diff options
| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:16:17 +0100 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:27:50 +0100 |
| commit | aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 (patch) | |
| tree | 7ca136834857c12449f50a1e086a589cc9b79e2e /docs/reference/read.TOXSWA_cwa.html | |
| parent | 64f629efbe666bae56f48a309adf33d1eb09c358 (diff) | |
Reorganise data generation
- Use inst/data_generation for R code generating data as in some of my other packages
- data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff
contents were not changed
- Remove ChangeLog, the history is in the git logs
- Update docs and some links contained therein
- use \doi{} markup
- Move logs to log directory
Diffstat (limited to 'docs/reference/read.TOXSWA_cwa.html')
| -rw-r--r-- | docs/reference/read.TOXSWA_cwa.html | 243 |
1 files changed, 88 insertions, 155 deletions
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 9c5c2a0..2685c21 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -1,69 +1,17 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" /> -<meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa"><meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (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." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- 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]> +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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,35 +22,21 @@ renamed to ConLiqWatLay in the out file." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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 --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Read TOXSWA surface water concentrations</h1> @@ -119,103 +53,102 @@ of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</p> </div> - <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>( - <span class='no'>filename</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span> -)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>filename</th> - <td><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></td> - </tr> - <tr> - <th>basedir</th> - <td><p>The path to the directory where the cwa file resides.</p></td> - </tr> - <tr> - <th>zipfile</th> - <td><p>Optional path to a zip file containing the cwa file.</p></td> - </tr> - <tr> - <th>segment</th> - <td><p>The segment for which the data should be read. Either "last", or -the segment number.</p></td> - </tr> - <tr> - <th>substance</th> - <td><p>For .out files, the default value "parent" leads + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read.TOXSWA_cwa</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> basedir <span class="op">=</span> <span class="st">"."</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> windows <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> thresholds <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>filename</dt> +<dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> + + +<dt>basedir</dt> +<dd><p>The path to the directory where the cwa file resides.</p></dd> + + +<dt>zipfile</dt> +<dd><p>Optional path to a zip file containing the cwa file.</p></dd> + + +<dt>segment</dt> +<dd><p>The segment for which the data should be read. Either "last", or +the segment number.</p></dd> + + +<dt>substance</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></td> - </tr> - <tr> - <th>total</th> - <td><p>Set this to TRUE in order to read total concentrations as well. This is +of interested can be selected by its code name.</p></dd> + + +<dt>total</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></td> - </tr> - <tr> - <th>windows</th> - <td><p>Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.</p></td> - </tr> - <tr> - <th>thresholds</th> - <td><p>Numeric vector of threshold concentrations in µg/L for -generating event statistics.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An instance of an R6 object of class -<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +files. For .cwa files, the total concentration is always read as well.</p></dd> + + +<dt>windows</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> +<dd><p>Numeric vector of threshold concentrations in µg/L for +generating event statistics.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>An instance of an R6 object of class +<code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu">read.TOXSWA_cwa</span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |