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class="external-link"><code>R/EFSA_GW_interception_2014.R</code></a></small> <div class="d-none name"><code>EFSA_GW_interception_2014.Rd</code></div> </div> @@ -78,23 +69,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + 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aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Subset of EFSA crop washoff default values</h1> + + <h1>Subset of EFSA crop washoff default values</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/EFSA_washoff_2017.R" class="external-link"><code>R/EFSA_washoff_2017.R</code></a></small> <div class="d-none name"><code>EFSA_washoff_2017.Rd</code></div> </div> @@ -78,23 +69,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> 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The +soil definitions are from page 46ff. from FOCUS (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)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav 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autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>A very small subset of the FOCUS Groundwater scenario definitions</h1> + + <h1>A very small subset of the FOCUS Groundwater scenario definitions</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/FOCUS_GW_scenarios_2012.R" class="external-link"><code>R/FOCUS_GW_scenarios_2012.R</code></a></small> <div class="d-none name"><code>FOCUS_GW_scenarios_2012.Rd</code></div> </div> @@ -130,23 +121,23 @@ http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index aab1d87..536b974 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,45 +1,36 @@ <!DOCTYPE html> -<!-- 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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" 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code shown below. +The text file is not included in the package as its licence is not clear."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - 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class="r-out co"><span class="r-pr">#></span> list()</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index b66cd35..1e0fd64 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,43 +1,34 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html 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</ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Actual and maximum moving window time average concentrations for FOMC kinetics</h1> + + <h1>Actual and maximum moving window time average concentrations for FOMC kinetics</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/FOMC_actual_twa.R" class="external-link"><code>R/FOMC_actual_twa.R</code></a></small> <div class="d-none name"><code>FOMC_actual_twa.Rd</code></div> </div> @@ -63,15 +54,17 @@ 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> - <dl><dt>alpha</dt> + + +<dl><dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a></dt> <dd><p>Parameter of the FOMC model</p></dd> -<dt>beta</dt> +<dt id="arg-beta">beta<a class="anchor" aria-label="anchor" href="#arg-beta"></a></dt> <dd><p>Parameter of the FOMC model</p></dd> -<dt>times</dt> +<dt id="arg-times">times<a class="anchor" aria-label="anchor" href="#arg-times"></a></dt> <dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> </dl></div> @@ -97,23 +90,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a 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calculated according to the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><!-- 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> +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" 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class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Groundwater ubiquity score based on Gustafson (1989)</h1> + + <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/GUS.R" class="external-link"><code>R/GUS.R</code></a></small> <div class="d-none name"><code>GUS.Rd</code></div> </div> @@ -56,10 +47,10 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> <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">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> +<span><span class="co"># S3 method for class 'numeric'</span></span> <span><span class="fu">GUS</span><span class="op">(</span><span class="va">DT50</span>, <span class="va">Koc</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for chent</span></span> +<span><span class="co"># S3 method for class 'chent'</span></span> <span><span class="fu">GUS</span><span class="op">(</span></span> <span> <span class="va">chent</span>,</span> <span> degradation_value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> @@ -71,18 +62,20 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for GUS_result</span></span> +<span><span class="co"># S3 method for class 'GUS_result'</span></span> <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> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>...</dt> + + +<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></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> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson @@ -90,7 +83,7 @@ did not refer to any normalisation procedure, but says the field study should be conducted under use conditions.</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is @@ -98,17 +91,17 @@ unclear at which reference concentration the Koc should be observed (and if the reference concentration would be in soil or in porewater).</p></dd> -<dt>chent</dt> +<dt id="arg-chent">chent<a class="anchor" aria-label="anchor" href="#arg-chent"></a></dt> <dd><p>If a chent is given with appropriate information present in its chyaml field, this information is used, with defaults specified below.</p></dd> -<dt>degradation_value</dt> +<dt id="arg-degradation-value">degradation_value<a class="anchor" aria-label="anchor" href="#arg-degradation-value"></a></dt> <dd><p>Which of the available degradation values should be used?</p></dd> -<dt>lab_field</dt> +<dt id="arg-lab-field">lab_field<a class="anchor" aria-label="anchor" href="#arg-lab-field"></a></dt> <dd><p>Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS @@ -116,11 +109,11 @@ values given by Gustafson (1989) is desired, non-normalised first-order field half-lives obtained under actual use conditions should be used.</p></dd> -<dt>redox</dt> +<dt id="arg-redox">redox<a class="anchor" aria-label="anchor" href="#arg-redox"></a></dt> <dd><p>Aerobic or anaerobic degradation data</p></dd> -<dt>sorption_value</dt> +<dt id="arg-sorption-value">sorption_value<a class="anchor" aria-label="anchor" href="#arg-sorption-value"></a></dt> <dd><p>Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference @@ -128,27 +121,25 @@ concentration of 1 mg/L in porewater, that means they would be expected to be Koc values at a concentration of 1 mg/L in the water phase.</p></dd> -<dt>degradation_aggregator</dt> +<dt id="arg-degradation-aggregator">degradation_aggregator<a class="anchor" aria-label="anchor" href="#arg-degradation-aggregator"></a></dt> <dd><p>Function for aggregating half-lives</p></dd> -<dt>sorption_aggregator</dt> +<dt id="arg-sorption-aggregator">sorption_aggregator<a class="anchor" aria-label="anchor" href="#arg-sorption-aggregator"></a></dt> <dd><p>Function for aggregation Koc values</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An object of class GUS_result to be printed</p></dd> -<dt>digits</dt> +<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt> <dd><p>The number of digits used in the print method</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A list with the DT50 and Koc used as well as the resulting score + <p>A list with the DT50 and Koc used as well as the resulting score of class GUS_result</p> </div> <div class="section level2"> @@ -162,23 +153,23 @@ toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> <p>Johannes Ranke</p> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/GUS.numeric.html b/docs/reference/GUS.numeric.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/GUS.numeric.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/GUS.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/GUS.html"> + </head> +</html> + diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 46c92f4..e86dd6d 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,51 +1,42 @@ <!DOCTYPE html> -<!-- 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 +<!-- 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>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil"><meta name="description" content="This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. 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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> +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate predicted environmental concentrations in soil</h1> + + <h1>Calculate predicted environmental concentrations in soil</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_soil.R" class="external-link"><code>R/PEC_soil.R</code></a></small> <div class="d-none name"><code>PEC_soil.Rd</code></div> </div> @@ -88,99 +79,101 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>rate</dt> + + +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>Application rate in units specified below</p></dd> -<dt>rate_units</dt> +<dt id="arg-rate-units">rate_units<a class="anchor" aria-label="anchor" href="#arg-rate-units"></a></dt> <dd><p>Defaults to g/ha</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>The fraction of the application rate that does not reach the soil</p></dd> -<dt>mixing_depth</dt> +<dt id="arg-mixing-depth">mixing_depth<a class="anchor" aria-label="anchor" href="#arg-mixing-depth"></a></dt> <dd><p>Mixing depth in cm</p></dd> -<dt>PEC_units</dt> +<dt id="arg-pec-units">PEC_units<a class="anchor" aria-label="anchor" href="#arg-pec-units"></a></dt> <dd><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></dd> -<dt>PEC_pw_units</dt> +<dt id="arg-pec-pw-units">PEC_pw_units<a class="anchor" aria-label="anchor" href="#arg-pec-pw-units"></a></dt> <dd><p>Only mg/L currently supported</p></dd> -<dt>interval</dt> +<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a></dt> <dd><p>Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation units are in days</p></dd> -<dt>n_periods</dt> +<dt id="arg-n-periods">n_periods<a class="anchor" aria-label="anchor" href="#arg-n-periods"></a></dt> <dd><p>Number of periods to be considered for long term PEC calculations</p></dd> -<dt>tillage_depth</dt> +<dt id="arg-tillage-depth">tillage_depth<a class="anchor" aria-label="anchor" href="#arg-tillage-depth"></a></dt> <dd><p>Periodic (see interval) deeper mixing in cm</p></dd> -<dt>leaching_depth</dt> +<dt id="arg-leaching-depth">leaching_depth<a class="anchor" aria-label="anchor" href="#arg-leaching-depth"></a></dt> <dd><p>EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage depth are taken into account in this implementation.