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/plot.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/plot.TOXSWA_cwa.html')
-rw-r--r-- | docs/reference/plot.TOXSWA_cwa.html | 258 |
1 files changed, 99 insertions, 159 deletions
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 1262c71..857b154 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -1,65 +1,13 @@ -<!-- 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>Plot TOXSWA surface water concentrations — plot.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> - 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- - - </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"> @@ -70,35 +18,21 @@ segment of a TOXSWA surface water body." /> </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>Plot TOXSWA surface water concentrations</h1> @@ -111,106 +45,112 @@ segment of a TOXSWA surface water body." /> segment of a TOXSWA surface water body.</p> </div> - <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, - <span class='no'>...</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>x</th> - <td><p>The TOXSWA_cwa object to be plotted.</p></td> - </tr> - <tr> - <th>time_column</th> - <td><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></td> - </tr> - <tr> - <th>xlab, ylab</th> - <td><p>Labels for x and y axis.</p></td> - </tr> - <tr> - <th>add</th> - <td><p>Should we add to an existing plot?</p></td> - </tr> - <tr> - <th>threshold_factor</th> - <td><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></td> - </tr> - <tr> - <th>thin_low</th> - <td><p>If an integer greater than 1, the data close to zero (smaller than + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for 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> +<span> xlab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> add <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> threshold_factor <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> thin_low <span class="op">=</span> <span class="fl">1</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> LC_TIME <span class="op">=</span> <span class="st">"C"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The TOXSWA_cwa object to be plotted.</p></dd> + + +<dt>time_column</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> +<dd><p>Labels for x and y axis.</p></dd> + + +<dt>add</dt> +<dd><p>Should we add to an existing plot?</p></dd> + + +<dt>threshold_factor</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> +<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></td> - </tr> - <tr> - <th>total</th> - <td><p>Should the total concentration in water be plotted, including substance sorbed -to suspended matter?</p></td> - </tr> - <tr> - <th>LC_TIME</th> - <td><p>Specification of the locale used to format dates</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></td> - </tr> - </table> - - - <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'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></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>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_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>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></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="#examples">Examples</a></li> - </ul> +in order to decrease the amount of data that is included in the plots</p></dd> + + +<dt>total</dt> +<dd><p>Should the total concentration in water be plotted, including substance sorbed +to suspended matter?</p></dd> + + +<dt>LC_TIME</dt> +<dd><p>Specification of the locale used to format dates</p></dd> + +<dt>...</dt> +<dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> + +</dl></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"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></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>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</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">H_sw_D4_pond</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-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="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-2.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="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_firstjan"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-3.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="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_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>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</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">H_sw_R1_stream</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></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> - 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