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diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index 63e1730..e1f9a53 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,4 +1,42 @@ <!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>Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • 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" 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+ <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Subset of EFSA crop interception default values for groundwater modelling</h1> +======= <!-- 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="Subset of EFSA crop interception default values for groundwater modelling"><title>Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • 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=" 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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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,13 +85,25 @@ <p>Subset of EFSA crop interception default values for groundwater modelling</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_GW_interception_2014</span></span></code></pre></div> + </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A matrix containing interception values, currently only for some selected crops</p> + </div> + <div id="source"> + <h2>Source</h2> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A matrix containing interception values, currently only for some selected crops</p> </div> <div class="section level2"> <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> +>>>>>>> refs/remotes/origin/main <p>European Food Safety Authority (2014) EFSA Guidance Document for evaluating laboratory and field dissipation studies to obtain DegT50 values of active substances of plant protection products and transformation @@ -60,6 +111,11 @@ products of these active substances in soil. <em>EFSA Journal</em> <b>12</b>(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662</p> </div> +<<<<<<< HEAD + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_GW_interception_2014</span></span></span> +======= <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="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> @@ -91,6 +147,7 @@ products of these active substances in soil. <em>EFSA Journal</em> <span class="r-in"><span> file <span class="op">=</span> <span class="st">"../data/EFSA_GW_interception_2014.RData"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="va">EFSA_GW_interception_2014</span></span></span> +>>>>>>> refs/remotes/origin/main <span class="r-out co"><span class="r-pr">#></span> BBCH</span> <span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> <span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80</span> @@ -102,6 +159,24 @@ products of these active substances in soil. <em>EFSA Journal</em> <span class="r-out co"><span class="r-pr">#></span> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -115,10 +190,16 @@ products of these active substances in soil. <em>EFSA Journal</em> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index b424de9..371f27e 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -1,4 +1,42 @@ <!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>Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" 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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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,7 +85,28 @@ <p>Subset of EFSA crop washoff default values</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_washoff_2017</span></span></code></pre></div> + </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A matrix containing wash-off factors, currently only for some selected crops</p> + </div> + <div id="source"> + <h2>Source</h2> + <p>European Food Safety Authority (2017) 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>15</b>(10) 4982 + doi:10.2903/j.efsa.2017.4982</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_washoff_2017</span></span></span> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A matrix containing wash-off factors, currently only for some selected crops</p> @@ -91,6 +151,7 @@ doi:10.2903/j.efsa.2017.4982</p> <span class="r-in"><span> file <span class="op">=</span> <span class="st">"../data/EFSA_washoff_2017.RData"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="va">EFSA_washoff_2017</span></span></span> +>>>>>>> refs/remotes/origin/main <span class="r-out co"><span class="r-pr">#></span> BBCH</span> <span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> <span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35</span> @@ -102,6 +163,24 @@ doi:10.2903/j.efsa.2017.4982</p> <span class="r-out co"><span class="r-pr">#></span> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -115,10 +194,16 @@ doi:10.2903/j.efsa.2017.4982</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 2e9982b..4b6b993 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,4 +1,43 @@ <!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>A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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The +soil definitions are from page 46ff. from FOCUS (2012)."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>A very small subset of the FOCUS Groundwater scenario definitions</h1> +======= <!-- 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="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012)."><title>A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • 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="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012"><meta property="og:description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012)."><!-- 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]> @@ -34,6 +73,7 @@ soil definitions are from page 46ff. from FOCUS (2012)."><!-- mathjax --><script </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -49,6 +89,104 @@ soil definitions are from page 46ff. from FOCUS (2012)."><!-- mathjax --><script soil definitions are from page 46ff. from FOCUS (2012).</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_GW_scenarios_2012</span></span></code></pre></div> + </div> + + <div id="format"> + <h2>Format</h2> + <p>An object of class <code>list</code> of length 2.</p> + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_GW_scenarios_2012</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $names</span> +<span class="r-out co"><span class="r-pr">#></span> Cha Ham Jok Kre Oke </span> +<span class="r-out co"><span class="r-pr">#></span> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" </span> +<span class="r-out co"><span class="r-pr">#></span> Pia Por Sev Thi </span> +<span class="r-out co"><span class="r-pr">#></span> "Piacenza" "Porto" "Sevilla" "Thiva" </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $soils</span> +<span class="r-out co"><span class="r-pr">#></span> location horizon number pH_H2O perc_clay perc_oc rel_deg</span> +<span class="r-out co"><span class="r-pr">#></span> 1 Cha Ap 1 8.0 30.0 1.39 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Cha B1 2 8.1 31.0 0.93 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 3 Cha B2 3 8.2 25.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 4 Cha II C1 4 8.5 26.0 0.30 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Cha II C1 5 8.5 26.0 0.30 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Cha II C2 6 8.5 24.0 0.27 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Cha M 7 8.3 31.0 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Ham Ap 1 6.4 7.2 1.50 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 9 Ham BvI 2 5.6 6.7 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 Ham BvII 3 5.6 0.9 0.20 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 12 Ham Cv 5 5.5 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 13 Ham Cv 6 5.5 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 14 Jok Ap 1 6.2 3.6 4.06 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 15 Jok Bs 2 5.6 1.8 0.84 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 16 Jok BC1 3 5.4 1.2 0.36 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 17 Jok BC2 4 5.4 1.7 0.29 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 18 Jok BC2 5 5.4 1.7 0.29 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 19 Jok Cg 6 5.3 1.9 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 Kre <NA> 1 7.7 14.0 3.60 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 21 Kre <NA> 2 7.0 25.0 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 22 Kre <NA> 3 7.1 27.0 0.50 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 23 Kre <NA> 4 7.1 27.0 0.50 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 24 Kre <NA> 5 7.1 27.0 0.50 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 25 Oke A 1 5.8 18.0 2.20 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 26 Oke Bw1 2 6.3 17.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 27 Oke BC 3 6.5 14.0 0.40 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 28 Oke C 4 6.6 9.0 0.10 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 29 Oke C 5 6.6 9.0 0.10 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 30 Pia Ap 1 7.0 15.0 1.26 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 31 Pia Ap 2 7.0 15.0 1.26 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 32 Pia Bw 3 6.3 7.0 0.47 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 33 Pia Bw 4 6.3 7.0 0.47 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 34 Pia 2C 5 6.4 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 35 Pia 2C 6 6.4 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 36 Por <NA> 1 4.9 10.0 1.42 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 37 Por <NA> 2 4.8 8.0 0.78 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 38 Por <NA> 3 4.8 8.0 0.78 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 39 Por <NA> 4 4.8 8.0 0.78 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 Sev <NA> 1 7.3 14.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 41 Sev <NA> 2 7.3 13.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 42 Sev <NA> 3 7.8 15.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 43 Sev <NA> 4 8.1 16.0 0.58 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 44 Sev <NA> 5 8.1 16.0 0.58 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 45 Sev <NA> 6 8.2 22.0 0.49 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 46 Thi Ap1 1 7.7 25.3 0.74 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 47 Thi Ap2 2 7.7 25.3 0.74 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 48 Thi Bw 3 7.8 29.6 0.57 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 49 Thi Bw 4 7.8 31.9 0.31 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 50 Thi Ck1 5 7.8 32.9 0.18 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 51 Thi Ck1 6 7.8 32.9 0.18 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_GW_scenarios_2012</span></span></code></pre></div> @@ -143,10 +281,16 @@ http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index bcf71ed..259e0c5 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,4 +1,43 @@ <!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>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • 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=" 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class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> +======= <!-- 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="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear."><title>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • 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="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios"><meta property="og:description" content="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear."><!-- 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]> @@ -34,6 +73,7 @@ The text file is not included in the package as its licence is not clear."><!-- </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -50,6 +90,75 @@ The text file is not included in the package as its licence is not clear.</p> </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A list containing the scenario names in a character vector called 'names', + the drift percentiles in a matrix called 'drift', interception percentages in + a matrix called 'interception' and the runoff/drainage percentages for Step 2 + calculations in a matrix called 'rd'.