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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 interception default values for groundwater modelling</h1> + + <h1>Subset of EFSA crop interception default values for groundwater modelling</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/EFSA_GW_interception_2014.R" 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 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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="">0.6.4</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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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..434a6aa 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 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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>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> + + <h1>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/FOCUS_Step_12_scenarios.R" class="external-link"><code>R/FOCUS_Step_12_scenarios.R</code></a></small> <div class="d-none name"><code>FOCUS_Step_12_scenarios.Rd</code></div> </div> @@ -101,23 +92,23 @@ calculations in a matrix called 'rd'.</p> <span 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 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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 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.chent.html b/docs/reference/GUS.chent.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/GUS.chent.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 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+<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> 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-53,42 +44,42 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>n</dt> + + +<dl><dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt> <dd><p>number of applications</p></dd> -<dt>interval</dt> +<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a></dt> <dd><p>Time between applications</p></dd> -<dt>FOMC</dt> +<dt id="arg-fomc">FOMC<a class="anchor" aria-label="anchor" href="#arg-fomc"></a></dt> <dd><p>Named numeric vector containing the FOMC parameters alpha and beta</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A numeric vector containing all n accumulation factors for the n applications</p> + <p>A numeric vector containing all n accumulation factors for the n applications</p> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this 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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="">0.6.4</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> @@ -88,100 +79,103 @@ 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> -<dd><p>If this is 'default', the DT50 will be used without correction +<dt id="arg-scenarios">scenarios<a class="anchor" aria-label="anchor" href="#arg-scenarios"></a></dt> +<dd><p>If this is 'default', a soil bulk density of 1.5 kg/L will +be used. The DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when @@ -190,12 +184,12 @@ 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 +199,7 @@ 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 +297,23 @@ 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 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_soil_mets.html b/docs/reference/PEC_soil_mets.html index 3bce8cc..f078454 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.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; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculate initial and 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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 and accumulation PEC soil for a set of metabolites</h1> + + <h1>Calculate initial and accumulation PEC soil for a set of metabolites</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_mets.Rd</code></div> </div> @@ -53,46 +44,48 @@ <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>mw_parent</dt> +<dt id="arg-mw-parent">mw_parent<a class="anchor" aria-label="anchor" href="#arg-mw-parent"></a></dt> <dd><p>The molecular weight of the parent compound</p></dd> -<dt>mets</dt> +<dt id="arg-mets">mets<a class="anchor" aria-label="anchor" href="#arg-mets"></a></dt> <dd><p>A dataframe with metabolite identifiers as rownames and columns "mw", "occ" and "DT50" holding their molecular weight, maximum occurrence in soil and their soil DT50</p></dd> -<dt>interval</dt> +<dt id="arg-interval">interval<a class="anchor" aria-label="anchor" href="#arg-interval"></a></dt> <dd><p>The interval for accumulation calculations</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments are passed to PEC_soil</p></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/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 3996f9c..54dbede 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -1,52 +1,46 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta 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Degradation before the start of the drainage period is taken into account if +latest_application is specified and the degradation parameters are given either as a soil_DT50 or a model."><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. Degradation before the start of the drainage period is taken into account if +latest_application is specified and the degradation parameters are given either as a soil_DT50 or a model."></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="">0.6.4</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> <div class="ref-description section level2"> <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website</p> +published on the CRC website. Degradation before the start of the drainage period is taken into account if +<code>latest_application</code> is specified and the degradation parameters are given either as a <code>soil_DT50</code> or a <code>model</code>.</p> </div> <div class="section level2"> @@ -64,40 +58,40 @@ 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> @@ -118,25 +112,28 @@ accessed 2019-09-27</p> <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_drainage_UK</span><span class="op">(</span><span class="fl">150</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</span> +<span class="r-in"><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span><span class="fl">60</span>, interception <span class="op">=</span> <span class="fl">0.5</span>, Koc <span class="op">=</span> <span class="fl">550</span>,</span></span> +<span class="r-in"><span> latest_application <span class="op">=</span> <span class="st">"01 July"</span>, soil_DT50 <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> [1] 0.8388303</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 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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_data_JKI.html">drift_data_JKI</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..ebcf7d1 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -1,56 +1,51 @@ <!