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diff --git a/docs/index.html b/docs/index.html index 590ed7b..e6da960 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,7 +8,9 @@ <title>Utilities for Pesticide Fate Modelling • pfm</title> <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"> -<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Utilities for Pesticide Fate Modelling"> +<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="Utilities for Pesticide Fate Modelling"> <meta name="description" content="Utilities for simple calculations of predicted environmental concentrations (PEC values) and for dealing with data from some FOCUS pesticide fate modelling software packages."> <meta property="og:description" content="Utilities for simple calculations of predicted environmental concentrations (PEC values) and for dealing with data from some FOCUS pesticide fate modelling software packages."> </head> @@ -20,7 +22,7 @@ <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="">0.6.3</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"> @@ -47,17 +49,22 @@ <main id="main" class="col-md-9"><div class="section level1"> <div class="page-header"><h1 id="pfm">pfm<a class="anchor" aria-label="anchor" href="#pfm"></a> </h1></div> -<p><a href="https://jranke.r-universe.dev/ui/#package:pfm" class="external-link"><img src="https://jranke.r-universe.dev/badges/pfm" alt="pfm status badge"></a> <a href="https://app.travis-ci.com/jranke/pfm" class="external-link"><img src="https://app.travis-ci.com/jranke/pfm.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main" alt="Build Status"></a> <a href="https://codecov.io/github/jranke/pfm" class="external-link"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></p> -<p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license.</p> +<p><a href="https://pkgdown.jrwb.de/pfm/"><img src="https://img.shields.io/badge/docs-jrwb.de-blue.svg" alt="Online documentation"></a> <a href="https://jranke.r-universe.dev/ui/#package:pfm" class="external-link"><img src="https://jranke.r-universe.dev/badges/pfm" alt="pfm status badge"></a> <a href="https://app.travis-ci.com/jranke/pfm" class="external-link"><img src="https://app.travis-ci.com/jranke/pfm.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main" alt="Build Status"></a> <a href="https://codecov.io/github/jranke/pfm" class="external-link"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></p> +<p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including simple routines for calculating predicted environmental concentrations (PEC) and some routines for dealing with FOCUS pesticide fate modelling tools made available under the GNU public license.</p> +<p>More specifically, <strong>pfm</strong> includes facilities for simple one-box modelling of the <a href="https://pkgdown.jrwb.de/pfm/reference/sawtooth.html">saw-tooth</a>-like curves resulting from multiple repeated applications, for calculation of <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html">PEC soil</a> based on the 1997 SANCO guidance and the first tiers of the EFSA PEC soil guidance from 2012 and 2015, as well as some functions for calculating <a href="https://pkgdown.jrwb.de/pfm/reference/sawtooth.html">PEC surface water</a>. The <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html">PEC drift</a> calculations can be based on the Rautmann drift percentiles published by JKI, the exponential formulas published by Rautmann to inter- or extrapolate to arbitrary distances, or on the integrated Rautmann formulas (integrated over the width of the surface water body) used in FOCUS drift calculations.</p> +<p>For PEC drainage calculations, the methods used by the <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_drainage_UK.html">UK at tier 1</a> and by <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html">Germany</a> are implemented. For runoff, the <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html">German</a> method used at tier 1 is available.</p> +<p>The output of FOCUS TOXSWA calculations can be read in, plotted, and evaluated using the <a href="https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html">TOXSWA cwa</a> class giving maximum time weighted average concentrations and peak statistics way as available when using the <a href="https://www.rifcon.com/en/downloads/software-2/" class="external-link">EPAT</a> tool.</p> <div class="section level2"> <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> </h2> <p>The easiest way to install the package is probably to use the <a href="https://jranke.r-universe.dev/pfm" class="external-link">r-universe repo</a>:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span>, repos <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">"https://jranke.r-universe.dev"</span>, <span class="st">"https://cran.r-project.org"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> -<p>Alternatively you can install the package using the <code>remotes</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span>,</span> +<span> repos <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">"https://jranke.r-universe.dev"</span>, <span class="st">"https://cran.r-project.org"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p>The packages at R-universe are provided with a slight delay. Alternatively, you can install the package directly from github, e.g. by using <a href="https://pak.r-lib.org" class="external-link"><code>pak</code></a>.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jranke/pfm"</span>, quick <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="co"># install.packages("pak")</span></span> +<span><span class="fu">pak</span><span class="fu">::</span><span class="fu">pak</span><span class="op">(</span><span class="st">"jranke/pfm"</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> <h2 id="use">Use<a class="anchor" aria-label="anchor" href="#use"></a> @@ -67,7 +74,7 @@ <div class="section level2"> <h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a> </h2> -<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html" class="external-link">here</a>.</p> +<p>One nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html" class="external-link">here</a>.</p> </div> <div class="section level2"> <h2 id="applications">Applications<a class="anchor" aria-label="anchor" href="#applications"></a> @@ -118,6 +125,7 @@ Korkaric M, Hanke I, Grossar D, Neuweiler R, Christ B, Wirth J, Hochstrasser M, <h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> <li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> +<li><a href="authors.html">More about authors...</a></li> </ul> </div> |