</p></dd> -<dt>crop</dt> +<dt id="arg-crop">crop<a class="anchor" aria-label="anchor" href="#arg-crop"></a></dt> <dd><p>Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping cycle per year are currently supported.</p></dd> -<dt>cultivation</dt> +<dt id="arg-cultivation">cultivation<a class="anchor" aria-label="anchor" href="#arg-cultivation"></a></dt> <dd><p>Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios other than EFSA_2017</p></dd> -<dt>chent</dt> +<dt id="arg-chent">chent<a class="anchor" aria-label="anchor" href="#arg-chent"></a></dt> <dd><p>An optional chent object holding substance specific information. Can also be a name for the substance as a character string</p></dd> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero degradation is assumed</p></dd> -<dt>FOMC</dt> +<dt id="arg-fomc">FOMC<a class="anchor" aria-label="anchor" href="#arg-fomc"></a></dt> <dd><p>If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC is calculated using these parameters without temperature correction</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>If specified, overrides Koc endpoints from a chent object</p></dd> -<dt>Kom</dt> +<dt id="arg-kom">Kom<a class="anchor" aria-label="anchor" href="#arg-kom"></a></dt> <dd><p>Calculated from Koc by default, but can explicitly be specified as Kom here</p></dd> -<dt>t_avg</dt> +<dt id="arg-t-avg">t_avg<a class="anchor" aria-label="anchor" href="#arg-t-avg"></a></dt> <dd><p>Averaging times for time weighted average concentrations</p></dd> -<dt>t_act</dt> +<dt id="arg-t-act">t_act<a class="anchor" aria-label="anchor" href="#arg-t-act"></a></dt> <dd><p>Time series for actual concentrations</p></dd> -<dt>scenarios</dt> +<dt id="arg-scenarios">scenarios<a class="anchor" aria-label="anchor" href="#arg-scenarios"></a></dt> <dd><p>If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", @@ -190,12 +183,12 @@ and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also model and scenario adjustment factors from the EFSA guidance are used.</p></dd> -<dt>leaching</dt> +<dt id="arg-leaching">leaching<a class="anchor" aria-label="anchor" href="#arg-leaching"></a></dt> <dd><p>Should leaching be taken into account? The default is FALSE, except when the EFSA_2017 scenarios are used.</p></dd> -<dt>porewater</dt> +<dt id="arg-porewater">porewater<a class="anchor" aria-label="anchor" href="#arg-porewater"></a></dt> <dd><p>Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion @@ -205,9 +198,7 @@ p. 13).</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The predicted concentration in soil</p> + <p>The predicted concentration in soil</p> </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> @@ -305,23 +296,23 @@ doi:10.2903/j.efsa.2015.4093</p> <span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div 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using the UK method — PEC_sw_drainage_UK • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK"><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"><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"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> + + <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_drainage_UK.R" class="external-link"><code>R/PEC_sw_drainage_UK.R</code></a></small> <div class="d-none name"><code>PEC_sw_drainage_UK.Rd</code></div> </div> @@ -64,40 +55,40 @@ published on the CRC website</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>rate</dt> + + +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>Application rate in g/ha</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>The fraction of the application rate that does not reach the soil</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> -<dt>latest_application</dt> +<dt id="arg-latest-application">latest_application<a class="anchor" aria-label="anchor" href="#arg-latest-application"></a></dt> <dd><p>Latest application date, formatted as e.g. "01 July"</p></dd> -<dt>soil_DT50</dt> +<dt id="arg-soil-dt-">soil_DT50<a class="anchor" aria-label="anchor" href="#arg-soil-dt-"></a></dt> <dd><p>Soil degradation half-life, if SFO kinetics are to be used</p></dd> -<dt>model</dt> +<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt> <dd><p>The soil degradation model to be used. Either one of "FOMC", "DFOP", "HS", or "IORE", or an mkinmod object</p></dd> -<dt>model_parms</dt> +<dt id="arg-model-parms">model_parms<a class="anchor" aria-label="anchor" href="#arg-model-parms"></a></dt> <dd><p>A named numeric vector containing the model parameters</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The predicted concentration in surface water in µg/L</p> + <p>The predicted concentration in surface water in µg/L</p> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> @@ -120,23 +111,23 @@ accessed 2019-09-27</p> <span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 1fe8465..2bd66df 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,47 +1,38 @@ <!DOCTYPE html> -<!-- 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, 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vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing -with input via spray drift."><!-- 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> +with input via spray drift."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar 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</ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate predicted environmental concentrations in surface water due to drift</h1> + + <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_drift.R" class="external-link"><code>R/PEC_sw_drift.R</code></a></small> <div class="d-none name"><code>PEC_sw_drift.Rd</code></div> </div> @@ -57,16 +48,16 @@ with input via spray drift.</p> <div 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> -<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fu">as_units</span><span class="op">(</span><span class="st">"30 cm"</span><span class="op">)</span>,</span> <span> drift_percentages <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> drift_data <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">"JKI"</span>, <span class="st">"RF"</span><span class="op">)</span>,</span> <span> crop_group_JKI <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">"Ackerbau"</span>, <span class="st">"Obstbau frueh"</span>, <span class="st">"Obstbau spaet"</span>, <span class="st">"Weinbau frueh"</span>,</span> <span> <span class="st">"Weinbau spaet"</span>, <span class="st">"Hopfenbau"</span>, <span class="st">"Flaechenkulturen > 900 l/ha"</span>, <span class="st">"Gleisanlagen"</span><span class="op">)</span>,</span> -<span> crop_group_focus <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">"arable"</span>, <span class="st">"hops"</span>, <span class="st">"vines, late"</span>, <span class="st">"vines, early"</span>, <span class="st">"fruit, late"</span>,</span> +<span> crop_group_RF <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">"arable"</span>, <span class="st">"hops"</span>, <span class="st">"vines, late"</span>, <span class="st">"vines, early"</span>, <span class="st">"fruit, late"</span>,</span> <span> <span class="st">"fruit, early"</span>, <span class="st">"aerial"</span><span class="op">)</span>,</span> <span> distances <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">5</span>, <span class="fl">10</span>, <span class="fl">20</span><span class="op">)</span>,</span> <span> formula <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">"Rautmann"</span>, <span class="st">"FOCUS"</span><span class="op">)</span>,</span> -<span> water_width <span class="op">=</span> <span class="fl">100</span>,</span> +<span> water_width <span class="op">=</span> <span class="fu">as_units</span><span class="op">(</span><span class="st">"100 cm"</span><span class="op">)</span>,</span> <span> side_angle <span class="op">=</span> <span class="fl">90</span>,</span> <span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> <span> PEC_units <span class="op">=</span> <span class="st">"µg/L"</span></span> @@ -75,71 +66,78 @@ with input via spray drift.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>rate</dt> -<dd><p>Application rate in units specified below</p></dd> -<dt>applications</dt> +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> +<dd><p>Application rate in units specified below, or with units defined via the +<code>units</code> package.</p></dd> + + +<dt id="arg-applications">applications<a class="anchor" aria-label="anchor" href="#arg-applications"></a></dt> <dd><p>Number of applications for selection of drift percentile</p></dd> -<dt>water_depth</dt> +<dt id="arg-water-depth">water_depth<a class="anchor" aria-label="anchor" href="#arg-water-depth"></a></dt> <dd><p>Depth of the water body in cm</p></dd> -<dt>drift_percentages</dt> +<dt id="arg-drift-percentages">drift_percentages<a class="anchor" aria-label="anchor" href="#arg-drift-percentages"></a></dt> <dd><p>Percentage drift values for which to calculate PECsw. Overrides 'drift_data' and 'distances' if not NULL.</p></dd> -<dt>drift_data</dt> +<dt id="arg-drift-data">drift_data<a class="anchor" aria-label="anchor" href="#arg-drift-data"></a></dt> <dd><p>Source of drift percentage data. If 'JKI', the <a href="drift_data_JKI.html">drift_data_JKI</a> included in the package is used. If 'RF', the Rautmann drift data are calculated either in the original form or integrated over the width of the water body, depending on the 'formula' argument.</p></dd> -<dt>crop_group_JKI</dt> +<dt id="arg-crop-group-jki">crop_group_JKI<a class="anchor" aria-label="anchor" href="#arg-crop-group-jki"></a></dt> <dd><p>When using the 'JKI' drift data, one of the German names -as used in <a href="drift_parameters_focus.html">drift_parameters_focus</a>.</p></dd> +as used in <a href="drift_parameters_focus.html">drift_parameters_focus</a>. Will only be used if drift_data is 'JKI'.</p></dd> -<dt>crop_group_focus</dt> +<dt id="arg-crop-group-rf">crop_group_RF<a class="anchor" aria-label="anchor" href="#arg-crop-group-rf"></a></dt> <dd><p>One of the crop groups as used in <a href="drift_parameters_focus.html">drift_parameters_focus</a></p></dd> -<dt>distances</dt> +<dt id="arg-distances">distances<a class="anchor" aria-label="anchor" href="#arg-distances"></a></dt> <dd><p>The distances in m for which to get PEC values</p></dd> -<dt>formula</dt> +<dt id="arg-formula">formula<a class="anchor" aria-label="anchor" href="#arg-formula"></a></dt> <dd><p>By default, the original Rautmann formula is used. If you specify "FOCUS", mean drift input over the width of the water body is calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance</p></dd> -<dt>water_width</dt> +<dt id="arg-water-width">water_width<a class="anchor" aria-label="anchor" href="#arg-water-width"></a></dt> <dd><p>Width of the water body in cm</p></dd> -<dt>side_angle</dt> +<dt id="arg-side-angle">side_angle<a class="anchor" aria-label="anchor" href="#arg-side-angle"></a></dt> <dd><p>The angle of the side of the water relative to the bottom which is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees here.</p></dd> -<dt>rate_units</dt> -<dd><p>Defaults to g/ha</p></dd> +<dt id="arg-rate-units">rate_units<a class="anchor" aria-label="anchor" href="#arg-rate-units"></a></dt> +<dd><p>Defaults to g/ha. For backwards compatibility, only used +if the specified rate does not have <a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">units::units</a>].</p></dd> -<dt>PEC_units</dt> +<dt id="arg-pec-units">PEC_units<a class="anchor" aria-label="anchor" href="#arg-pec-units"></a></dt> <dd><p>Requested units for the calculated PEC. Only µg/L currently supported</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The predicted concentration in surface water</p> + <p>The predicted concentration in surface water</p> + </div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>It is recommened to specify the arguments <code>rate</code>, <code>water_depth</code> and +<code>water_width</code> using <a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">units::units</a> from the <code>units</code> package.</p> </div> <div class="section level2"> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> @@ -153,24 +151,28 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her <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="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> Units: [µg/L]</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> <span class="r-in"><span><span class="co"># Alternatively, we can use the formula for a single application to</span></span></span> <span class="r-in"><span><span class="co"># "Ackerbau" from the paper</span></span></span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</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> 0.91976667 0.19064473 0.09680051 0.04915079 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># This makes it possible to also use different distances</span></span></span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <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">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</span> <span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> <span class="r-out co"><span class="r-pr">#></span> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 </span> <span class="r-out co"><span class="r-pr">#></span> 100 m </span> <span class="r-out co"><span class="r-pr">#></span> 0.01018774 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># or consider aerial application</span></span></span> -<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <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">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>, </span></span> -<span class="r-in"><span> crop_group_focus <span class="op">=</span> <span class="st">"aerial"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <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">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>,</span></span> +<span class="r-in"><span> crop_group_RF <span class="op">=</span> <span class="st">"aerial"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</span> <span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> <span class="r-out co"><span class="r-pr">#></span> 16.8233333 11.0585820 9.0986174 8.4866460 6.9825178 4.7004640 1.8820816 </span> <span class="r-out co"><span class="r-pr">#></span> 100 m </span> @@ -178,47 +180,53 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Using custom drift percentages is also supported</span></span></span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_percentages <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">2.77</span>, <span class="fl">0.95</span>, <span class="fl">0.57</span>, <span class="fl">0.48</span>, <span class="fl">0.29</span>, <span class="fl">0.15</span>, <span class="fl">0.06</span>, <span class="fl">0.03</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</span> <span class="r-out co"><span class="r-pr">#></span> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % </span> <span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 </span> <span class="r-out co"><span class="r-pr">#></span> 0.03 % </span> <span class="r-out co"><span class="r-pr">#></span> 0.01000000 </span> <span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># The influence of assuming a 45° angle of the sides of the waterbody and the width of the </span></span></span> +<span class="r-in"><span><span class="co"># The influence of assuming a 45° angle of the sides of the waterbody and the width of the</span></span></span> <span class="r-in"><span><span class="co"># waterbody can be illustrated</span></span></span> <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> Units: [µg/L]</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> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</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> 0.91976667 0.19064473 0.09680051 0.04915079 </span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>, formula <span class="op">=</span> <span class="st">"FOCUS"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</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> 0.64246407 0.17414541 0.09235842 0.04798749 </span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>, formula <span class="op">=</span> <span class="st">"FOCUS"</span>, side_angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</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> 0.91780582 0.24877916 0.13194060 0.06855356 </span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>, formula <span class="op">=</span> <span class="st">"FOCUS"</span>, side_angle <span class="op">=</span> <span class="fl">45</span>, water_width <span class="op">=</span> <span class="fl">200</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</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> 0.30085000 0.09468652 0.05201349 0.02758547 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.60169999 0.18937304 0.10402698 0.05517095 </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 5da26c6..a2dab7e 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -1,56 +1,47 @@ <!DOCTYPE html> -<!-- 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, +<!-- 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>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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></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 name="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 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 -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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate 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, +details, see the discussion of the function arguments below.'><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 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 -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> +details, see the discussion of the function arguments below.'