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><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.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. 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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. +It is recommened to specify the arguments rate, Koc, DT50, t_drainage, +V_ditch and V_drainage using units::units from the units package.'></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="">0.6.4</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> @@ -61,7 +56,9 @@ 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.</p> +details, see the discussion of the function arguments below. +It is recommened to specify the arguments <code>rate</code>, <code>Koc</code>, <code>DT50</code>, <code>t_drainage</code>, +<code>V_ditch</code> and <code>V_drainage</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"> @@ -71,10 +68,10 @@ details, see the discussion of the function arguments below.</p> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> <span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> <span> mobility <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="cn">NA</span>, <span class="st">"low"</span>, <span class="st">"high"</span><span class="op">)</span>,</span> -<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> -<span> t_drainage <span class="op">=</span> <span class="fl">3</span>,</span> -<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> -<span> V_drainage <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>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</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_drainage <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> 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_drainage <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</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> @@ -86,57 +83,57 @@ 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> @@ -157,28 +154,29 @@ 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> 12.5 25.0 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $PEC_sw_drainage</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> spring autumn </span> <span class="r-out co"><span class="r-pr">#></span> 1.562500 4.807692 </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_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 21731f3..869c170 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,46 +1,37 @@ <!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, -in the worksheet "Konzept Runoff".'><title>Calculate PEC surface water due to runoff and erosion as in Exposit 3 — 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calculation described in the Exposit 3.02 spreadsheet file, +in the worksheet "Konzept Runoff".'><meta property="og:description" content='This is a reimplementation of the calculation described in the Exposit 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="">0.6.4</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" 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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..9f8fc6c 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="">0.6.4</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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<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="">0.6.4</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" 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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 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/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex 8269e66..5b79a08 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff 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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..f554693 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -1,45 +1,36 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta 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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>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 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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="">0.6.4</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-1.png b/docs/reference/TSCF-1.png Binary files differindex 82c0ea8..788f4d3 100644 --- a/docs/reference/TSCF-1.png +++ b/docs/reference/TSCF-1.png diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html index 8391cb4..92fec23 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><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.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. 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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="">0.6.4</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/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index df9df8b..5f6fe6c 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,43 +1,34 @@ <!DOCTYPE html> -<!-- 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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>Create a chemical compound object for FOCUS Step 1 calculations</h1> + + <h1>Create a chemical compound object for FOCUS Step 1 calculations</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>chent_focus_sw.Rd</code></div> </div> @@ -64,72 +55,72 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>name</dt> + + +<dl><dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt> <dd><p>Length one character vector containing the name</p></dd> -<dt>Koc</dt> +<dt id="arg-koc">Koc<a class="anchor" aria-label="anchor" href="#arg-koc"></a></dt> <dd><p>Partition coefficient between organic carbon and water in L/kg.</p></dd> -<dt>DT50_ws</dt> +<dt id="arg-dt-ws">DT50_ws<a class="anchor" aria-label="anchor" href="#arg-dt-ws"></a></dt> <dd><p>Half-life in water/sediment systems in days</p></dd> -<dt>DT50_soil</dt> +<dt id="arg-dt-soil">DT50_soil<a class="anchor" aria-label="anchor" href="#arg-dt-soil"></a></dt> <dd><p>Half-life in soil in days</p></dd> -<dt>DT50_water</dt> +<dt id="arg-dt-water">DT50_water<a class="anchor" aria-label="anchor" href="#arg-dt-water"></a></dt> <dd><p>Half-life in water in days (Step 2)</p></dd> -<dt>DT50_sediment</dt> +<dt id="arg-dt-sediment">DT50_sediment<a class="anchor" aria-label="anchor" href="#arg-dt-sediment"></a></dt> <dd><p>Half-life in sediment in days (Step 2)</p></dd> -<dt>cwsat</dt> +<dt id="arg-cwsat">cwsat<a class="anchor" aria-label="anchor" href="#arg-cwsat"></a></dt> <dd><p>Water solubility in mg/L</p></dd> -<dt>mw</dt> +<dt id="arg-mw">mw<a class="anchor" aria-label="anchor" href="#arg-mw"></a></dt> <dd><p>Molar weight in g/mol.</p></dd> -<dt>max_soil</dt> +<dt id="arg-max-soil">max_soil<a class="anchor" aria-label="anchor" href="#arg-max-soil"></a></dt> <dd><p>Maximum observed fraction (dimensionless) in soil</p></dd> -<dt>max_ws</dt> +<dt id="arg-max-ws">max_ws<a class="anchor" aria-label="anchor" href="#arg-max-ws"></a></dt> <dd><p>Maximum observed fraction (dimensionless) in water/sediment systems</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 substance specific properties</p> + <p>A list with the substance specific properties</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/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 5d9c11e..c8a2d1d 100644 --- 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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="">0.6.4</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-1.png b/docs/reference/drift_percentages_rautmann-1.png Binary files differindex ae57141..139b22f 100644 --- a/docs/reference/drift_percentages_rautmann-1.png +++ 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class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Calculate drift percentages based on Rautmann data</h1> + + <h1>Calculate drift percentages based on Rautmann data</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>drift_percentages_rautmann.Rd</code></div> </div> @@ -51,7 +42,7 @@ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span></span> <span> <span class="va">distances</span>,</span> <span> applications <span class="op">=</span> <span class="fl">1</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> 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> widths <span class="op">=</span> <span class="fl">1</span></span> @@ -60,25 +51,27 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>distances</dt> + + +<dl><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>applications</dt> +<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>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>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>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> @@ -95,7 +88,7 @@ FOrum for the Co-ordination of pesticde fate models and their USe. <div class="section level2"> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Compare JKI data with Rautmann formula</span></span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Compare JKI data with Rautmann and FOCUS formulas for arable crops (default)</span></span></span> <span class="r-in"><span><span class="co"># One application on field crops, for 1 m, 3 m and 5 m distance</span></span></span> <span class="r-in"><span><span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span>, <span class="st">"Ackerbau"</span><span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 1 3 5 </span> @@ -109,49 +102,49 @@ FOrum for the Co-ordination of pesticde fate models and their USe. <span class="r-in"><span><span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span><span class="op">)</span>, <span class="st">"Obstbau frueh"</span><span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 3 5 20 50 </span> <span class="r-out co"><span class="r-pr">#></span> 29.20 19.89 2.77 0.30 </span> -<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group <span class="op">=</span> <span class="st">"fruit, early"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group_RF <span class="op">=</span> <span class="st">"fruit, early"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 29.1973659 19.8844422 2.7618138 0.3012008</span> -<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group <span class="op">=</span> <span class="st">"fruit, early"</span>,</span></span> +<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group_RF <span class="op">=</span> <span class="st">"fruit, early"</span>,</span></span> <span class="r-in"><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> [1] 26.1193421 18.5428680 2.6038558 0.2940792</span> <span class="r-in"><span><span class="va">drift_data_JKI</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span><span class="op">)</span>, <span class="st">"Obstbau spaet"</span><span class="op">]</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 3 5 20 50 </span> <span class="r-out co"><span class="r-pr">#></span> 15.73 8.41 1.09 0.22 </span> -<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group <span class="op">=</span> <span class="st">"fruit, late"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group_RF <span class="op">=</span> <span class="st">"fruit, late"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 15.7246994 8.4108487 1.0813887 0.2155992</span> -<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group <span class="op">=</span> <span class="st">"fruit, late"</span>,</span></span> +<span class="r-in"><span><span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, crop_group_RF <span class="op">=</span> <span class="st">"fruit, late"</span>,</span></span> <span class="r-in"><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> [1] 13.1414350 7.5123244 1.0359007 0.2118734</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We get a continuum if the waterbody covers the hinge distance</span></span></span> <span class="r-in"><span><span class="co"># (11.4 m for 1 early app to fruit)</span></span></span> <span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">30</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="va">d</span> <span class="op"><-</span> <span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="va">x</span>, crop_group <span class="op">=</span> <span class="st">"fruit, early"</span>, formula <span class="op">=</span> <span class="st">"FOCUS"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d</span> <span