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<title>Set non-detects in residue series without replicates — set_nd • pfm</title>
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<meta property="og:description" content="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." />
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<h1>Set non-detects in residue series without replicates</h1>
<div class="hidden name"><code>set_nd.Rd</code></div>
</div>
<div class="ref-description">
<p>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 or zero values 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</code>: Set non-detects in residues series</p></li>
<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) Generic Guidance for Estimating Persistence and Degradation
Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
18 December 2014, p. 251</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># FOCUS (2014) p. 75/76 and 131/132</span>
<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>
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<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>
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