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| 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.one_box.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.one_box.html')
| -rw-r--r-- | docs/reference/plot.one_box.html | 242 |
1 files changed, 90 insertions, 152 deletions
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 75b8fe9..2fc946e 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -1,64 +1,12 @@ -<!-- 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 time series of decline data — plot.one_box • 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 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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" 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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"> @@ -69,35 +17,21 @@ </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 time series of decline data</h1> @@ -109,97 +43,101 @@ <p>Plot time series of decline data</p> </div> - <pre class="usage"><span class='co'># S3 method for one_box</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, - <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</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 object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>Limits for the x axis</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>Limits for the y axis</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis</p></td> - </tr> - <tr> - <th>max_twa</th> - <td><p>If a numeric value is given, the maximum time weighted -average concentration(s) is/are shown in the graph.</p></td> - </tr> - <tr> - <th>max_twa_var</th> - <td><p>Variable for which the maximum time weighted average should -be shown if max_twa is not NULL.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-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='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a fitted mkinfit model</span> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.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="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</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> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> ylim <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="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> max_twa <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> max_twa_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">]</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 object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> + + +<dt>xlim</dt> +<dd><p>Limits for the x axis</p></dd> + + +<dt>ylim</dt> +<dd><p>Limits for the y axis</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis</p></dd> + +<dt>ylab</dt> +<dd><p>Label for the y axis</p></dd> + + +<dt>max_twa</dt> +<dd><p>If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.</p></dd> + + +<dt>max_twa_var</dt> +<dd><p>Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <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>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</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">dfop_pred</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-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="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</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">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-3.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> + 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