></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate PEC surface water due to drainage as in Exposit 3</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit_runoff.R" class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + + <h1>Calculate PEC surface water due to drainage as in Exposit 3</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit.R" class="external-link"><code>R/PEC_sw_exposit.R</code></a></small> <div class="d-none name"><code>PEC_sw_exposit_drainage.Rd</code></div> </div> @@ -86,57 +77,57 @@ 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> - <dl><dt>rate</dt> + + +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>The application rate in g/ha</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>The fraction intercepted by the crop</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></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> -<dt>mobility</dt> +<dt id="arg-mobility">mobility<a class="anchor" aria-label="anchor" href="#arg-mobility"></a></dt> <dd><p>Overrides what is determined from the Koc.</p></dd> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>The soil half-life in days</p></dd> -<dt>t_drainage</dt> +<dt id="arg-t-drainage">t_drainage<a class="anchor" aria-label="anchor" href="#arg-t-drainage"></a></dt> <dd><p>The time between application and the drainage event, where degradation occurs, in days</p></dd> -<dt>V_ditch</dt> +<dt id="arg-v-ditch">V_ditch<a class="anchor" aria-label="anchor" href="#arg-v-ditch"></a></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> +<dt id="arg-v-drainage">V_drainage<a class="anchor" aria-label="anchor" href="#arg-v-drainage"></a></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> +<dt id="arg-dilution">dilution<a class="anchor" aria-label="anchor" href="#arg-dilution"></a></dt> <dd><p>The dilution factor</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A list containing the following components</p><dl><dt>perc_runoff</dt> -<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + <p>A list containing the following components</p><dl><dt>perc_drainage_total</dt> +<dd><p>Gesamtaustrag (total fraction of the residue drained)</p></dd> -<dt>runoff</dt> -<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> +<dt>perc_peak</dt> +<dd><p>Stoßbelastung (fraction drained at event)</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> +<dt>PEC_sw_drainage</dt> +<dd><p>A matrix containing PEC values for the spring and autumn +scenarios. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> </dl></div> @@ -162,23 +153,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 21731f3..cd57c99 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,46 +1,37 @@ 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3.02 spreadsheet file, +in the worksheet "Konzept Runoff".'></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li 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aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate PEC surface water due to runoff and erosion as in Exposit 3</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit_runoff.R" class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + + <h1>Calculate PEC surface water due to runoff and erosion as in Exposit 3</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit.R" class="external-link"><code>R/PEC_sw_exposit.R</code></a></small> <div class="d-none name"><code>PEC_sw_exposit_runoff.Rd</code></div> </div> @@ -55,11 +46,11 @@ in the worksheet "Konzept Runoff".</p> <span> <span class="va">rate</span>,</span> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> <span> <span class="va">Koc</span>,</span> -<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> -<span> t_runoff <span class="op">=</span> <span class="fl">3</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="cn">Inf</span>, <span class="st">"d"</span><span class="op">)</span>,</span> +<span> t_runoff <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">3</span>, <span class="st">"days"</span><span class="op">)</span>,</span> <span> exposit_reduction_version <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">"3.02"</span>, <span class="st">"3.01a"</span>, <span class="st">"3.01a2"</span>, <span class="st">"2.0"</span><span class="op">)</span>,</span> -<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> -<span> V_event <span class="op">=</span> <span class="fl">100</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">30</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> +<span> V_event <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> <span> dilution <span class="op">=</span> <span class="fl">2</span></span> <span><span class="op">)</span></span></code></pre></div> </div> @@ -71,27 +62,29 @@ 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> - <dl><dt>rate</dt> + + +<dl><dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>The application rate in g/ha</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>The fraction intercepted by the crop</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>The sorption coefficient to soil organic carbon</p></dd> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>The soil half-life in days</p></dd> -<dt>t_runoff</dt> +<dt id="arg-t-runoff">t_runoff<a class="anchor" aria-label="anchor" href="#arg-t-runoff"></a></dt> <dd><p>The time between application and the runoff event, where degradation occurs, in days</p></dd> -<dt>exposit_reduction_version</dt> +<dt id="arg-exposit-reduction-version">exposit_reduction_version<a class="anchor" aria-label="anchor" href="#arg-exposit-reduction-version"></a></dt> <dd><p>The version of the reduction factors to be used. "3.02" is the current version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations @@ -99,23 +92,21 @@ performed for a 3 m buffer zone in Switzerland, with the same reduction being ap and the bound fraction.</p></dd> -<dt>V_ditch</dt> +<dt id="arg-v-ditch">V_ditch<a class="anchor" aria-label="anchor" href="#arg-v-ditch"></a></dt> <dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> -<dt>V_event</dt> +<dt id="arg-v-event">V_event<a class="anchor" aria-label="anchor" href="#arg-v-event"></a></dt> <dd><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></dd> -<dt>dilution</dt> +<dt id="arg-dilution">dilution<a class="anchor" aria-label="anchor" href="#arg-dilution"></a></dt> <dd><p>The dilution factor</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A list containing the following components</p><dl><dt>perc_runoff</dt> + <p>A list containing the following components</p><dl><dt>perc_runoff</dt> <dd><p>The runoff percentages for dissolved and bound substance</p></dd> <dt>runoff</dt> @@ -128,6 +119,11 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic </dl></div> <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>It is recommened to specify the arguments <code>rate</code>, <code>Koc</code>, <code>DT50</code>, <code>t_runoff</code>, <code>V_ditch</code> and <code>V_event</code> +using <a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">units::units</a> from the <code>units</code> package.</p> + </div> + <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="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> @@ -140,18 +136,18 @@ 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> 0.248 0.001 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $runoff</span> -<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> -<span class="r-out co"><span class="r-pr">#></span> No buffer 1.240 0.00500 1.24500</span> -<span class="r-out co"><span class="r-pr">#></span> 5 m 0.744 0.00300 0.74700</span> -<span class="r-out co"><span class="r-pr">#></span> 10 m 0.496 0.00075 0.49675</span> -<span class="r-out co"><span class="r-pr">#></span> 20 m 0.248 0.00025 0.24825</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 1.240 [g] 0.00500 [g] 1.24500 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.744 [g] 0.00300 [g] 0.74700 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.496 [g] 0.00075 [g] 0.49675 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.248 [g] 0.00025 [g] 0.24825 [g]</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> -<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> -<span class="r-out co"><span class="r-pr">#></span> No buffer 4.769231 0.019230769 4.788462</span> -<span class="r-out co"><span class="r-pr">#></span> 5 m 4.133333 0.016666667 4.150000</span> -<span class="r-out co"><span class="r-pr">#></span> 10 m 3.542857 0.005357143 3.548214</span> -<span class="r-out co"><span class="r-pr">#></span> 20 m 2.480000 0.002500000 2.482500</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 4.769231 [µg/L] 0.019230769 [µg/L] 4.788462 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 4.133333 [µg/L] 0.016666667 [µg/L] 4.150000 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 3.542857 [µg/L] 0.005357143 [µg/L] 3.548214 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 2.480000 [µg/L] 0.002500000 [µg/L] 2.482500 [µg/L]</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">600</span>, Koc <span class="op">=</span> <span class="fl">10000</span>, DT50 <span class="op">=</span> <span class="fl">195</span>, exposit <span class="op">=</span> <span class="st">"3.01a"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> @@ -159,42 +155,42 @@ 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> 0.037 0.159 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $runoff</span> -<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> -<span class="r-out co"><span class="r-pr">#></span> No buffer 0.21964521 0.94388078 1.16352600</span> -<span class="r-out co"><span class="r-pr">#></span> 3 m 0.16473391 0.66071655 0.82545046</span> -<span class="r-out co"><span class="r-pr">#></span> 5 m 0.13178713 0.56632847 0.69811560</span> -<span class="r-out co"><span class="r-pr">#></span> 6 m 0.12080487 0.42474635 0.54555122</span> -<span class="r-out co"><span class="r-pr">#></span> 10 m 0.08785809 0.14158212 0.22944020</span> -<span class="r-out co"><span class="r-pr">#></span> 20 m 0.04392904 0.04719404 0.09112308</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.21964521 [g] 0.94388078 [g] 1.16352600 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.16473391 [g] 0.66071655 [g] 0.82545046 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.13178713 [g] 0.56632847 [g] 0.69811560 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.12080487 [g] 0.42474635 [g] 0.54555122 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.08785809 [g] 0.14158212 [g] 0.22944020 [g]</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.04392904 [g] 0.04719404 [g] 0.09112308 [g]</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> -<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> -<span class="r-out co"><span class="r-pr">#></span> No buffer 0.8447893 3.6303107 4.4751000</span> -<span class="r-out co"><span class="r-pr">#></span> 3 m 0.7844472 3.1462693 3.9307165</span> -<span class="r-out co"><span class="r-pr">#></span> 5 m 0.7321507 3.1462693 3.8784200</span> -<span class="r-out co"><span class="r-pr">#></span> 6 m 0.7106169 2.4985080 3.2091248</span> -<span class="r-out co"><span class="r-pr">#></span> 10 m 0.6275578 1.0113008 1.6388586</span> -<span class="r-out co"><span class="r-pr">#></span> 20 m 0.4392904 0.4719404 0.9112308</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.8447893 [µg/L] 3.6303107 [µg/L] 4.4751000 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.7844472 [µg/L] 3.1462693 [µg/L] 3.9307165 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.7321507 [µg/L] 3.1462693 [µg/L] 3.8784200 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.7106169 [µg/L] 2.4985080 [µg/L] 3.2091248 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.6275578 [µg/L] 1.0113008 [µg/L] 1.6388586 [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.4392904 [µg/L] 0.4719404 [µg/L] 0.9112308 [µg/L]</span> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index d9d06de..d91d957 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,55 +1,46 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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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 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> +the FOCUS calculator."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate PEC surface water at FOCUS Step 1</h1> + + <h1>Calculate PEC surface water at FOCUS Step 1</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_focus.R" class="external-link"><code>R/PEC_sw_focus.R</code></a></small> <div class="d-none name"><code>PEC_sw_focus.Rd</code></div> </div> @@ -89,85 +80,87 @@ the FOCUS calculator.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>parent</dt> + + +<dl><dt id="arg-parent">parent<a class="anchor" aria-label="anchor" href="#arg-parent"></a></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> -<dt>rate</dt> +<dt id="arg-rate">rate<a class="anchor" aria-label="anchor" href="#arg-rate"></a></dt> <dd><p>The application rate in g/ha. Overriden when applications are given explicitly</p></dd> -<dt>n</dt> +<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt> <dd><p>The number of applications</p></dd> -<dt>i</dt> +<dt id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></dt> <dd><p>The application interval</p></dd> -<dt>comment</dt> +<dt id="arg-comment">comment<a class="anchor" aria-label="anchor" href="#arg-comment"></a></dt> <dd><p>A comment for the input file</p></dd> -<dt>met</dt> +<dt id="arg-met">met<a class="anchor" aria-label="anchor" href="#arg-met"></a></dt> <dd><p>A list containing metabolite specific parameters. e.g. conveniently generated by <a href="chent_focus_sw.html">chent_focus_sw</a>. If not NULL, the PEC is calculated for this compound, not the parent.</p></dd> -<dt>f_drift</dt> +<dt id="arg-f-drift">f_drift<a class="anchor" aria-label="anchor" href="#arg-f-drift"></a></dt> <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 <a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd> -<dt>f_rd</dt> +<dt id="arg-f-rd">f_rd<a class="anchor" aria-label="anchor" href="#arg-f-rd"></a></dt> <dd><p>The fraction of the amount applied reaching the waterbody via runoff/drainage. At Step 1, it is assumed to be 10%, be it the parent or a metabolite</p></dd> -<dt>scenario</dt> +<dt id="arg-scenario">scenario<a class="anchor" aria-label="anchor" href="#arg-scenario"></a></dt> <dd><p>The name of the scenario. Must be one of the scenario names given in <a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd> -<dt>region</dt> +<dt id="arg-region">region<a class="anchor" aria-label="anchor" href="#arg-region"></a></dt> <dd><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only Step 1 PECsw are calculated</p></dd> -<dt>season</dt> +<dt id="arg-season">season<a class="anchor" aria-label="anchor" href="#arg-season"></a></dt> <dd><p>'of' for October to February, 'mm' for March to May, and 'js' for June to September. If NA, only step 1 PECsw are calculated</p></dd> -<dt>interception</dt> +<dt id="arg-interception">interception<a class="anchor" aria-label="anchor" href="#arg-interception"></a></dt> <dd><p>One of 'no interception' (default), 'minimal crop cover', 'average crop cover' or 'full canopy'</p></dd> -<dt>met_form_water</dt> +<dt id="arg-met-form-water">met_form_water<a class="anchor" aria-label="anchor" href="#arg-met-form-water"></a></dt> <dd><p>Should the metabolite formation in water be taken into account? This can be switched off to check the influence and to compare with previous versions of the Steps 12 calculator</p></dd> -<dt>txt_file</dt> +<dt id="arg-txt-file">txt_file<a class="anchor" aria-label="anchor" href="#arg-txt-file"></a></dt> <dd><p>the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) should be written</p></dd> -<dt>overwrite</dt> +<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt> <dd><p>Should an existing file a the location specified in <code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></dd> -<dt>append</dt> +<dt id="arg-append">append<a class="anchor" aria-label="anchor" href="#arg-append"></a></dt> <dd><p>Should the input text file be appended, if it exists?</p></dd> </dl></div> @@ -294,23 +287,23 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - 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— PEC_sw_sed"><meta name="description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator"><meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" 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href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate predicted environmental concentrations in sediment from surface -water concentrations</h1> + + <h1>Calculate predicted environmental concentrations in sediment from surface water concentrations</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_sed.R" class="external-link"><code>R/PEC_sw_sed.R</code></a></small> <div class="d-none name"><code>PEC_sw_sed.Rd</code></div> </div> @@ -58,50 +46,50 @@ PEC calculator</p> <span> <span class="va">PEC_sw</span>,</span> <span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> <span> method <span class="op">=</span> <span class="st">"percentage"</span>,</span> -<span> sediment_depth <span class="op">=</span> <span class="fl">5</span>,</span> -<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> -<span> sediment_density <span class="op">=</span> <span class="fl">1.3</span>,</span> +<span> sediment_depth <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">5</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">30</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> +<span> sediment_density <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">1.3</span>, <span class="st">"kg/L"</span><span class="op">)</span>,</span> <span> PEC_sed_units <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">"µg/kg"</span>, <span class="st">"mg/kg"</span><span class="op">)</span></span> <span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>PEC_sw</dt> + + +<dl><dt id="arg-pec-sw">PEC_sw<a class="anchor" aria-label="anchor" href="#arg-pec-sw"></a></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> -<dt>percentage</dt> +<dt id="arg-percentage">percentage<a class="anchor" aria-label="anchor" href="#arg-percentage"></a></dt> <dd><p>The percentage in sediment, used for the percentage method</p></dd> -<dt>method</dt> +<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt> <dd><p>The method used for the calculation</p></dd> -<dt>sediment_depth</dt> +<dt id="arg-sediment-depth">sediment_depth<a class="anchor" aria-label="anchor" href="#arg-sediment-depth"></a></dt> <dd><p>Depth of the sediment layer</p></dd> -<dt>water_depth</dt> +<dt id="arg-water-depth">water_depth<a class="anchor" aria-label="anchor" href="#arg-water-depth"></a></dt> <dd><p>Depth of the water body in cm</p></dd> -<dt>sediment_density</dt> -<dd><p>The density of the sediment in L/kg (equivalent to +<dt id="arg-sediment-density">sediment_density<a class="anchor" aria-label="anchor" href="#arg-sediment-density"></a></dt> +<dd><p>The density of the sediment in kg/L (equivalent to g/cm3)</p></dd> -<dt>PEC_sed_units</dt> +<dt id="arg-pec-sed-units">PEC_sed_units<a class="anchor" aria-label="anchor" href="#arg-pec-sed-units"></a></dt> <dd><p>The units of the estimated sediment PEC value</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The predicted concentration in sediment</p> + <p>The predicted concentration in sediment</p> </div> <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> @@ -110,28 +98,30 @@ g/cm3)</p></dd> <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> - <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> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/pfm">pfm</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://r-quantities.github.io/units/" class="external-link">units</a></span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> udunits database from /usr/share/xml/udunits/udunits2.xml</span> +<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> 2.130769 [µg/kg]</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a 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window time average concentrations for SFO kinetics</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/SFO_actual_twa.R" class="external-link"><code>R/SFO_actual_twa.R</code></a></small> <div class="d-none name"><code>SFO_actual_twa.Rd</code></div> </div> @@ -59,11 +50,13 @@ 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> - <dl><dt>DT50</dt> + + +<dl><dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>The half-life.