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span> +<span class="r-in"><span> <span class="va">scenario_path</span> <span class="op"><-</span> <span class="st">"inst/extdata/FOCUS_Step_12_scenarios.txt"</span></span></span> +<span class="r-in"><span> <span class="va">scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">9</span><span class="op">:</span><span class="fl">38</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sce</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'scenarios' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op"><-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">sce_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">rd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce_2' not found</span> +<span class="r-in"><span> <span class="va">rd_mat</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory'</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in gzfile(file, "wb"):</span> cannot open the connection</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And this is the resulting data</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_Step_12_scenarios</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> list()</span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list containing the scenario names in a character vector called 'names', @@ -246,10 +355,16 @@ calculations in a matrix called 'rd'.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 226d44f..6c46259 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,4 +1,42 @@ <!DOCTYPE html> +<<<<<<< HEAD +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta 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src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,8 +85,12 @@ <p>Actual and maximum moving window time average concentrations for FOMC kinetics</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">FOMC_actual_twa</span><span class="op">(</span></span> <span> alpha <span class="op">=</span> <span class="fl">1.0001</span>,</span> <span> beta <span class="op">=</span> <span class="fl">10</span>,</span> @@ -55,6 +98,16 @@ <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation @@ -63,6 +116,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>alpha</dt> <dd><p>Parameter of the FOMC model</p></dd> @@ -75,6 +129,15 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> </dl></div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -82,6 +145,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span>alpha <span class="op">=</span> <span class="fl">1.0001</span>, beta <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> actual twa</span> <span class="r-out co"><span class="r-pr">#></span> 0 1.00000000 NaN</span> @@ -97,6 +161,24 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <span class="r-out co"><span class="r-pr">#></span> 100 0.09088729 0.2397608</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -110,10 +192,16 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index e3a451e..b68df33 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,4 +1,44 @@ <!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>Groundwater ubiquity score based on Gustafson (1989) — GUS • 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" 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title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> +======= <!-- 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="The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><title>Groundwater ubiquity score 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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">GUS</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for numeric</span></span> @@ -75,8 +120,13 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>...</dt> <dd><p>Included in the generic to allow for further arguments later. Therefore this also had to be added to the specific methods.</p></dd> @@ -104,7 +154,11 @@ chyaml field, this information is used, with defaults specified below.</p></dd> <dt>degradation_value</dt> +<<<<<<< HEAD +<dd><p>Which of the available degradation values should +======= <dd><p>Which of the available degradation values should +>>>>>>> refs/remotes/origin/main be used?</p></dd> @@ -144,6 +198,17 @@ be Koc values at a concentration of 1 mg/L in the water phase.</p></dd> <dd><p>The number of digits used in the print method</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> + + +<p>A list with the DT50 and Koc used as well as the resulting score + of class GUS_result</p> + </div> + <div id="references"> + <h2>References</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> @@ -153,10 +218,34 @@ of class GUS_result</p> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> +>>>>>>> refs/remotes/origin/main <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. <em>Environmental toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> </div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -175,10 +264,16 @@ toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= 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+ <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Get the relative accumulation of an FOMC model over multiples of an interval</h1> + + <div class="hidden name"><code>PEC_FOMC_accu_rel.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Get the relative accumulation of an FOMC model over multiples of an interval</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_FOMC_accu_rel</span><span class="op">(</span><span class="va">n</span>, <span class="va">interval</span>, <span class="va">FOMC</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <!-- 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="Get the relative accumulation of an FOMC model over multiples of an interval"><title>Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • 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, 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src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -53,6 +105,7 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>n</dt> <dd><p>number of applications</p></dd> @@ -65,13 +118,36 @@ <dd><p>Named numeric vector containing the FOMC parameters alpha and beta</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>A numeric vector containing all n accumulation factors for the n applications</p> </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -85,10 +161,16 @@ </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 98ac3ac..447e01d 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,4 +1,46 @@ <!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 predicted environmental concentrations in soil — PEC_soil • 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" 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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]> +<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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in soil</h1> +======= <!-- 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 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 @@ -40,6 +82,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- math </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -58,8 +101,12 @@ 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).</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_soil</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> @@ -86,8 +133,13 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>Application rate in units specified below</p></dd> @@ -203,14 +255,24 @@ soil concentrations? Based on equation (7) given in the PPR panel opinion p. 13).</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The predicted concentration in soil</p> </div> +<<<<<<< HEAD + <div id="details"> + <h2>Details</h2> +======= <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> +>>>>>>> refs/remotes/origin/main <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 (EFSA PPR panel 2012), only temperature correction using the @@ -218,8 +280,13 @@ Arrhenius equation is performed.</p> <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.</p> </div> +<<<<<<< HEAD + <div id="note"> + <h2>Note</h2> +======= <div class="section level2"> <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> +>>>>>>> refs/remotes/origin/main <p>While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -231,12 +298,21 @@ place. However, as the amount leaching below the evaluation depth (often 5 cm) will partly be mixed back during tillage, the default in this function is to use the tillage depth for the calculation of the leaching rate.</p> <p>If temperature information is available in the selected scenarios, as +<<<<<<< HEAD + 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 id="references"> + <h2>References</h2> +======= 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="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> +>>>>>>> refs/remotes/origin/main <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 @@ -248,6 +324,20 @@ protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 doi:10.2903/j.efsa.2017.4982</p> <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for +<<<<<<< HEAD + 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> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= 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 @@ -260,6 +350,7 @@ doi:10.2903/j.efsa.2015.4093</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> scenario</span> <span class="r-out co"><span class="r-pr">#></span> t_avg default</span> @@ -305,6 +396,24 @@ 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> +<<<<<<< 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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -318,10 +427,16 @@ doi:10.2903/j.efsa.2015.4093</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index ddaa9d1..4119861 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -1,4 +1,56 @@ <!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 initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • 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 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class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate initial and accumulation PEC soil for a set of metabolites</h1> + + <div class="hidden name"><code>PEC_soil_mets.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Calculate initial and accumulation PEC soil for a set of metabolites</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil_mets</span><span class="op">(</span><span class="va">rate</span>, <span class="va">mw_parent</span>, <span class="va">mets</span>, interval <span class="op">=</span> <span class="fl">365</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <!-- 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" 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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> @@ -53,6 +105,7 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>Application rate in units specified below</p></dd> @@ -66,6 +119,34 @@ and columns "mw", "occ" and "DT50" holding their molecular weight, maximum occurrence in soil and their soil DT50</p></dd> +<<<<<<< HEAD + +<dt>interval</dt> +<dd><p>The interval for accumulation calculations</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments are passed to PEC_soil</p></dd> + +</dl></div> + + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <dt>interval</dt> <dd><p>The interval for accumulation calculations</p></dd> @@ -89,10 +170,16 @@ maximum occurrence in soil and their soil DT50</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 5068319..f8ee95d 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ 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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]> @@ -34,6 +73,7 @@ published on the CRC website"><!-- mathjax --><script src="https://cdnjs.cloudfl </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -49,8 +89,12 @@ published on the CRC website"><!