class="op"><-</span> <span class="fu">drift_percentages_rautmann</span><span class="op">(</span><span class="va">x</span>, crop_group_RF <span class="op">=</span> <span class="st">"fruit, early"</span>, formula <span class="op">=</span> <span class="st">"FOCUS"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">d</span>, type <span class="op">=</span> <span class="st">"l"</span>,</span></span> -<span class="r-in"><span> xlab <span class="op">=</span> <span class="st">"Distance of near edge [m]"</span>, </span></span> +<span class="r-in"><span> xlab <span class="op">=</span> <span class="st">"Distance of near edge [m]"</span>,</span></span> <span class="r-in"><span> ylab <span class="op">=</span> <span class="st">"Mean drift percentage over waterbody width"</span>,</span></span> <span class="r-in"><span> main <span class="op">=</span> <span class="st">"One application to fruit, early"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/abline.html" class="external-link">abline</a></span><span class="op">(</span>v <span class="op">=</span> <span class="fl">11.4</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <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/" 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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="">0.6.4</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/geomean.html b/docs/reference/geomean.html index 347d9d7..1307a93 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.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="Based on some posts in a thread on Stackoverflow +<!-- 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 the geometric mean — geomean • 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><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the geometric mean — geomean"><meta name="description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. -If at least one element of the vector is 0, it returns 0."><title>Calculate the geometric mean — geomean • 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 the geometric mean — geomean"><meta property="og:description" content="Based on some posts in a thread on Stackoverflow +If at least one element of the vector is 0, it returns 0."><meta property="og:description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. -If at least one element of the vector is 0, it returns 0."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body> +If at least one element of the vector is 0, it returns 0."></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="">0.6.4</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" 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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 the geometric mean</h1> + + <h1>Calculate the geometric mean</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/geomean.R" class="external-link"><code>R/geomean.R</code></a></small> <div class="d-none name"><code>geomean.Rd</code></div> </div> @@ -65,19 +56,19 @@ If at least one element of the vector is 0, it returns 0.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>x</dt> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>Vector of numbers</p></dd> -<dt>na.rm</dt> +<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt> <dd><p>Should NA values be omitted?</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The geometric mean</p> + <p>The geometric mean</p> </div> <div class="section level2"> <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> @@ -94,23 +85,23 @@ If at least one element of the vector is 0, it returns 0.</p> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in geomean(c(1, -3, 9)):</span> Only defined for positive numbers</span> </code></pre></div> </div> - </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/get_vertex.html b/docs/reference/get_vertex.html index d0eff28..45a3408 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.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="This was inspired by an answer on stackoverflow -https://stackoverflow.com/a/717791"><title>Fit a parabola through three points — get_vertex • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" 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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>Fit a parabola through three points</h1> + + <h1>Fit a parabola through three points</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>get_vertex.Rd</code></div> </div> @@ -56,32 +47,34 @@ https://stackoverflow.com/a/717791</p> <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>Three x coordinates</p></dd> -<dt>y</dt> +<dt id="arg-y">y<a class="anchor" aria-label="anchor" href="#arg-y"></a></dt> <dd><p>Three y coordinates</p></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/index.html b/docs/reference/index.html index aaa499d..0586b68 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" 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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="">0.6.4</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/" 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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..02c8320 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" 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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="">0.6.4</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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me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</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 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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>one_box.Rd</code></div> </div> @@ -50,19 +41,21 @@ <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">one_box</span><span class="op">(</span><span class="va">x</span>, <span class="va">ini</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</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">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for character</span></span> +<span><span class="co"># S3 method for class 'character'</span></span> <span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">parms</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="co"># S3 method for class 'mkinfit'</span></span> <span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="st">"model"</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</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>x</dt> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. @@ -70,7 +63,7 @@ If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" c object.