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Diffstat (limited to 'docs')
| -rw-r--r-- | docs/reference/index.html | 15 | ||||
| -rw-r--r-- | docs/reference/set_nd.html | 247 | ||||
| -rw-r--r-- | docs/sitemap.xml | 3 |
3 files changed, 265 insertions, 0 deletions
diff --git a/docs/reference/index.html b/docs/reference/index.html index e1acfc1..a704ad0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -167,6 +167,21 @@ <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> + </tr><tr> + + <td> + <p><code><a href="set_nd.html">set_nd()</a></code> <code><a href="set_nd.html">set_nd_focus()</a></code> </p> + </td> + <td><p>Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq.</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html new file mode 100644 index 0000000..32ac155 --- /dev/null +++ b/docs/reference/set_nd.html @@ -0,0 +1,247 @@ +<!-- 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>Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq. — set_nd • 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="Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq. — set_nd" /> + +<meta property="og:description" content="Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq." /> +<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]> +<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="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> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq.</h1> + + <div class="hidden name"><code>set_nd.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>Set non-detects in residue series without replicates +Sets non-detects directly before or directly after detects to NA. Values between +lod and loq are set to their mean value if an loq is specified. +If 'time_zero' is set to TRUE, the residue series is assumed to start with time +zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the +set_nd_focus variant, this is zero, otherwise this argument has NA as default +value. +If stopping after the first non-detection is requested, as in in the FOCUS +variant of the function, an loq has to be specified in order to decide +if any later detections are above the loq.</p> + + </div> + + <pre class="usage"><span class='fu'>set_nd</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>time_zero_nd_value</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>stop_after_first_nondetect</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + +<span class='fu'>set_nd_focus</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>r</th> + <td><p>A character vector of sequential residues without replicates, with +non-detects specified as 'nd' and unquantified values above the limit of +detection specified as 'nq', otherwise coercible to numeric</p></td> + </tr> + <tr> + <th>lod</th> + <td><p>Limit of detection (numeric)</p></td> + </tr> + <tr> + <th>loq</th> + <td><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to +stop after the first non-detection is to be applied</p></td> + </tr> + <tr> + <th>time_zero</th> + <td><p>Is the first value in the series a time zero value?</p></td> + </tr> + <tr> + <th>time_zero_nd_value</th> + <td><p>Which value should we use for non-detects at time zero?</p></td> + </tr> + <tr> + <th>stop_after_first_nondetect</th> + <td><p>Should we really stop after the first non-detection?</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2> + + +<ul> +<li><p><code>set_nd_focus</code>: Set non-detects in residues series according to FOCUS rules</p></li> +</ul> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>FOCUS (2014) p. 75, 76, 131, 132</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>parent_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) +<span class='fu'>set_nd</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) +<span class='fu'>set_nd</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</div><div class='input'><span class='no'>parent_3</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.06</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) +<span class='fu'>set_nd</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</div><div class='input'><span class='no'>metabolite</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>0.03</span>, <span class='fl'>0.06</span>, <span class='fl'>0.10</span>, <span class='fl'>0.11</span>, <span class='fl'>0.10</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>) +<span class='fu'>set_nd</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</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="#functions">Functions</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + + <footer> + <div class="copyright"> + <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> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 6eff936..79d9b14 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -100,6 +100,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/sawtooth.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/set_nd.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html</loc> </url> <url> |