-- mathjax --><script src="https://cdnjs.cloudfl published on the CRC website</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_drainage_UK</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> @@ -62,8 +106,13 @@ published on the CRC website</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>Application rate in g/ha</p></dd> @@ -93,12 +142,36 @@ published on the CRC website</p> <dd><p>A named numeric vector containing the model parameters</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The predicted concentration in surface water in µg/L</p> </div> +<<<<<<< HEAD + <div id="references"> + <h2>References</h2> + <p>HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + accessed 2019-09-27</p> +<p>Drainage PECs Version 1.0 (2015) Spreadsheet published at + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + accessed 2019-09-27</p> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance @@ -116,10 +189,29 @@ accessed 2019-09-27</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span><span class="fl">150</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -133,10 +225,16 @@ accessed 2019-09-27</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index d7e940c..2111058 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,4 +1,44 @@ <!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 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</div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> +======= <!-- 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 basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing with input via spray drift."><title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • 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, 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class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drift</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> applications <span class="op">=</span> <span class="fl">1</span>,</span> @@ -67,8 +112,13 @@ with input via spray drift.</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>Application rate in units specified below</p></dd> @@ -87,7 +137,11 @@ with input via spray drift.</p> <dt>drift_data</dt> +<<<<<<< HEAD +<dd><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] +======= <dd><p>Source of drift percentage data. If 'JKI', the <a href="drift_data_JKI.html">drift_data_JKI</a> +>>>>>>> refs/remotes/origin/main included in the package is used. If 'RF', the Rautmann formula is used, if implemented for the crop type and number of applications</p></dd> @@ -108,12 +162,26 @@ implemented for the crop type and number of applications</p></dd> <dd><p>Requested units for the calculated PEC. Only µg/L currently supported</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The predicted concentration in surface water</p> </div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -121,6 +189,7 @@ implemented for the crop type and number of applications</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> <span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.19000000 0.09666667 0.05000000 </span> @@ -144,6 +213,24 @@ implemented for the crop type and number of applications</p></dd> <span class="r-out co"><span class="r-pr">#></span> 0.01000000 </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -157,10 +244,16 @@ implemented for the crop type and number of applications</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index f57fc56..a1e135b 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -1,10 +1,52 @@ <!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 due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • 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 due to drainage as in Exposit 3 — PEC_sw_exposit_drainage"><meta property="og:description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, +======= <!-- 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 calculation described in the Exposit 3.02 spreadsheet file, +>>>>>>> refs/remotes/origin/main in the worksheet "Konzept Drainage". Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the calculations, between compounds with low mobility (group 1) and compounds with modest to high mobility (groups 2, 3 and 4). In this implementation, the group is derived only from the Koc, if not given explicitly. For +<<<<<<< HEAD +details, see the discussion of the function arguments below.'><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate PEC surface water due to drainage as in Exposit 3</h1> +======= details, see the discussion of the function arguments below.'><title>Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • 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 due to drainage as in Exposit 3 — PEC_sw_exposit_drainage"><meta property="og:description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Drainage". Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the @@ -44,6 +86,7 @@ details, see the discussion of the function arguments below.'><!-- mathjax --><s </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -64,8 +107,12 @@ the group is derived only from the Koc, if not given explicitly. For details, see the discussion of the function arguments below.</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_exposit_drainage</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> @@ -79,6 +126,15 @@ details, see the discussion of the function arguments below.</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Excel 3.02 spreadsheet available from @@ -86,6 +142,7 @@ details, see the discussion of the function arguments below.</p> </div> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>The application rate in g/ha</p></dd> @@ -97,6 +154,60 @@ details, see the discussion of the function arguments below.</p> <dt>Koc</dt> <dd><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger value of 550 L/kg is used in order to decide if Koc >> 500.</p></dd> +<<<<<<< HEAD + + +<dt>mobility</dt> +<dd><p>Overrides what is determined from the Koc.</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_drainage</dt> +<dd><p>The time between application and the drainage event, where degradation occurs, in days</p></dd> + + +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> + + +<dt>V_drainage</dt> +<dd><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for +autumn/winter/early spring.</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance + for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <dt>mobility</dt> @@ -147,6 +258,7 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $perc_drainage_total</span> <span class="r-out co"><span class="r-pr">#></span> spring autumn </span> @@ -162,6 +274,24 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -175,10 +305,16 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 73e3e43..db121b4 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,4 +1,43 @@ <!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 due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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described in the Exposit 3.02 spreadsheet file, +in the worksheet "Konzept Runoff".'><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" 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described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Runoff".'><!-- 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]> @@ -34,6 +73,7 @@ in the worksheet "Konzept Runoff".'><!-- mathjax --><script src="https://cdnjs.c </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -49,8 +89,12 @@ in the worksheet "Konzept Runoff".'><!-- mathjax --><script src="https://cdnjs.c in the worksheet "Konzept Runoff".</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_exposit_runoff</span><span class="op">(</span></span> <span> <span class="va">rate</span>,</span> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> @@ -64,6 +108,15 @@ in the worksheet "Konzept Runoff".</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Excel 3.02 spreadsheet available from @@ -71,6 +124,7 @@ in the worksheet "Konzept Runoff".</p> </div> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>rate</dt> <dd><p>The application rate in g/ha</p></dd> @@ -109,6 +163,35 @@ and the bound fraction.</p></dd> <dt>dilution</dt> <dd><p>The dilution factor</p></dd> +<<<<<<< HEAD + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance + for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= </dl></div> <div class="section level2"> @@ -134,6 +217,7 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> <span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> @@ -178,6 +262,24 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -191,10 +293,16 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index e758347..c5efeb9 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,9 +1,52 @@ <!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> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <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 @@ -44,6 +87,7 @@ to be used with the FOCUS calculator."><!-- mathjax --><script src="https://cdnj </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -60,12 +104,16 @@ 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.</p> +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> @@ -83,6 +131,17 @@ to be used with 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> + + <div id="arguments"> + <h2>Arguments</h2> + <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> @@ -92,6 +151,7 @@ to be used with the FOCUS calculator.</p> <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> @@ -113,7 +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> @@ -121,18 +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> @@ -168,11 +244,19 @@ 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 @@ -181,12 +265,28 @@ 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> <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> + + <div id="ref-examples"> + <h2>Examples</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"><-</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> @@ -196,6 +296,7 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> <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"><-</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">#></span> $f_drift</span> <span class="r-out co"><span class="r-pr">#></span> [1] 0</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -294,6 +395,24 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -307,10 +426,16 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 3432a75..c733ff8 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -1,11 +1,52 @@ <!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" 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crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface +>>>>>>> refs/remotes/origin/main water concentrations — PEC_sw_sed"><meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC 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> +<<<<<<< HEAD +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in sediment from surface +water concentrations</h1> +======= <![endif]--></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -36,6 +77,7 @@ PEC calculator"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -52,8 +94,12 @@ water concentrations</h1> PEC 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_sed</span><span class="op">(</span></span> <span> <span class="va">PEC_sw</span>,</span> <span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> @@ -65,8 +111,13 @@ PEC calculator</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>PEC_sw</dt> <dd><p>Numeric vector or matrix of surface water concentrations in µg/L for which the corresponding sediment concentration is to be estimated</p></dd> @@ -97,12 +148,26 @@ g/cm3)</p></dd> <dd><p>The units of the estimated sediment PEC value</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The predicted concentration in sediment</p> </div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -110,11 +175,30 @@ g/cm3)</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_sed</span><span class="op">(</span><span class="fu"><a href="PEC_sw_drift.html">PEC_sw_drift</a></span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, percentage <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 1 m </span> <span class="r-out co"><span class="r-pr">#></span> 2.130769 </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -128,10 +212,16 @@ g/cm3)</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex a32c4ab..8269e66 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex a32c4ab..8269e66 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 5973602..9ec61d5 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 2db42a3..02941cf 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index 0c3813f..dc25585 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -1,4 +1,42 @@ <!