</p></dd> -<dt>ini</dt> +<dt id="arg-ini">ini<a class="anchor" aria-label="anchor" href="#arg-ini"></a></dt> <dd><p>The initial amount. If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and @@ -78,27 +71,25 @@ initial values of metabolites are zero, otherwise, it must give values for all observed variables.</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments passed to methods</p></dd> -<dt>t_end</dt> +<dt id="arg-t-end">t_end<a class="anchor" aria-label="anchor" href="#arg-t-end"></a></dt> <dd><p>End of the time series</p></dd> -<dt>res</dt> +<dt id="arg-res">res<a class="anchor" aria-label="anchor" href="#arg-res"></a></dt> <dd><p>Resolution of the time series</p></dd> -<dt>parms</dt> +<dt id="arg-parms">parms<a class="anchor" aria-label="anchor" href="#arg-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>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> + <p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> </div> <div class="section level2"> @@ -125,23 +116,23 @@ all observed variables.</p></dd> <span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </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> 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class="page-header"> - <img src="" class="logo" alt=""><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_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 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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/pfm_degradation.html b/docs/reference/pfm_degradation.html index 8b21cf5..2540333 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -1,43 +1,34 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta 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href="https://github.com/jranke/pfm/blob/HEAD/R/pfm_degradation.R" class="external-link"><code>R/pfm_degradation.R</code></a></small> <div class="d-none name"><code>pfm_degradation.Rd</code></div> </div> @@ -60,29 +51,31 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>model</dt> + + +<dl><dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt> <dd><p>The degradation model to be used. Either a parent only model like 'SFO' or 'FOMC', or an mkinmod object</p></dd> -<dt>DT50</dt> +<dt id="arg-dt-">DT50<a class="anchor" aria-label="anchor" href="#arg-dt-"></a></dt> <dd><p>The half-life. This is only used when simple exponential decline is calculated (SFO model).</p></dd> -<dt>parms</dt> +<dt id="arg-parms">parms<a class="anchor" aria-label="anchor" href="#arg-parms"></a></dt> <dd><p>The parameters used for the degradation model</p></dd> -<dt>years</dt> +<dt id="arg-years">years<a class="anchor" aria-label="anchor" href="#arg-years"></a></dt> <dd><p>For how many years should the degradation be predicted?</p></dd> -<dt>step_days</dt> +<dt id="arg-step-days">step_days<a class="anchor" aria-label="anchor" href="#arg-step-days"></a></dt> <dd><p>What step size in days should the output have?</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</p></dd> </dl></div> @@ -103,23 +96,23 @@ is calculated (SFO model).</p></dd> <span class="r-out co"><span class="r-pr">#></span> 5 5 0.7071068</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + 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<div class="d-none name"><code>plot.TOXSWA_cwa.Rd</code></div> </div> @@ -51,7 +42,7 @@ segment of a TOXSWA surface water body.</p> <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for TOXSWA_cwa</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'TOXSWA_cwa'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> <span> time_column <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">"datetime"</span>, <span class="st">"t"</span>, <span class="st">"t_firstjan"</span>, <span class="st">"t_rel_to_max"</span><span class="op">)</span>,</span> @@ -68,44 +59,46 @@ segment of a TOXSWA surface water body.</p> <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>The TOXSWA_cwa object to be plotted.</p></dd> -<dt>time_column</dt> +<dt id="arg-time-column">time_column<a class="anchor" aria-label="anchor" href="#arg-time-column"></a></dt> <dd><p>What should be used for the time axis. If "t_firstjan" is chosen, the time is given in days relative to the first of January in the first year.</p></dd> -<dt>xlab, ylab</dt> +<dt id="arg-xlab-ylab">xlab, ylab<a class="anchor" aria-label="anchor" href="#arg-xlab-ylab"></a></dt> <dd><p>Labels for x and y axis.</p></dd> -<dt>add</dt> +<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt> <dd><p>Should we add to an existing plot?</p></dd> -<dt>threshold_factor</dt> +<dt id="arg-threshold-factor">threshold_factor<a class="anchor" aria-label="anchor" href="#arg-threshold-factor"></a></dt> <dd><p>The factor by which the data have to be lower than the maximum in order to get thinned for plotting (see next argument).</p></dd> -<dt>thin_low</dt> +<dt id="arg-thin-low">thin_low<a class="anchor" aria-label="anchor" href="#arg-thin-low"></a></dt> <dd><p>If an integer greater than 1, the data close to zero (smaller than 1/threshold_factor of the maximum) in the series will be thinned by this factor in order to decrease the amount of data that is included in the plots</p></dd> -<dt>total</dt> +<dt id="arg-total">total<a class="anchor" aria-label="anchor" href="#arg-total"></a></dt> <dd><p>Should the total concentration in water be plotted, including substance sorbed to suspended matter?</p></dd> -<dt>LC_TIME</dt> +<dt id="arg-lc-time">LC_TIME<a class="anchor" aria-label="anchor" href="#arg-lc-time"></a></dt> <dd><p>Specification of the locale used to format dates</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> </dl></div> @@ -135,23 +128,23 @@ to suspended matter?