</p></dd> -<dt>times</dt> +<dt id="arg-times">times<a class="anchor" aria-label="anchor" href="#arg-times"></a></dt> <dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> </dl></div> @@ -89,23 +82,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 1874128..3463b3c 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -1,45 +1,36 @@ 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class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> + + <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/SSLRC_mobility_classification.R" class="external-link"><code>R/SSLRC_mobility_classification.R</code></a></small> <div class="d-none name"><code>SSLRC_mobility_classification.Rd</code></div> </div> @@ -56,15 +47,15 @@ checked against the spreadsheet published on the CRD website</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>Koc</dt> + + +<dl><dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A list containing the classification and the percentage of the + <p>A list containing the classification and the percentage of the compound transported per 10 mm drain water</p> </div> <div class="section level2"> @@ -100,23 +91,23 @@ accessed 2019-09-27</p> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 281315a..f620349 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,51 +1,42 @@ <!DOCTYPE html> -<!-- 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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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> +by read.TOXSWA_cwa."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> + + <h1>R6 class for holding TOXSWA water concentration data and associated statistics</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/TOXSWA_cwa.R" class="external-link"><code>R/TOXSWA_cwa.R</code></a></small> <div class="d-none name"><code>TOXSWA_cwa.Rd</code></div> </div> @@ -61,7 +52,7 @@ by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> <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> + <p>An <code><a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6Class</a></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> @@ -103,7 +94,7 @@ for the requested moving window sizes in days.</p></dd> </div> <div class="section level2"> <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2> - + <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> @@ -264,23 +255,23 @@ suspended matter will be used.</p></dd> <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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html index 8391cb4..f611a53 100644 --- a/docs/reference/TSCF.html +++ b/docs/reference/TSCF.html @@ -1,53 +1,44 @@ <!DOCTYPE html> -<!-- 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 +<!-- 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>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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Estimation of the transpiration stream concentration factor — TSCF"><meta name="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 equation is stated to be produced for non-ionic compounds, suggesting that the compound should not be ionogenic (weak acid/base) -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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="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 +or ionic."><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 equation is stated to be produced for non-ionic compounds, suggesting that the compound should not be ionogenic (weak acid/base) -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> +or ionic."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Estimation of the transpiration stream concentration factor</h1> + + <h1>Estimation of the transpiration stream concentration factor</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/TSCF.R" class="external-link"><code>R/TSCF.R</code></a></small> <div class="d-none name"><code>TSCF.Rd</code></div> </div> @@ -68,11 +59,13 @@ or ionic.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>log_Kow</dt> + + +<dl><dt id="arg-log-kow">log_Kow<a class="anchor" aria-label="anchor" href="#arg-log-kow"></a></dt> <dd><p>The decadic logarithm of the octanol-water partition constant</p></dd> -<dt>method</dt> +<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt> <dd><p>Short name of the estimation method.</p></dd> </dl></div> @@ -98,23 +91,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 5d9c11e..064264f 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -1,48 +1,36 @@ <!DOCTYPE html> -<!-- 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drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse 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name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Deposition from spray drift expressed as percent of the applied dose as -published by the JKI</h1> + + <h1>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/drift_data_JKI.R" class="external-link"><code>R/drift_data_JKI.R</code></a></small> <div class="d-none name"><code>drift_data_JKI.Rd</code></div> </div> @@ -288,23 +276,23 @@ included.</p> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/drift_parameters_focus.html b/docs/reference/drift_parameters_focus.html index 3f54160..6d3f679 100644 --- a/docs/reference/drift_parameters_focus.html +++ b/docs/reference/drift_parameters_focus.html @@ -1,49 +1,40 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit 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The appendix itself 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]> -<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> +as its licence is not clear."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Regression parameters for the Rautmann drift data</h1> + + <h1>Regression parameters for the Rautmann drift data</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/drift_parameters_focus.R" class="external-link"><code>R/drift_parameters_focus.R</code></a></small> <div class="d-none name"><code>drift_parameters_focus.Rd</code></div> </div> @@ -111,23 +102,23 @@ Bundesanst. Land- Forstwirtsch. 383, 133-141</p> <span class="r-out co"><span class="r-pr">#></span> [6] "fruit, early" "aerial" </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/drift_percentages_rautmann.html b/docs/reference/drift_percentages_rautmann.html index ae5ca03..bee0e60 100644 --- a/docs/reference/drift_percentages_rautmann.html +++ b/docs/reference/drift_percentages_rautmann.html @@ -1,43 +1,34 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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If you specify "FOCUS", mean drift input over the width of the water body is calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance</p></dd> -<dt>widths</dt> +<dt id="arg-widths">widths<a class="anchor" aria-label="anchor" href="#arg-widths"></a></dt> <dd><p>The widths of the water bodies (only used in the FOCUS formula)</p></dd> </dl></div> @@ -135,23 +128,23 @@ FOrum for the Co-ordination of pesticde fate models and their USe. <span class="r-plt img"><img src="drift_percentages_rautmann-1.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 6705770..228d77f 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,49 +1,40 @@ <!DOCTYPE html> -<!-- 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 +<!-- 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>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint"><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. 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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> +this function."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Retrieve endpoint information from the chyaml field of a chent object</h1> + + <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/endpoint.R" class="external-link"><code>R/endpoint.R</code></a></small> <div class="d-none name"><code>endpoint.Rd</code></div> </div> @@ -94,59 +85,59 @@ this function.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>chent</dt> + + +<dl><dt id="arg-chent">chent<a class="anchor" aria-label="anchor" href="#arg-chent"></a></dt> <dd><p>The chent object to get the information from</p></dd> -<dt>medium</dt> +<dt id="arg-medium">medium<a class="anchor" aria-label="anchor" href="#arg-medium"></a></dt> <dd><p>The medium for which information is sought</p></dd> -<dt>type</dt> +<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt> <dd><p>The information type</p></dd> -<dt>lab_field</dt> +<dt id="arg-lab-field">lab_field<a class="anchor" aria-label="anchor" href="#arg-lab-field"></a></dt> <dd><p>If not NA, do we want laboratory or field endpoints</p></dd> -<dt>redox</dt> +<dt id="arg-redox">redox<a class="anchor" aria-label="anchor" href="#arg-redox"></a></dt> <dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd> -<dt>value</dt> +<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt> <dd><p>The name of the value we want. The list given in the usage section is not exclusive</p></dd> -<dt>aggregator</dt> +<dt id="arg-aggregator">aggregator<a class="anchor" aria-label="anchor" href="#arg-aggregator"></a></dt> <dd><p>The aggregator function. Can be mean, <code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd> -<dt>raw</dt> +<dt id="arg-raw">raw<a class="anchor" aria-label="anchor" href="#arg-raw"></a></dt> <dd><p>Should the number(s) be returned as stored in the chent object (could be a character value) to retain original information about precision?