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 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maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa"><meta property="og:description" content="Actual and maximum moving window time average concentrations for SFO kinetics"><!-- 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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,6 +85,20 @@ <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO_actual_twa</span><span class="op">(</span>DT50 <span class="op">=</span> <span class="fl">1000</span>, times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, + 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO_actual_twa</span><span class="op">(</span>DT50 <span class="op">=</span> <span class="fl">1000</span>, times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> @@ -59,6 +112,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>DT50</dt> <dd><p>The half-life.</p></dd> @@ -67,6 +121,15 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> </dl></div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -74,6 +137,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SFO_actual_twa</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> actual twa</span> <span class="r-out co"><span class="r-pr">#></span> 0 1.0000000000 NaN</span> @@ -89,6 +153,24 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <span class="r-out co"><span class="r-pr">#></span> 100 0.0009765625 0.1441286</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -102,10 +184,16 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 0530260..3ea5599 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -1,4 +1,43 @@ <!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>Determine the SSLRC mobility classification for a 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a chemical substance from its Koc — SSLRC_mobility_classification"><meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website"><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" 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for a chemical substance from its Koc</h1> +======= <!-- 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 implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website"><title>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • 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 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SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification"><meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website"><!-- 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]> @@ -34,6 +73,7 @@ checked against the spreadsheet published on the CRC website"><!-- mathjax --><s </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -44,11 +84,23 @@ checked against the spreadsheet published on the CRC website"><!-- mathjax --><s <div class="d-none name"><code>SSLRC_mobility_classification.Rd</code></div> </div> +<<<<<<< HEAD + <div class="ref-description"> +======= <div class="ref-description section level2"> +>>>>>>> refs/remotes/origin/main <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="va">Koc</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="va">Koc</span><span class="op">)</span></span></code></pre></div> @@ -56,10 +108,37 @@ checked against the spreadsheet published on the CRC website</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>Koc</dt> <dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the classification and the percentage of the + compound transported per 10 mm drain water</p> + </div> + <div id="references"> + <h2>References</h2> + <p>HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + accessed 2019-09-27</p> +<p>Drainage PECs Version 1.0 (2015) Spreadsheet published at + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + accessed 2019-09-27</p> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> @@ -84,6 +163,7 @@ accessed 2019-09-27</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> <span class="r-out co"><span class="r-pr">#></span> [1] "Moderately mobile"</span> @@ -100,6 +180,24 @@ accessed 2019-09-27</p> <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -113,10 +211,16 @@ accessed 2019-09-27</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 8908748..18e5cdd 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,4 +1,46 @@ <!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>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • 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TOXSWA_cwa"><meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data +and some associated statistics. like maximum moving window average +concentrations, and dataframes holding the events exceeding specified +thresholds. Usually, an instance of this class will be generated +by read.TOXSWA_cwa."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> +======= <!-- 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="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified @@ -40,6 +82,7 @@ by read.TOXSWA_cwa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/a </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -59,12 +102,21 @@ by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object.</p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <code>R6Class</code> generator object.</p> </div> <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> +>>>>>>> refs/remotes/origin/main <p></p><div class="r6-fields"><dl><dt><code>filename</code></dt> <dd><p>Length one character vector holding the filename.</p></dd> @@ -101,8 +153,13 @@ for the requested moving window sizes in days.</p></dd> </dl><p></p></div> </div> +<<<<<<< HEAD + <div id="methods"> + <h2>Methods</h2> +======= <div class="section level2"> <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> @@ -157,7 +214,11 @@ for the requested moving window sizes in days.</p></dd> </div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> <h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3> +<<<<<<< HEAD +<p>Add to the `windows` field described above.</p><div class="section"> +======= <p>Add to the <code>windows</code> field described above.</p><div class="section"> +>>>>>>> refs/remotes/origin/main <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -179,7 +240,11 @@ suspended matter will be used.</p></dd> </div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> <h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified +<<<<<<< HEAD +threshold value. The resulting dataframe is stored in the `events` +======= threshold value. The resulting dataframe is stored in the <code>events</code> +>>>>>>> refs/remotes/origin/main field of the object.</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> @@ -201,7 +266,11 @@ suspended matter will be used.</p></dd> </div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> <h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> +<<<<<<< HEAD +<p>Print a `TOXSWA_cwa` object</p><div class="section"> +======= <p>Print a <code>TOXSWA_cwa</code> object</p><div class="section"> +>>>>>>> refs/remotes/origin/main <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -212,6 +281,76 @@ suspended matter will be used.</p></dd> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +<<<<<<< HEAD +</div> + +<div class="section"> +<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> + + +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span> +<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span> +<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 0</span> +<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span> +<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span> +<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span> +<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </div> <div class="section"> @@ -277,10 +416,16 @@ suspended matter will be used.</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/TSCF-1.png b/docs/reference/TSCF-1.png Binary files differindex 788f4d3..82c0ea8 100644 --- a/docs/reference/TSCF-1.png +++ b/docs/reference/TSCF-1.png diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html index 6ac2f56..9155ce9 100644 --- a/docs/reference/TSCF.html +++ b/docs/reference/TSCF.html @@ -1,9 +1,51 @@ <!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 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Estimation of the transpiration stream concentration factor — TSCF"><meta property="og:description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +======= <!-- 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="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +>>>>>>> refs/remotes/origin/main log Kow for neutral pH must be available in order to apply the Briggs equation. It is not clarified when it can be regarded reliable, but the equation is stated to be produced for non-ionic compounds, suggesting that the compound should not be ionogenic (weak acid/base) +<<<<<<< HEAD +or ionic."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Estimation of the transpiration stream concentration factor</h1> +======= or ionic."><title>Estimation of the transpiration stream concentration factor — TSCF • 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="Estimation of the transpiration stream concentration factor — TSCF"><meta property="og:description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured log Kow for neutral pH must be available in order to apply the Briggs equation. It is not clarified when it can be regarded reliable, but the @@ -42,6 +84,7 @@ or ionic."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/m </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -61,6 +104,14 @@ the compound should not be ionogenic (weak acid/base) or ionic.</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TSCF</span><span class="op">(</span><span class="va">log_Kow</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"briggs82"</span>, <span class="st">"dettenmaier09"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TSCF</span><span class="op">(</span><span class="va">log_Kow</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"briggs82"</span>, <span class="st">"dettenmaier09"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> @@ -68,6 +119,7 @@ or ionic.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>log_Kow</dt> <dd><p>The decadic logarithm of the octanol-water partition constant</p></dd> @@ -76,20 +128,34 @@ or ionic.</p> <dd><p>Short name of the estimation method.</p></dd> </dl></div> +<<<<<<< HEAD + <div id="details"> + <h2>Details</h2> + <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> + </div> + <div id="references"> + <h2>References</h2> +======= <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> </div> <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 Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake by plant roots. Environ. Sci. Technol 43, 324 - 329</p> </div> +<<<<<<< HEAD + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">TSCF</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, xlab <span class="op">=</span> <span class="st">"log Kow"</span>, ylab <span class="op">=</span> <span class="st">"TSCF"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">TSCF_2</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">TSCF</span><span class="op">(</span><span class="va">x</span>, method <span class="op">=</span> <span class="st">"dettenmaier09"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/curve.html" class="external-link">curve</a></span><span class="op">(</span><span class="va">TSCF_2</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> @@ -98,6 +164,24 @@ by plant roots. Environ. Sci. Technol 43, 324 - 329</p> <span class="r-plt img"><img src="TSCF-1.png" alt="" width="700" height="433"></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -111,10 +195,16 @@ by plant roots. Environ. Sci. Technol 43, 324 - 329</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 5ffa6b4..828c71a 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,4 +1,42 @@ <!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>Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • 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 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</button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Create a chemical compound object for FOCUS Step 1 calculations</h1> +======= <!