</p></dd> <span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </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 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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="">0.6.4</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 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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>Plot time series of decline data</h1> + + <h1>Plot time series of decline data</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>plot.one_box.Rd</code></div> </div> @@ -48,7 +39,7 @@ <div class="section level2"> <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'one_box'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> <span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> @@ -63,37 +54,39 @@ <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>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> -<dt>xlim</dt> +<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt> <dd><p>Limits for the x axis</p></dd> -<dt>ylim</dt> +<dt id="arg-ylim">ylim<a class="anchor" aria-label="anchor" href="#arg-ylim"></a></dt> <dd><p>Limits for the y axis</p></dd> -<dt>xlab</dt> +<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt> <dd><p>Label for the x axis</p></dd> -<dt>ylab</dt> +<dt id="arg-ylab">ylab<a class="anchor" aria-label="anchor" href="#arg-ylab"></a></dt> <dd><p>Label for the y axis</p></dd> -<dt>max_twa</dt> +<dt id="arg-max-twa">max_twa<a class="anchor" aria-label="anchor" href="#arg-max-twa"></a></dt> <dd><p>If a numeric value is given, the maximum time weighted average concentration(s) is/are shown in the graph.</p></dd> -<dt>max_twa_var</dt> +<dt id="arg-max-twa-var">max_twa_var<a class="anchor" aria-label="anchor" href="#arg-max-twa-var"></a></dt> <dd><p>Variable for which the maximum time weighted average should be shown if max_twa is not NULL.</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments passed to methods</p></dd> </dl></div> @@ -109,6 +102,7 @@ be shown if max_twa is not NULL.</p></dd> <span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> <span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -117,27 +111,29 @@ be shown if max_twa is not NULL.</p></dd> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="plot.one_box-4.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="plot.one_box-5.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> 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charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific +<!-- 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>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" 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Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was -renamed to ConLiqWatLay in the out file."><title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/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="Read TOXSWA surface water concentrations — read.TOXSWA_cwa"><meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific +renamed to ConLiqWatLay in the out file."><meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was -renamed to ConLiqWatLay in the out file."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body> +renamed to ConLiqWatLay in the out file."></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="">0.6.4</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>Read TOXSWA surface water concentrations</h1> + + <h1>Read TOXSWA surface water concentrations</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>read.TOXSWA_cwa.Rd</code></div> </div> @@ -77,51 +68,51 @@ renamed to ConLiqWatLay in the out file.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>filename</dt> + + +<dl><dt id="arg-filename">filename<a class="anchor" aria-label="anchor" href="#arg-filename"></a></dt> <dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> -<dt>basedir</dt> +<dt id="arg-basedir">basedir<a class="anchor" aria-label="anchor" href="#arg-basedir"></a></dt> <dd><p>The path to the directory where the cwa file resides.</p></dd> -<dt>zipfile</dt> +<dt id="arg-zipfile">zipfile<a class="anchor" aria-label="anchor" href="#arg-zipfile"></a></dt> <dd><p>Optional path to a zip file containing the cwa file.</p></dd> -<dt>segment</dt> +<dt id="arg-segment">segment<a class="anchor" aria-label="anchor" href="#arg-segment"></a></dt> <dd><p>The segment for which the data should be read. Either "last", or the segment number.</p></dd> -<dt>substance</dt> +<dt id="arg-substance">substance<a class="anchor" aria-label="anchor" href="#arg-substance"></a></dt> <dd><p>For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance of interested can be selected by its code name.</p></dd> -<dt>total</dt> +<dt id="arg-total">total<a class="anchor" aria-label="anchor" href="#arg-total"></a></dt> <dd><p>Set this to TRUE in order to read total concentrations as well. This is only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa files. For .cwa files, the total concentration is always read as well.</p></dd> -<dt>windows</dt> +<dt id="arg-windows">windows<a class="anchor" aria-label="anchor" href="#arg-windows"></a></dt> <dd><p>Numeric vector of width of moving windows in days, for calculating maximum time weighted average concentrations and areas under the curve.</p></dd> -<dt>thresholds</dt> +<dt id="arg-thresholds">thresholds<a class="anchor" aria-label="anchor" href="#arg-thresholds"></a></dt> <dd><p>Numeric vector of threshold concentrations in µg/L for generating event statistics.</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>An instance of an R6 object of class + <p>An instance of an R6 object of class <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> </div> <div class="section level2"> @@ -137,23 +128,23 @@ generating event statistics.</p></dd> <span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> </code></pre></div> </div> - </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/reexports.html b/docs/reference/reexports.html index 8507c78..82d8303 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,57 +1,48 @@ <!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="These objects are imported from other packages. Follow the links +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Objects exported from other packages — reexports • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Objects exported from other packages — reexports"><meta name="description" content="These objects are imported from other packages. 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Follow the links below to see their documentation. mkin set_nd_nq, set_nd_nq_focus -"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body> +"></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="">0.6.4</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>Objects exported from other packages</h1> + + <h1>Objects exported from other packages</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/reexports.R" class="external-link"><code>R/reexports.R</code></a></small> <div class="d-none name"><code>reexports.Rd</code></div> </div> @@ -71,18 +62,18 @@ below to see their documentation.