dd>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
</code></pre></div>
</div>
+<<<<<<< HEAD
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
@@ -300,11 +412,30 @@ should be written</p></dd>
</div>
</footer></div>
+=======
+ </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+ </nav></aside></div>
+
+
+ <footer><div class="pkgdown-footer-left">
+ <p></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>
+</div>
+
+ </footer></div>
+>>>>>>> refs/remotes/origin/main
+
+<<<<<<< HEAD
+=======
+>>>>>>> refs/remotes/origin/main
</body></html>

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