-- 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 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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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,8 +85,12 @@ <p>Create a chemical compound object for FOCUS Step 1 calculations</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">chent_focus_sw</span><span class="op">(</span></span> <span> <span class="va">name</span>,</span> <span> <span class="va">Koc</span>,</span> @@ -62,8 +105,13 @@ <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>name</dt> <dd><p>Length one character vector containing the name</p></dd> @@ -72,6 +120,65 @@ <dd><p>Partition coefficient between organic carbon and water in L/kg.</p></dd> +<<<<<<< HEAD + +<dt>DT50_ws</dt> +<dd><p>Half-life in water/sediment systems in days</p></dd> + + +<dt>DT50_soil</dt> +<dd><p>Half-life in soil in days</p></dd> + + +<dt>DT50_water</dt> +<dd><p>Half-life in water in days (Step 2)</p></dd> + + +<dt>DT50_sediment</dt> +<dd><p>Half-life in sediment in days (Step 2)</p></dd> + + +<dt>cwsat</dt> +<dd><p>Water solubility in mg/L</p></dd> + + +<dt>mw</dt> +<dd><p>Molar weight in g/mol.</p></dd> + + +<dt>max_soil</dt> +<dd><p>Maximum observed fraction (dimensionless) in soil</p></dd> + + +<dt>max_ws</dt> +<dd><p>Maximum observed fraction (dimensionless) in water/sediment +systems</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list with the substance specific properties</p> + </div> + + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <dt>DT50_ws</dt> <dd><p>Half-life in water/sediment systems in days</p></dd> @@ -126,10 +233,16 @@ systems</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git 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class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Deposition from spray drift expressed as percent of the applied dose as +published by the JKI</h1> +======= <![endif]--></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -36,6 +77,7 @@ published by the German Julius-Kühn Institute (JKI)."><!-- mathjax --><script s </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -53,24 +95,39 @@ published by the German Julius-Kühn Institute (JKI).</p> </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> +>>>>>>> refs/remotes/origin/main <p>A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late (Obstbau frueh, spaet).</p> </div> +<<<<<<< HEAD + <div id="source"> + <h2>Source</h2> +======= <div class="section level2"> <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> +>>>>>>> refs/remotes/origin/main <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11</p> +on 2015-06-11, not present any more 2024-01-31</p> <p>Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141</p> </div> +<<<<<<< HEAD + <div id="details"> + <h2>Details</h2> +======= <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The data were extracted from the spreadsheet cited below using the R code given in the example section. The spreadsheet is not included in the package as its licence is not clear.</p> @@ -86,6 +143,11 @@ equipment (tragbare Spritz- und Sprühgerate).</p> included.</p> </div> +<<<<<<< HEAD + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">drift_data_JKI</span></span></span> +======= <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></span> @@ -136,6 +198,7 @@ included.</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># And these are the resulting data</span></span></span> <span class="r-in"><span><span class="va">drift_data_JKI</span></span></span> +>>>>>>> refs/remotes/origin/main <span class="r-out co"><span class="r-pr">#></span> [[1]]</span> <span class="r-out co"><span class="r-pr">#></span> crop</span> <span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> @@ -330,6 +393,24 @@ included.</p> <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -343,10 +424,16 @@ included.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index b17611e..0f012a0 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,4 +1,45 @@ <!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>Retrieve endpoint information from the chyaml field of a chent object — endpoint • 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="Retrieve endpoint information from the chyaml field of a chent object — endpoint"><meta property="og:description" content="R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> +======= <!-- 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="R6 class objects of class chent represent chemical entities and can hold a list of information loaded from a chemical yaml file in their chyaml field. Such information is extracted and optionally aggregated by @@ -38,6 +79,7 @@ this function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -55,8 +97,12 @@ chyaml field. Such information is extracted and optionally aggregated by this function.</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">endpoint</span><span class="op">(</span></span> <span> <span class="va">chent</span>,</span> <span> medium <span class="op">=</span> <span class="st">"soil"</span>,</span> @@ -92,8 +138,13 @@ this function.</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>chent</dt> <dd><p>The chent object to get the information from</p></dd> @@ -115,12 +166,20 @@ this function.</p> <dt>value</dt> +<<<<<<< HEAD +<dd><p>The name of the value we want. The list given in the +======= <dd><p>The name of the value we want. The list given in the +>>>>>>> refs/remotes/origin/main usage section is not exclusive</p></dd> <dt>aggregator</dt> +<<<<<<< HEAD +<dd><p>The aggregator function. Can be mean, +======= <dd><p>The aggregator function. Can be mean, +>>>>>>> refs/remotes/origin/main <code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd> @@ -142,6 +201,20 @@ about precision?</p></dd> <dd><p>A named vector of aggregator functions to be used</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> + + +<p>The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present.</p> + </div> + <div id="details"> + <h2>Details</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> @@ -154,12 +227,31 @@ information on precision that may be present.</p> </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. For the Freundlich exponent, the capital letter <code>N</code> is used in order to facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.</p> </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -173,10 +265,16 @@ exponent is often called 1/n.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 20ee17d..0dbc6d1 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -1,4 +1,46 @@ <!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 the geometric mean — geomean • 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 the geometric mean — geomean"><meta property="og:description" content="Based on some posts in a thread on Stackoverflow +http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in +This function returns NA if NA values are present and na.rm = FALSE +(default). If negative values are present, it gives an error message. +If at least one element of the vector is 0, it returns 0."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate the geometric mean</h1> +======= <!-- 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="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE @@ -40,6 +82,7 @@ If at least one element of the vector is 0, it returns 0."><!-- mathjax --><scri </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -58,6 +101,14 @@ This function returns NA if NA values are present and na.rm = FALSE If at least one element of the vector is 0, it returns 0.</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">geomean</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">geomean</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> @@ -65,6 +116,7 @@ If at least one element of the vector is 0, it returns 0.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>x</dt> <dd><p>Vector of numbers</p></dd> @@ -73,12 +125,26 @@ If at least one element of the vector is 0, it returns 0.</p> <dd><p>Should NA values be omitted?</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The geometric mean</p> </div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -86,10 +152,33 @@ If at least one element of the vector is 0, it returns 0.</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 3</span> <span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="cn">NA</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<<<<<<< HEAD +<span class="r-in"><span><span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="op">-</span><span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span> <span class="co"># returns an error</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in geomean(c(1, -3, 9)):</span> Only defined for positive numbers</span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">geomean</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="op">-</span><span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span> <span class="co"># returns an error</span></span></span> </code></pre></div> </div> @@ -106,10 +195,16 @@ If at least one element of the vector is 0, it returns 0.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index aee1a70..6a03c3c 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -1,4 +1,43 @@ <!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>Fit a parabola through three points — get_vertex • 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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]> @@ -34,6 +73,7 @@ https://stackoverflow.com/a/717791"><!-- mathjax --><script src="https://cdnjs.c </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -44,11 +84,48 @@ https://stackoverflow.com/a/717791"><!-- mathjax --><script src="https://cdnjs.c <div class="d-none name"><code>get_vertex.Rd</code></div> </div> +<<<<<<< HEAD + <div class="ref-description"> +======= <div class="ref-description section level2"> +>>>>>>> refs/remotes/origin/main <p>This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_vertex</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Three x coordinates</p></dd> + + +<dt>y</dt> +<dd><p>Three y coordinates</p></dd> + +</dl></div> + + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_vertex</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div> @@ -78,10 +155,16 @@ https://stackoverflow.com/a/717791</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/index.html b/docs/reference/index.html index f41d356..3e5be55 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,4 +1,239 @@ <!