</p></dd> -<dt>signif</dt> +<dt id="arg-signif">signif<a class="anchor" aria-label="anchor" href="#arg-signif"></a></dt> <dd><p>How many significant digits do we want</p></dd> -<dt>values</dt> +<dt id="arg-values">values<a class="anchor" aria-label="anchor" href="#arg-values"></a></dt> <dd><p>The values to be returned</p></dd> -<dt>aggregators</dt> +<dt id="arg-aggregators">aggregators<a class="anchor" aria-label="anchor" href="#arg-aggregators"></a></dt> <dd><p>A named vector of aggregator functions to be used</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The result from applying the aggregator function to + <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 @@ -160,23 +151,23 @@ facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.</p> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/index.html b/docs/reference/index.html index aaa499d..97f59b5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,337 +1,365 @@ <!DOCTYPE html> -<!-- 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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- 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> +<!-- 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>Package index • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.2</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - 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+ </div> </nav><div class="container template-reference-index"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Function reference</h1> + + <h1>Package index</h1> </div> <div class="section level2"> <h2 id="general-utility-functions">General utility functions<a class="anchor" aria-label="anchor" href="#general-utility-functions"></a></h2> - - <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="geomean.html">geomean()</a></code> + + <code><a href="geomean.html">geomean()</a></code> + </dt> <dd>Calculate the geometric mean</dd> </dl><dl><dt> - - <code><a href="one_box.html">one_box()</a></code> + + <code><a href="one_box.html">one_box()</a></code> + </dt> <dd>Create a time series of decline data</dd> </dl><dl><dt> - - <code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> + + <code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> + </dt> <dd>Plot time series of decline data</dd> </dl><dl><dt> - - <code><a href="sawtooth.html">sawtooth()</a></code> + + <code><a href="sawtooth.html">sawtooth()</a></code> + </dt> <dd>Create decline time series for multiple applications</dd> </dl><dl><dt> - - <code><a href="twa.html">twa()</a></code> + + <code><a href="twa.html">twa()</a></code> + </dt> <dd>Calculate a time weighted average concentration</dd> </dl><dl><dt> - - <code><a href="max_twa.html">max_twa()</a></code> + + <code><a href="max_twa.html">max_twa()</a></code> + </dt> <dd>The maximum time weighted average concentration for a moving window</dd> </dl><dl><dt> - - <code><a href="pfm_degradation.html">pfm_degradation()</a></code> + + <code><a href="pfm_degradation.html">pfm_degradation()</a></code> + </dt> <dd>Calculate a time course of relative concentrations based on an mkinmod model</dd> </dl><dl><dt> - - <code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> + + <code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> + </dt> <dd>Actual and maximum moving window time average concentrations for SFO kinetics</dd> </dl><dl><dt> - - <code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> + + <code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> + </dt> <dd>Actual and maximum moving window time average concentrations for FOMC kinetics</dd> </dl><dl><dt> - - <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> + + <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> + </dt> <dd>Objects exported from other packages</dd> </dl><dl><dt> - - <code><a href="TSCF.html">TSCF()</a></code> + + <code><a href="TSCF.html">TSCF()</a></code> + </dt> <dd>Estimation of the transpiration stream concentration factor</dd> </dl></div><div class="section level2"> <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-soil"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="PEC_soil.html">PEC_soil()</a></code> + + <code><a href="PEC_soil.html">PEC_soil()</a></code> + </dt> <dd>Calculate predicted environmental concentrations in soil</dd> </dl><dl><dt> - - <code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> + + <code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> + </dt> <dd>Calculate initial and accumulation PEC soil for a set of metabolites</dd> </dl><dl><dt> - - <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> + + <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> + </dt> <dd>Properties of the predefined scenarios from the EFSA guidance from 2015</dd> </dl><dl><dt> - - <code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> + + <code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> + </dt> <dd>Properties of the predefined scenarios from the EFSA guidance from 2017</dd> </dl><dl><dt> - - <code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> + + <code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> + </dt> <dd>Get the relative accumulation of an FOMC model over multiples of an interval</dd> </dl><dl><dt> - - <code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> + + <code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> + </dt> <dd>Subset of EFSA crop washoff default values</dd> </dl></div><div class="section level2"> <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-groundwater"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> + + <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> + </dt> <dd>A very small subset of the FOCUS Groundwater scenario definitions</dd> </dl><dl><dt> - - <code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> + + <code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> + </dt> <dd>Subset of EFSA crop interception default values for groundwater modelling</dd> </dl></div><div class="section level2"> <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water<a class="anchor" aria-label="anchor" href="#predicted-environmental-concentrations-in-surface-water"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> + + <code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> + </dt> <dd>Calculate predicted environmental concentrations in surface water due to drift</dd> </dl><dl><dt> - - <code><a href="drift_data_JKI.html">drift_data_JKI</a></code> + + <code><a href="drift_data_JKI.html">drift_data_JKI</a></code> + </dt> - <dd>Deposition from spray drift expressed as percent of the applied dose as -published by the JKI</dd> + <dd>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</dd> </dl><dl><dt> - - <code><a href="drift_parameters_focus.html">drift_parameters_focus</a></code> + + <code><a href="drift_parameters_focus.html">drift_parameters_focus</a></code> + </dt> <dd>Regression parameters for the Rautmann drift data</dd> </dl><dl><dt> - - <code><a href="drift_percentages_rautmann.html">drift_percentages_rautmann()</a></code> + + <code><a href="drift_percentages_rautmann.html">drift_percentages_rautmann()</a></code> + </dt> <dd>Calculate drift percentages based on Rautmann data</dd> </dl><dl><dt> - - <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> + + <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> + </dt> <dd>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</dd> </dl><dl><dt> - - <code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> + + <code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> + </dt> - <dd>Calculate predicted environmental concentrations in sediment from surface -water concentrations</dd> + <dd>Calculate predicted environmental concentrations in sediment from surface water concentrations</dd> </dl><dl><dt> - - <code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> + + <code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> + </dt> <dd>Calculate PEC surface water at FOCUS Step 1</dd> </dl><dl><dt> - - <code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> + + <code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> + </dt> <dd>Create a chemical compound object for FOCUS Step 1 calculations</dd> </dl><dl><dt> - - <code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> + + <code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> + </dt> <dd>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</dd> </dl><dl><dt> - - <code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> + + <code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> + </dt> <dd>Calculate PEC surface water due to drainage as in Exposit 3</dd> </dl><dl><dt> - - <code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> + + <code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> + </dt> <dd>Calculate PEC surface water due to runoff and erosion as in Exposit 3</dd> </dl><dl><dt> - - <code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> + + <code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> + </dt> <dd>Runoff loss percentages as used in Exposit 3</dd> </dl><dl><dt> - - <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> + + <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> + </dt> <dd>Runoff reduction percentages as used in Exposit</dd> </dl><dl><dt> - - <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> + + <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> + </dt> <dd>R6 class for holding TOXSWA water concentration data