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diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 9c5c2a0..32a9b1d 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -1,116 +1,58 @@ -<!-- 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, shrink-to-fit=no"><meta name="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" /> - +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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/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 +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> + <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"> + + <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="">0.6.0</small> -<!-- 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> + + <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> -<!--[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> - <div class="container template-reference-topic"> - <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"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </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> - </div> + <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> - <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> + <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> -<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 --> + </ul></div> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Read TOXSWA surface water concentrations</h1> - <div class="hidden name"><code>read.TOXSWA_cwa.Rd</code></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> + <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> - <div class="ref-description"> + <div class="ref-description section level2"> <p>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 @@ -119,103 +61,99 @@ 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 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="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 class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></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> - - <h2>Author</h2> +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 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 +<code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> - </div> -</div> + </div> + <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="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> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + + <footer><div class="pkgdown-footer-left"> + <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> +<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> </div> - </footer> - </div> + </footer></div> + - </body> -</html> - + </body></html> |