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>Function reference • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="contents col-md-9"> + <div class="page-header"> + <h1>Reference</h1> + </div> + + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="general-utility-functions">General utility functions <a href="#general-utility-functions" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="geomean.html">geomean()</a></code> </p> + </td> + <td><p>Calculate the geometric mean</p></td> + </tr><tr><td> + <p><code><a href="one_box.html">one_box()</a></code> </p> + </td> + <td><p>Create a time series of decline data</p></td> + </tr><tr><td> + <p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p> + </td> + <td><p>Plot time series of decline data</p></td> + </tr><tr><td> + <p><code><a href="sawtooth.html">sawtooth()</a></code> </p> + </td> + <td><p>Create decline time series for multiple applications</p></td> + </tr><tr><td> + <p><code><a href="twa.html">twa()</a></code> </p> + </td> + <td><p>Calculate a time weighted average concentration</p></td> + </tr><tr><td> + <p><code><a href="max_twa.html">max_twa()</a></code> </p> + </td> + <td><p>The maximum time weighted average concentration for a moving window</p></td> + </tr><tr><td> + <p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p> + </td> + <td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td> + </tr><tr><td> + <p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p> + </td> + <td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td> + </tr><tr><td> + <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> + </td> + <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> + </tr><tr><td> + <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </p> + </td> + <td><p>Objects exported from other packages</p></td> + </tr><tr><td> + <p><code><a href="TSCF.html">TSCF()</a></code> </p> + </td> + <td><p>Estimation of the transpiration stream concentration factor</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil <a href="#predicted-environmental-concentrations-in-soil" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in soil</p></td> + </tr><tr><td> + <p><code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p> + </td> + <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</p></td> + </tr><tr><td> + <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> + </td> + <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> + </tr><tr><td> + <p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p> + </td> + <td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td> + </tr><tr><td> + <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> + </td> + <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> + </tr><tr><td> + <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> + </td> + <td><p>Subset of EFSA crop washoff default values</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater <a href="#predicted-environmental-concentrations-in-groundwater" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> + </td> + <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> + </tr><tr><td> + <p><code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> + </td> + <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water <a href="#predicted-environmental-concentrations-in-surface-water" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> + </tr><tr><td> + <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> + </td> + <td><p>Deposition from spray drift expressed as percent of the applied dose as +published by the JKI</p></td> + </tr><tr><td> + <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p> + </td> + <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> + </tr><tr><td> + <p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p> + </td> + <td><p>Calculate predicted environmental concentrations in sediment from surface +water concentrations</p></td> + </tr><tr><td> + <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p> + </td> + <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> + </tr><tr><td> + <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p> + </td> + <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td> + </tr><tr><td> + <p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p> + </td> + <td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td> + </tr><tr><td> + <p><code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p> + </td> + <td><p>Calculate PEC surface water due to drainage as in Exposit 3</p></td> + </tr><tr><td> + <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p> + </td> + <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> + </tr><tr><td> + <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p> + </td> + <td><p>Runoff loss percentages as used in Exposit 3</p></td> + </tr><tr><td> + <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p> + </td> + <td><p>Runoff reduction percentages as used in Exposit</p></td> + </tr><tr><td> + <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> + </td> + <td><p>R6 class for holding TOXSWA water concentration data and associated statistics</p></td> + </tr><tr><td> + <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p> + </td> + <td><p>Read TOXSWA surface water concentrations</p></td> + </tr><tr><td> + <p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p> + </td> + <td><p>Plot TOXSWA surface water concentrations</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="classifications-and-indicators">Classifications and indicators <a href="#classifications-and-indicators" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p> + </td> + <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> + </tr><tr><td> + <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p> + </td> + <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information <a href="#work-with-chent-objects-containing-relevant-information" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> + </td> + <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p> + </th> + </tr></tbody><tbody><tr><td> + <p><code><a href="get_vertex.html">get_vertex()</a></code> </p> + </td> + <td><p>Fit a parabola through three points</p></td> + </tr></tbody></table></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <!-- 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"><title>Function reference • 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 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+<<<<<<< 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>The maximum time weighted average concentration for a moving window — max_twa • 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=" 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It is therefore recommended to check this using +plot.one_box using the window size for the argument +max_twa."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>The maximum time weighted average concentration for a moving window</h1> +======= <!-- 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="If you generate your time series using sawtooth, you need to make sure that the length of the time series allows for finding the maximum. It is therefore recommended to check this using @@ -40,6 +82,7 @@ max_twa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -50,7 +93,11 @@ max_twa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <div class="d-none name"><code>max_twa.Rd</code></div> </div> +<<<<<<< HEAD + <div class="ref-description"> +======= <div class="ref-description section level2"> +>>>>>>> refs/remotes/origin/main <p>If you generate your time series using <code><a href="sawtooth.html">sawtooth</a></code>, you need to make sure that the length of the time series allows for finding the maximum. It is therefore recommended to check this using @@ -58,6 +105,14 @@ for finding the maximum. It is therefore recommended to check this using <code>max_twa</code>.</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> @@ -65,6 +120,7 @@ for finding the maximum. It is therefore recommended to check this using <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>x</dt> <dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> @@ -73,12 +129,34 @@ for finding the maximum. It is therefore recommended to check this using <dd><p>The size of the moving window</p></dd> </dl></div> +<<<<<<< HEAD + <div id="details"> + <h2>Details</h2> +======= <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> +>>>>>>> refs/remotes/origin/main <p>The method working directly on fitted <code>mkinfit</code> objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound</p> </div> +<<<<<<< HEAD + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="twa.html">twa</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -94,6 +172,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> <span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> @@ -115,6 +194,24 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-out co"><span class="r-pr">#></span> 18.22124 </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -128,10 +225,16 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png Binary files differindex b280532..eb4d2ee 100644 --- a/docs/reference/one_box-1.png +++ b/docs/reference/one_box-1.png diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png Binary files differindex 8c8188c..1b34c2d 100644 --- a/docs/reference/one_box-2.png +++ b/docs/reference/one_box-2.png diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png Binary files differindex 3d77b8e..e4e41ea 100644 --- a/docs/reference/one_box-3.png +++ b/docs/reference/one_box-3.png diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index d143079..3e5f7bb 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -1,4 +1,42 @@ <!DOCTYPE html> +<<<<<<< HEAD +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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When a character string specifying a parent decline model is given @@ -80,8 +128,13 @@ all observed variables.</p></dd> <dt>...</dt> <dd><p>Further arguments passed to methods</p></dd> +<<<<<<< HEAD +======= + + +>>>>>>> refs/remotes/origin/main <dt>t_end</dt> <dd><p>End of the time series</p></dd> @@ -94,15 +147,25 @@ all observed variables.</p></dd> <dd><p>A named numeric vector containing the model parameters</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> </div> +<<<<<<< HEAD + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Only use a half-life</span></span></span> <span class="r-in"><span><span class="va">pred_0</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_0</span><span class="op">)</span></span></span> @@ -125,6 +188,24 @@ all observed variables.</p></dd> <span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -138,10 +219,16 @@ all observed variables.</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index ba35561..4f3c3e8 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -1,4 +1,42 @@ <!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" 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class="page-header"> + <h1>Runoff loss percentages as used in Exposit 3</h1> +======= <!-- 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="A table of the loss percentages used in Exposit 3 for the twelve different Koc classes"><title>Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • 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" 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used in Exposit 3 — perc_runoff_exposit"><meta property="og:description" content="A table of the loss percentages used in Exposit 3 for the twelve different Koc classes"><!-- 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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,7 +85,36 @@ <p>A table of the loss percentages used in Exposit 3 for the twelve different Koc classes</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_exposit</span></span></code></pre></div> + </div> + +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A data frame with percentage values for the dissolved fraction and the fraction + bound to eroding particles, with Koc classes used as row names</p><dl><dt>Koc_lower_bound</dt> +<dd><p>The lower bound of the Koc class</p></dd> + + <dt>dissolved</dt> +<dd><p>The percentage of the applied substance transferred to an + adjacent water body in the dissolved phase</p></dd> + + <dt>bound</dt> +<dd><p>The percentage of the applied substance transferred to an + adjacent water body bound to eroding particles</p></dd> + + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with percentage values for the dissolved fraction and the fraction @@ -71,6 +139,7 @@ adjacent water body bound to eroding particles</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_exposit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Koc_lower_bound dissolved bound</span> <span class="r-out co"><span class="r-pr">#></span> 0-20 0 0.110 0.000</span> @@ -87,6 +156,24 @@ adjacent water body bound to eroding particles</p></dd> <span class="r-out co"><span class="r-pr">#></span> >50000 50000 0.001 0.451</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -100,10 +187,16 @@ adjacent water body bound to eroding particles</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> 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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="Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit"><meta property="og:description" content="A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths"><!-- 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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,6 +85,14 @@ <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> </div> +<<<<<<< HEAD + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_reduction_exposit</span></span></code></pre></div> + </div> + + <div id="format"> + <h2>Format</h2> +======= <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_reduction_exposit</span></span></code></pre></div> @@ -53,12 +100,30 @@ <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> +>>>>>>> refs/remotes/origin/main <p>A named list of data frames with reduction percentage values for the dissolved fraction and the fraction bound to eroding particles, with vegetated buffer widths as row names. The names of the list items are the Exposit versions from which the values were taken.</p><dl><dt>dissolved</dt> <dd><p>The reduction percentage for the dissolved phase</p></dd> +<<<<<<< HEAD + <dt>bound</dt> +<dd><p>The reduction percentage for the particulate phase</p></dd> + + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> +<p>Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). + The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <dt>bound</dt> <dd><p>The reduction percentage for the particulate phase</p></dd> @@ -74,6 +139,7 @@ The variant 3.01a2 was introduced for consistency with previous calculations per <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">perc_runoff_reduction_exposit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $`3.02`</span> <span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> @@ -103,6 +169,24 @@ The variant 3.01a2 was introduced for consistency with previous calculations per <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -116,10 +200,16 @@ The variant 3.01a2 was introduced for consistency with previous calculations per </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt deleted file mode 100644 index 4618e8b..0000000 --- a/docs/reference/pesticide.txt +++ /dev/null @@ -1,3 +0,0 @@ -Active Substance Compound Comment Mol mass a.i. Mol mass met. Water solubility KOC assessed compound KOC parent compound DT50 Max. in Water Max. in Soil asessed compound App. Rate Number of App. Time between app. App. Type DT50 soil parent compound DT50 soil DT50 water DT50 sediment Region / Season Interception class -Dummy 1 cereals, spring n NA Dummy 1 cereals, spring n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 -M1 cereals, winter n NA M1 cereals, winter n NA 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 0ae35ba..5ed36f9 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -1,4 +1,42 @@ <!DOCTYPE html> +<<<<<<< HEAD +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1> +======= <!-- 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="Calculate a time course of relative concentrations based on an mkinmod model"><title>Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • 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 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src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,8 +85,12 @@ <p>Calculate a time course of relative concentrations based on an mkinmod model</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">pfm_degradation</span><span class="op">(</span></span> <span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span> <span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span> @@ -58,8 +101,13 @@ <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>model</dt> <dd><p>The degradation model to be used. Either a parent only model like 'SFO' or 'FOMC', or an mkinmod object</p></dd> @@ -86,6 +134,41 @@ is calculated (SFO model).</p></dd> <dd><p>The output times</p></dd> </dl></div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 1.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 0.9330330</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 0.8705506</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 0.8122524</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 0.7578583</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 0.7071068</span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -110,10 +193,16 @@ is calculated (SFO model).</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png Binary files differindex 19dfbe6..11a34cc 100644 --- a/docs/reference/plot.TOXSWA_cwa-1.png +++ b/docs/reference/plot.TOXSWA_cwa-1.png diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png Binary files differindex 85ffe4b..327a21b 100644 --- a/docs/reference/plot.TOXSWA_cwa-2.png +++ b/docs/reference/plot.TOXSWA_cwa-2.png diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png Binary files differindex f2bb9cf..65524b5 100644 --- a/docs/reference/plot.TOXSWA_cwa-3.png +++ b/docs/reference/plot.TOXSWA_cwa-3.png diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png Binary files differindex 6ee8f66..1d82cfc 100644 --- a/docs/reference/plot.TOXSWA_cwa-4.png +++ b/docs/reference/plot.TOXSWA_cwa-4.png diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png Binary files differindex 989f777..d28c87c 100644 --- a/docs/reference/plot.TOXSWA_cwa-5.png +++ b/docs/reference/plot.TOXSWA_cwa-5.png diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 09e9258..6cde064 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -1,4 +1,43 @@ <!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>Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" 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+ <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot TOXSWA surface water concentrations</h1> +======= <!-- 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, 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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]> @@ -34,6 +73,7 @@ segment of a TOXSWA surface water body."><!-- mathjax --><script src="https://cd </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -49,8 +89,12 @@ segment of a TOXSWA surface water body."><!-- mathjax --><script src="https://cd segment of a TOXSWA surface water body.</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="co"># S3 method for TOXSWA_cwa</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> @@ -66,8 +110,13 @@ segment of a TOXSWA surface water body.</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>x</dt> <dd><p>The TOXSWA_cwa object to be plotted.</p></dd> @@ -109,6 +158,15 @@ to suspended matter?</p></dd> <dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> </dl></div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -116,6 +174,7 @@ to suspended matter?</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> <span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> <span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -135,6 +194,24 @@ to suspended matter?</p></dd> <span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -148,10 +225,16 @@ to suspended matter?</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png Binary files differindex 5149343..066f466 100644 --- a/docs/reference/plot.one_box-1.png +++ b/docs/reference/plot.one_box-1.png diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png Binary files differindex 685384e..307dc3c 100644 --- a/docs/reference/plot.one_box-2.png +++ b/docs/reference/plot.one_box-2.png diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png Binary files differindex 5c9fbcc..cea8b0b 100644 --- a/docs/reference/plot.one_box-3.png +++ b/docs/reference/plot.one_box-3.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 9236503..a9048fd 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -1,4 +1,42 @@ <!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" 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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="Plot time series of decline data"><title>Plot time series of decline data — plot.one_box • 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" 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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> @@ -32,6 +70,7 @@ </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -46,8 +85,12 @@ <p>Plot time series of decline data</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="co"># S3 method for one_box</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> @@ -61,16 +104,26 @@ <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>x</dt> <dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> <dt>xlim</dt> <dd><p>Limits for the x axis</p></dd> +<<<<<<< HEAD + +======= + +>>>>>>> refs/remotes/origin/main <dt>ylim</dt> <dd><p>Limits for the y axis</p></dd> @@ -97,6 +150,15 @@ be shown if max_twa is not NULL.</p></dd> <dd><p>Further arguments passed to methods</p></dd> </dl></div> +<<<<<<< HEAD + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> @@ -104,6 +166,7 @@ be shown if max_twa is not NULL.</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pred</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span> @@ -121,6 +184,24 @@ be shown if max_twa is not NULL.</p></dd> <span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -134,10 +215,16 @@ be shown if max_twa is not NULL.</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 32a9b1d..7b60b4c 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -1,9 +1,51 @@ <!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>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • 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" 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property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa"><meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific +======= <!-- 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="Read TOXSWA hourly concentrations of a chemical substance in a specific +>>>>>>> refs/remotes/origin/main segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +<<<<<<< HEAD +renamed to ConLiqWatLay in the out file."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Read TOXSWA surface water concentrations</h1> +======= renamed to ConLiqWatLay in the out file."><title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • 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="Read TOXSWA surface water concentrations — read.TOXSWA_cwa"><meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour @@ -42,6 +84,7 @@ renamed to ConLiqWatLay in the out file."><!-- mathjax --><script src="https://c </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -61,8 +104,12 @@ of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</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">read.TOXSWA_cwa</span><span class="op">(</span></span> <span> <span class="va">filename</span>,</span> <span> basedir <span class="op">=</span> <span class="st">"."</span>,</span> @@ -75,8 +122,13 @@ renamed to ConLiqWatLay in the out file.</p> <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>filename</dt> <dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> @@ -117,13 +169,27 @@ maximum time weighted average concentrations and areas under the curve.</p></dd> generating event statistics.</p></dd> </dl></div> +<<<<<<< HEAD + <div id="value"> + <h2>Value</h2> +======= <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> +>>>>>>> refs/remotes/origin/main <p>An instance of an R6 object of class <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> </div> +<<<<<<< HEAD + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> @@ -131,12 +197,31 @@ generating event statistics.</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu">read.TOXSWA_cwa</span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> <span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> <span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> <span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -150,10 +235,16 @@ generating event statistics.</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index a98a861..a88fe65 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,4 +1,7 @@ <!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>Objects exported from other packages — reexports • 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="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. Follow the links +======= <!-- 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="These objects are imported from other packages. Follow the links below to see their documentation. @@ -7,6 +10,7 @@ set_nd_nq, set_nd_nq_focus "><title>Objects exported from other packages — reexports • 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="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. Follow the links +>>>>>>> refs/remotes/origin/main below to see their documentation. mkin @@ -16,6 +20,46 @@ set_nd_nq, set_nd_nq_focus "><!-- 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> +<<<<<<< HEAD +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Objects exported from other packages</h1> + + <div class="hidden name"><code>reexports.Rd</code></div> + </div> + + <div class="ref-description"> +======= <![endif]--></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -57,6 +101,7 @@ set_nd_nq, set_nd_nq_focus </div> <div class="ref-description section level2"> +>>>>>>> refs/remotes/origin/main <p>These objects are imported from other packages. Follow the links below to see their documentation.