and associated statistics</dd> </dl><dl><dt> - - <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> + + <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> + </dt> <dd>Read TOXSWA surface water concentrations</dd> </dl><dl><dt> - - <code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> + + <code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> + </dt> <dd>Plot TOXSWA surface water concentrations</dd> </dl></div><div class="section level2"> <h2 id="classifications-and-indicators">Classifications and indicators<a class="anchor" aria-label="anchor" href="#classifications-and-indicators"></a></h2> - - <p class="section-desc"></p><p>Evaluating environmental fate properties</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Evaluating environmental fate properties</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> + + <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> + </dt> <dd>Determine the SSLRC mobility classification for a chemical substance from its Koc</dd> </dl><dl><dt> - - <code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> + + <code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> + </dt> <dd>Groundwater ubiquity score based on Gustafson (1989)</dd> </dl></div><div class="section level2"> <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information<a class="anchor" aria-label="anchor" href="#work-with-chent-objects-containing-relevant-information"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <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> + + <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> + </dt> <dd>Retrieve endpoint information from the chyaml field of a chent object</dd> </dl></div><div class="section level2"> <h2 id="utilities">Utilities<a class="anchor" aria-label="anchor" href="#utilities"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="get_vertex.html">get_vertex()</a></code> + + <code><a href="get_vertex.html">get_vertex()</a></code> + </dt> <dd>Fit a parabola through three points</dd> </dl></div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 4d469eb..74eeb46 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -1,51 +1,42 @@ <!DOCTYPE html> -<!-- 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, +<!-- 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>The maximum time weighted average concentration for a moving window — max_twa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The maximum time weighted average concentration for a moving window — max_twa"><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. 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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> +max_twa."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>The maximum time weighted average concentration for a moving window</h1> + + <h1>The maximum time weighted average concentration for a moving window</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/twa.R" class="external-link"><code>R/twa.R</code></a></small> <div class="d-none name"><code>max_twa.Rd</code></div> </div> @@ -65,17 +56,19 @@ 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> - <dl><dt>x</dt> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> -<dt>window</dt> +<dt id="arg-window">window<a class="anchor" aria-label="anchor" href="#arg-window"></a></dt> <dd><p>The size of the moving window</p></dd> </dl></div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> - <p>The method working directly on fitted <code>mkinfit</code> objects uses the + <p>The method working directly on fitted <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></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> @@ -109,29 +102,29 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-out co"><span class="r-pr">#></span> parent </span> <span class="r-out co"><span class="r-pr">#></span> 21 </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span><span class="va">pred_FOMC</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_FOMC</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</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_FOMC</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 21 </span> <span class="r-out co"><span class="r-pr">#></span> 18.22124 </span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git 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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github 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href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit_runoff.R" class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + + <h1>Runoff loss percentages as used in Exposit 3</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit.R" class="external-link"><code>R/PEC_sw_exposit.R</code></a></small> <div class="d-none name"><code>perc_runoff_exposit.Rd</code></div> </div> @@ -77,37 +68,37 @@ adjacent water body bound to eroding particles</p></dd> <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="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> -<span class="r-out co"><span class="r-pr">#></span> >20-50 20 0.151 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> >50-100 50 0.197 0.000</span> -<span class="r-out co"><span class="r-pr">#></span> >100-200 100 0.248 0.001</span> -<span class="r-out co"><span class="r-pr">#></span> >200-500 200 0.224 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> >500-1000 500 0.184 0.020</span> -<span class="r-out co"><span class="r-pr">#></span> >1000-2000 1000 0.133 0.042</span> -<span class="r-out co"><span class="r-pr">#></span> >2000-5000 2000 0.084 0.091</span> -<span class="r-out co"><span class="r-pr">#></span> >5000-10000 5000 0.037 0.159</span> -<span class="r-out co"><span class="r-pr">#></span> >10000-20000 10000 0.031 0.192</span> -<span class="r-out co"><span class="r-pr">#></span> >20000-50000 20000 0.014 0.291</span> -<span class="r-out co"><span class="r-pr">#></span> >50000 50000 0.001 0.451</span> +<span class="r-out co"><span class="r-pr">#></span> 0-20 0 [L/kg] 0.110 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >20-50 20 [L/kg] 0.151 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >50-100 50 [L/kg] 0.197 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >100-200 100 [L/kg] 0.248 0.001</span> +<span class="r-out co"><span class="r-pr">#></span> >200-500 200 [L/kg] 0.224 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> >500-1000 500 [L/kg] 0.184 0.020</span> +<span class="r-out co"><span class="r-pr">#></span> >1000-2000 1000 [L/kg] 0.133 0.042</span> +<span class="r-out co"><span class="r-pr">#></span> >2000-5000 2000 [L/kg] 0.084 0.091</span> +<span class="r-out co"><span class="r-pr">#></span> >5000-10000 5000 [L/kg] 0.037 0.159</span> +<span class="r-out co"><span class="r-pr">#></span> >10000-20000 10000 [L/kg] 0.031 0.192</span> +<span class="r-out co"><span class="r-pr">#></span> >20000-50000 20000 [L/kg] 0.014 0.291</span> +<span class="r-out co"><span class="r-pr">#></span> >50000 50000 [L/kg] 0.001 0.451</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 24a199e..5bb3a57 100644 --- 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data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Runoff reduction percentages as used in Exposit</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit_runoff.R" class="external-link"><code>R/PEC_sw_exposit_runoff.R</code></a></small> + + <h1>Runoff reduction percentages as used in Exposit</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/PEC_sw_exposit.R" class="external-link"><code>R/PEC_sw_exposit.R</code></a></small> <div class="d-none name"><code>perc_runoff_reduction_exposit.Rd</code></div> </div> @@ -103,23 +94,23 @@ 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> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/print.GUS_result.html b/docs/reference/print.GUS_result.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/print.GUS_result.html @@ -0,0 +1,8 @@ +<html> + <head> + 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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> +scenario and model adjustment factors from p. 15 and p. 17 are included."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.3</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> + + <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/soil_scenario_data_EFSA_2015.R" class="external-link"><code>R/soil_scenario_data_EFSA_2015.R</code></a></small> <div class="d-none name"><code>soil_scenario_data_EFSA_2015.Rd</code></div> </div> @@ -91,23 +82,23 @@ active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 <span class="r-out co"><span class="r-pr">#></span> CLS 4</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index b1adfab..1a6157a 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,47 +1,38 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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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> +scenario and model adjustment factors from p. 16 and p. 18 are included."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">pfm</a> - 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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/soil_sorption.html b/docs/reference/soil_sorption.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_sorption.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/endpoint.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/endpoint.html"> + </head> +</html> + diff --git a/docs/reference/twa.one_box.html b/docs/reference/twa.one_box.html new file mode 100644 index 0000000..9372dd5 --- /dev/null +++ b/docs/reference/twa.one_box.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/twa.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/twa.html"> + </head> +</html> + |