</p> <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/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 062202c..6cf67ed 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex cea8b0b..3a4e7a2 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth-3.png b/docs/reference/sawtooth-3.png Binary files differnew file mode 100644 index 0000000..77e8eed --- /dev/null +++ b/docs/reference/sawtooth-3.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index f373ffb..36fbb77 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.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; 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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>Create decline time series for multiple applications — sawtooth • 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><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create decline time series for multiple applications — sawtooth"><meta name="description" content="If the application pattern is specified in applications, +n and i are disregarded."><meta property="og:description" content="If the application pattern is specified in applications, +n and i are disregarded."></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="">0.6.4</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>Create decline time series for multiple applications</h1> + + <h1>Create decline time series for multiple applications</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>sawtooth.Rd</code></div> </div> @@ -61,20 +52,22 @@ n and i are disregarded."><!-- mathjax --><script src="https://cdnjs.cloudflare. <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>A <code><a href="one_box.html">one_box</a></code> object</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. If <code>applications</code> is specified, <code>n</code> is ignored</p></dd> -<dt>i</dt> +<dt id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></dt> <dd><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> is ignored</p></dd> -<dt>applications</dt> +<dt id="arg-applications">applications<a class="anchor" aria-label="anchor" href="#arg-applications"></a></dt> <dd><p>A data frame holding the application times in the first column and the corresponding amounts applied in the second column.</p></dd> @@ -95,6 +88,7 @@ the corresponding amounts applied in the second column.</p></dd> <span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="sawtooth-2.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="sawtooth-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred_2_saw</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $max</span> @@ -111,23 +105,23 @@ the corresponding amounts applied in the second column.</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </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/set_nd_nq.html b/docs/reference/set_nd_nq.html new file mode 100644 index 0000000..2291be7 --- /dev/null +++ b/docs/reference/set_nd_nq.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/reexports.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/reexports.html"> + </head> +</html> + diff --git a/docs/reference/set_nd_nq_focus.html b/docs/reference/set_nd_nq_focus.html new file mode 100644 index 0000000..2291be7 --- /dev/null +++ b/docs/reference/set_nd_nq_focus.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/reexports.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/reexports.html"> + </head> +</html> + diff --git a/docs/reference/soil_DT50.html b/docs/reference/soil_DT50.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_DT50.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/soil_Kfoc.html b/docs/reference/soil_Kfoc.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_Kfoc.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/soil_N.html b/docs/reference/soil_N.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_N.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/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 41f1078..22e30e5 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.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="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +<!-- 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>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • 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><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015"><meta name="description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). 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Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included."><!-- 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="">0.6.4</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..fb866b9 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" 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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>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> + + <h1>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/soil_scenario_data_EFSA_2017.R" class="external-link"><code>R/soil_scenario_data_EFSA_2017.R</code></a></small> <div class="d-none name"><code>soil_scenario_data_EFSA_2017.Rd</code></div> </div> @@ -124,23 +115,23 @@ active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 <span class="r-out co"><span class="r-pr">#></span> And 3 more differences ...</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> 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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> +is after one window has passed."></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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src="" class="logo" alt=""><h1>Calculate a time weighted average concentration</h1> + + <h1>Calculate a time weighted average concentration</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>twa.Rd</code></div> </div> @@ -56,17 +47,19 @@ is after one window has passed.</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">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for one_box</span></span> +<span><span class="co"># S3 method for class 'one_box'</span></span> <span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> </div> <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> @@ -94,23 +87,23 @@ is after one window has passed.</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 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