</p> <dl><dt>mkin</dt> @@ -67,6 +112,28 @@ below to see their documentation.</p> +<<<<<<< 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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> + + + + +======= </main></div> @@ -82,6 +149,7 @@ below to see their documentation.</p> +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 6cf67ed..062202c 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary 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</button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Create decline time series for multiple applications</h1> +======= <!-- 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" 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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]> @@ -34,6 +73,7 @@ n and i are disregarded."><!-- mathjax --><script src="https://cdnjs.cloudflare. </li> </ul></div> +>>>>>>> refs/remotes/origin/main </div> </nav><div class="container template-reference-topic"> @@ -49,8 +89,12 @@ n and i are disregarded."><!-- mathjax --><script src="https://cdnjs.cloudflare. <code>n</code> and <code>i</code> are disregarded.</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">sawtooth</span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> <span> n <span class="op">=</span> <span class="fl">1</span>,</span> @@ -59,8 +103,13 @@ n and i are disregarded."><!-- mathjax --><script src="https://cdnjs.cloudflare. <span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> +>>>>>>> refs/remotes/origin/main <dl><dt>x</dt> <dd><p>A <code><a href="one_box.html">one_box</a></code> object</p></dd> @@ -80,8 +129,13 @@ the corresponding amounts applied in the second column.</p></dd> </dl></div> +<<<<<<< HEAD + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">applications</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">14</span>, by <span class="op">=</span> <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred</span>, applications <span class="op">=</span> <span class="va">applications</span><span class="op">)</span><span class="op">)</span></span></span> @@ -111,6 +165,24 @@ the corresponding amounts applied in the second column.</p></dd> <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -124,10 +196,16 @@ the corresponding amounts applied in the second column.</p></dd> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 79cfc68..90ebba1 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -1,4 +1,44 @@ <!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>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • 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" 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soil_scenario_data_EFSA_2015"><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> +======= <!-- 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="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). 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Also, the scenario and model adjustment factors from p. 15 and p. 17 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2015</span></span></code></pre></div> + </div> +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> + </div> + <div id="source"> + <h2>Source</h2> + <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 + <a href="https://doi.org/10.2903/j.efsa.2015.4093" class="external-link">doi:10.2903/j.efsa.2015.4093</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, @@ -91,6 +155,7 @@ doi:10.2903/j.efsa.2015.4093</p> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># And this is the resulting dataframe</span></span></span> <span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span> +>>>>>>> refs/remotes/origin/main <span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce</span> <span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0</span> <span class="r-out co"><span class="r-pr">#></span> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0</span> @@ -107,6 +172,24 @@ doi:10.2903/j.efsa.2015.4093</p> <span class="r-out co"><span class="r-pr">#></span> CLS 4</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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -120,10 +203,16 @@ doi:10.2903/j.efsa.2015.4093</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index 11eaa53..1d61136 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,4 +1,44 @@ <!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>Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • 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="Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017"><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the +scenario and model adjustment factors from p. 16 and p. 18 are included."><!-- 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 data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">pfm</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> +======= <!-- 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="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2017, p. 14/15). 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Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2017</span></span></code></pre></div> + </div> + +<<<<<<< HEAD + <div id="format"> + <h2>Format</h2> + <p>A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> + </div> + <div id="source"> + <h2>Source</h2> + <p>EFSA (European Food Safety Authority) (2017) + 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>15</b>(10) 4982 + <a href="https://doi.org/10.2903/j.efsa.2017.4982" class="external-link">doi:10.2903/j.efsa.2017.4982</a></p> + </div> + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, @@ -70,6 +133,7 @@ doi:10.2903/j.efsa.2017.4982</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2017</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod</span> <span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3</span> @@ -85,6 +149,59 @@ doi:10.2903/j.efsa.2017.4982</p> <span class="r-out co"><span class="r-pr">#></span> CLN Hamburg 602</span> <span class="r-out co"><span class="r-pr">#></span> CLC Châteaudun 589</span> <span class="r-out co"><span class="r-pr">#></span> CLS Sevilla 526</span> +<<<<<<< HEAD +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">waldo</span><span class="fu">::</span><span class="fu"><a href="https://waldo.r-lib.org/reference/compare.html" class="external-link">compare</a></span><span class="op">(</span><span class="va">soil_scenario_data_EFSA_2017</span>, <span class="va">soil_scenario_data_EFSA_2015</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> `old` is length 12</span> +<span class="r-out co"><span class="r-pr">#></span> `new` is length 10</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `names(old)[8:12]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> <span style="color: #BBBB00;">"FOCUS_zone"</span> <span style="color: #BBBB00;">"prec"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `names(new)[8:10]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Poland"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Austria"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Germany"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Czech Republik"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arit`: <span style="color: #00BB00;">5.7</span> <span style="color: #00BB00;">7.4</span> <span style="color: #00BB00;">10.2</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">15.4</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arit`: <span style="color: #00BB00;">4.7</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">11.0</span> <span style="color: #00BB00;">8.2</span> <span style="color: #00BB00;">9.1</span> <span style="color: #00BB00;">12.8</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arr`: <span style="color: #00BB00;">7.6</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">11.7</span> <span style="color: #00BB00;">9.2</span> <span style="color: #00BB00;">11.3</span> <span style="color: #00BB00;">16.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arr`: <span style="color: #00BB00;">7.0</span> <span style="color: #00BB00;">10.1</span> <span style="color: #00BB00;">12.3</span> <span style="color: #00BB00;">9.8</span> <span style="color: #00BB00;">11.2</span> <span style="color: #00BB00;">14.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium fine"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_om`: <span style="color: #00BB00;">0.220</span> <span style="color: #00BB00;">0.122</span> <span style="color: #00BB00;">0.070</span> <span style="color: #00BB00;">0.025</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.010</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_om`: <span style="color: #00BB00;">0.118</span> <span style="color: #00BB00;">0.086</span> <span style="color: #00BB00;">0.048</span> <span style="color: #00BB00;">0.023</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.011</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.385</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$rho`: <span style="color: #00BB00;">0.707</span> <span style="color: #00BB00;">0.934</span> <span style="color: #00BB00;">1.117</span> <span style="color: #00BB00;">1.371</span> <span style="color: #00BB00;">1.432</span> <span style="color: #00BB00;">1.521</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$rho`: <span style="color: #00BB00;">0.950</span> <span style="color: #00BB00;">1.050</span> <span style="color: #00BB00;">1.220</span> <span style="color: #00BB00;">1.390</span> <span style="color: #00BB00;">1.430</span> <span style="color: #00BB00;">1.510</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_sce`: <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_sce`: <span style="color: #00BB00;">3.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">1.5</span> <span style="color: #00BB00;">1.5</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> And 3 more differences ...</span> +</code></pre></div> + </div> + </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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </code></pre></div> </div> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> @@ -100,10 +217,16 @@ doi:10.2903/j.efsa.2017.4982</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> diff --git a/docs/reference/twa.html b/docs/reference/twa.html index fbcbe9a..767b2b6 100644 --- a/docs/reference/twa.html 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title="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Reference</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate a time weighted average concentration</h1> +======= <!-- 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="The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has 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<div class="ref-description"> +======= <div class="ref-description section level2"> +>>>>>>> refs/remotes/origin/main <p>The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has passed.</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">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for one_box</span></span> <span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> </div> +<<<<<<< HEAD + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> + + +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="max_twa.html">max_twa</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> +======= <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> @@ -77,6 +145,7 @@ is after one window has passed.</p> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> +>>>>>>> refs/remotes/origin/main <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> <span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> @@ -94,6 +163,24 @@ is after one window has passed.</p> <span class="r-out co"><span class="r-pr">#></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> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> +======= </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> </nav></aside></div> @@ -107,10 +194,16 @@ is after one window has passed.</p> </div> </footer></div> +>>>>>>> refs/remotes/origin/main + + +<<<<<<< HEAD +======= +>>>>>>> refs/remotes/origin/main </body></html> |
