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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:41:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:50:14 +0100 |
| commit | a76221d87485029444c8e684022ca606a0c7e68d (patch) | |
| tree | c95052ee51b35f6c5ab87bd6f27ef2877f536838 /docs/index.html | |
| parent | a1d9f93138c2cfed92a683e37e72c737d52b7ad7 (diff) | |
Update static docs using pkgdown
- Add _pkgdown.yml for a structured function/data reference
- Make seealso links active
- Make mkinfit calls quiet
- Use pkgdown branch from pull request hadley/pkgdown#229 to have topics
ordered
Diffstat (limited to 'docs/index.html')
| -rw-r--r-- | docs/index.html | 257 |
1 files changed, 112 insertions, 145 deletions
diff --git a/docs/index.html b/docs/index.html index a82dcae..4aa129c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,65 +1,55 @@ <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Home. pfm 0.3-8</title> +<!-- Generated by pkgdown: do not edit by hand --><html> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<title>Utilities for Pesticide Fate Modelling • pfm</title> +<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></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]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> +</head> +<body> + <div class="container template-home"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">pfm</a> </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> +<li> + <a href="reference/index.html">Reference</a> +</li> + </ul> +<ul class="nav navbar-nav navbar-right"></ul> +</div> +<!--/.nav-collapse --> </div> +<!--/.container --> </div> +<!--/.navbar --> - - <div class="container"> - <header> - - </header> - <div class="row"> - <div class="span8"> - <h1>pfm</h1> - -<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools, -(currently only TOXSWA cwa and out files), made available under the GNU public license. -This means:</p> - -<pre><code>This program is free software: you can redistribute it and/or modify it under + </header><div class="row"> + <div class="contents col-md-9"> + <div id="pfm" class="section level1"> +<div class="page-header"><h1 class="hasAnchor"> +<a href="#pfm" class="anchor"> </a>pfm</h1></div> +<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license. This means:</p> +<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software:<span class="st"> </span>you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software -Foundation, either version 3 of the License, or (at your option) any later +Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT @@ -68,49 +58,32 @@ FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with -this program. If not, see <http://www.gnu.org/licenses/> -</code></pre> - -<h2>Installation</h2> - -<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. -using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, -multiple-architecture builds, demos, and vignettes, to make installation as -fast and painless as possible.</p> - -<pre><code class="r">library(devtools) -install_github("jranke/pfm", subdir = "pkg", quick = TRUE) -</code></pre> - -<h2>Use</h2> - -<h3>Analyse TOXSWA output</h3> - +this program. If not, see <http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">></span></code></pre></div> +<div id="installation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#installation" class="anchor"> </a>Installation</h2> +<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools) +<span class="kw">install_github</span>(<span class="st">"jranke/pfm"</span>, <span class="dt">subdir =</span> <span class="st">"pkg"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</code></pre></div> +</div> +<div id="use" class="section level2"> +<h2 class="hasAnchor"> +<a href="#use" class="anchor"> </a>Use</h2> +<div id="analyse-toxswa-output" class="section level3"> +<h3 class="hasAnchor"> +<a href="#analyse-toxswa-output" class="anchor"> </a>Analyse TOXSWA output</h3> <p>Read in and analyse a cwa file:</p> - -<pre><code class="r">library(pfm, quietly = TRUE) -</code></pre> - +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(pfm, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</code></pre></div> <pre><code>## ## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) -## [GCC 4.9.2] -</code></pre> - -<pre><code class="r">example_cwa <- read.TOXSWA_cwa("00003s_pa.cwa") -plot(example_cwa) -</code></pre> - -<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p> - -<p>Get events above thresholds of 20 and 100 µg/L, -and do a moving window analysis for windows of 7 days -and 21 days, print the results:</p> - -<pre><code class="r">example_cwa$get_events(c(20, 100)) -example_cwa$moving_windows(c(7, 21)) -print(example_cwa) -</code></pre> - +## [GCC 4.9.2]</code></pre> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa <-<span class="st"> </span><span class="kw"><a href="reference/read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span>(<span class="st">"00003s_pa.cwa"</span>) +<span class="kw">plot</span>(example_cwa)</code></pre></div> +<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672"></p> +<p>Get events above thresholds of 20 and 100 µg/L, and do a moving window analysis for windows of 7 days and 21 days, print the results:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa$<span class="kw">get_events</span>(<span class="kw">c</span>(<span class="dv">20</span>, <span class="dv">100</span>)) +example_cwa$<span class="kw">moving_windows</span>(<span class="kw">c</span>(<span class="dv">7</span>, <span class="dv">21</span>)) +<span class="kw">print</span>(example_cwa)</code></pre></div> <pre><code>## <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 ## datetime t t_firstjan t_rel_to_max cwa_mug_per_L ## 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 @@ -134,35 +107,23 @@ print(example_cwa) ## t_start cwa_max duration pre_interval AUC_h AUC_d ## 1 55.083 40.58401 0.417 55.083 365.7912 15.2413 ## Event statistics for threshold 100 -## No events found -</code></pre> - -<p>This can also be done with out files, the function reads -out files from current TOXSWA versions as well as cwa files -from old TOXSWA versions.</p> - -<h3>Calculate PEC soil</h3> - -<p>Simple PEC soil calculation for an application rate of 100 g/ha and -25% interception, assuming complete mixing into 5 cm and a soil bulk -density of 1.5 kg/L, output in mg/kg:</p> - -<pre><code class="r">PEC_soil(100, interception = 0.25) -</code></pre> - +## No events found</code></pre> +<p>This can also be done with out files, the function reads out files from current TOXSWA versions as well as cwa files from old TOXSWA versions.</p> +</div> +<div id="calculate-pec-soil" class="section level3"> +<h3 class="hasAnchor"> +<a href="#calculate-pec-soil" class="anchor"> </a>Calculate PEC soil</h3> +<p>Simple PEC soil calculation for an application rate of 100 g/ha and 25% interception, assuming complete mixing into 5 cm and a soil bulk density of 1.5 kg/L, output in mg/kg:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_soil.html">PEC_soil</a></span>(<span class="dv">100</span>, <span class="dt">interception =</span> <span class="fl">0.25</span>)</code></pre></div> <pre><code>## scenario ## t_avg default -## 0 0.1 -</code></pre> - -<h3>Rautmann drift data</h3> - -<p>Some of the drift percentage data published by the JKI are included. To -see the data for one application:</p> - -<pre><code class="r">drift_data_JKI[1] -</code></pre> - +## 0 0.1</code></pre> +</div> +<div id="rautmann-drift-data" class="section level3"> +<h3 class="hasAnchor"> +<a href="#rautmann-drift-data" class="anchor"> </a>Rautmann drift data</h3> +<p>Some of the drift percentage data published by the JKI are included. To see the data for one application:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">drift_data_JKI[<span class="dv">1</span>]</code></pre></div> <pre><code>## [[1]] ## crop ## distance Ackerbau Obstbau frueh Obstbau spaet @@ -174,35 +135,41 @@ see the data for one application:</p> ## 20 0.15 2.77 1.09 ## 30 0.10 1.04 0.54 ## 40 0.07 0.52 0.32 -## 50 0.06 0.30 0.22 -</code></pre> - -<h3>PEC surface water due to drift</h3> - -<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm -deep water body are obtained using</p> +## 50 0.06 0.30 0.22</code></pre> +</div> +<div id="pec-surface-water-due-to-drift" class="section level3"> +<h3 class="hasAnchor"> +<a href="#pec-surface-water-due-to-drift" class="anchor"> </a>PEC surface water due to drift</h3> +<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm deep water body are obtained using</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_sw_drift.html">PEC_sw_drift</a></span>(<span class="dv">100</span>, <span class="dt">applications =</span> <span class="dv">1</span>)</code></pre></div> +<pre><code>## 1 m 5 m 10 m 20 m +## 0.92333333 0.19000000 0.09666667 0.05000000</code></pre> +</div> +</div> +</div> + </div> -<pre><code class="r">PEC_sw_drift(100, applications = 1) -</code></pre> + <div class="col-md-3" id="sidebar"> + <h2>License</h2> +<p>GPL</p> +<h2>Developers</h2> +<ul class="list-unstyled"> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +</ul> +</div> +</div> -<pre><code>## 1 m 5 m 10 m 20 m -## 0.92333333 0.19000000 0.09666667 0.05000000 -</code></pre> - </div> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> - <div class="span3 offset1 sidebar"> - <h2>Authors</h2> - <ul> - <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li> - </ul> - </div> +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> </div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> + </footer> - </div> +</div> + </body> -</html>
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