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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 14:09:50 +0100
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2024-01-31 14:09:50 +0100
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-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015)." />
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- <h1>Set non-detects and unquantified values in residue series without replicates</h1>
-
- <div class="hidden name"><code>set_nd_nq.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>This function automates replacing unquantified values in residue time and
-depth series. For time series, the function performs part of the residue
-processing proposed in the FOCUS kinetics guidance for parent compounds
-and metabolites. For two-dimensional residue series over time and depth,
-it automates the proposal of Boesten et al (2015).</p>
- </div>
-
- <pre class="usage"><span class='fu'>set_nd_nq</span>(<span class='no'>res_raw</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_presence</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>set_nd_nq_focus</span>(
- <span class='no'>res_raw</span>,
- <span class='no'>lod</span>,
- <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
- <span class='kw'>set_first_sample_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>first_sample_nd_value</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>ignore_below_loq_after_first_nd</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>res_raw</th>
- <td><p>Character vector of a residue time series, or matrix of
-residue values with rows representing depth profiles for a specific sampling
-time, and columns representing time series of residues at the same depth.
-Values below the limit of detection (lod) have to be coded as "nd", values
-between the limit of detection and the limit of quantification, if any, have
-to be coded as "nq". Samples not analysed have to be coded as "na". All
-values that are not "na", "nd" or "nq" have to be 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_presence</th>
- <td><p>Do we assume that residues occur at time zero?
-This only affects samples from the first sampling time that have been
-reported as "nd" (not detected).</p></td>
- </tr>
- <tr>
- <th>set_first_sample_nd</th>
- <td><p>Should the first sample be set to "first_sample_nd_value"
-in case it is a non-detection?</p></td>
- </tr>
- <tr>
- <th>first_sample_nd_value</th>
- <td><p>Value to be used for the first sample if it is a non-detection</p></td>
- </tr>
- <tr>
- <th>ignore_below_loq_after_first_nd</th>
- <td><p>Should we ignore values below the LOQ after the first
-non-detection that occurs after the quantified values?</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p>
- <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
-
-
-<ul>
-<li><p><code>set_nd_nq_focus</code>: Set non-detects in residue time series according to FOCUS rules</p></li>
-</ul>
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
- <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
-J. and Pol, J. W. (2015). Leaching of plant protection products and their
-transformation products; Proposals for improving the assessment of leaching
-to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
-Wageningen UR (University &amp; Research centre)</p>
-<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'>&lt;-</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_nq</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [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'>&lt;-</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_nq</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [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_nq_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'>#&gt; [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'>&lt;-</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_nq</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [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_nq_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'>#&gt; [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'>&lt;-</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_nq</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt; [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><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>, <span class='fl'>0.05</span>)</div><div class='output co'>#&gt; [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</div><div class='input'><span class='co'>#</span>
-<span class='co'># Boesten et al. (2015), p. 57/58</span>
-<span class='no'>table_8</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
- <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nq"</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>2</span>),
- <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>,
- <span class='st'>"nq"</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
- <span class='st'>"nd"</span>, <span class='st'>"nq"</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
- <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>)),
- <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>set_nd_nq</span>(<span class='no'>table_8</span>, <span class='fl'>0.5</span>, <span class='fl'>1.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; [,1] [,2] [,3] [,4] [,5] [,6]
-#&gt; [1,] 10.00 10.00 0.25 0.25 NA NA
-#&gt; [2,] 10.00 10.00 1.00 1.00 0.25 NA
-#&gt; [3,] 10.00 10.00 10.00 1.00 0.25 NA
-#&gt; [4,] 1.00 10.00 1.00 0.25 NA NA
-#&gt; [5,] 0.25 1.00 1.00 0.25 NA NA
-#&gt; [6,] NA 0.25 0.25 NA NA NA
-#&gt; [7,] NA NA NA NA NA NA</div><div class='input'><span class='no'>table_10</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
- <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
- <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
- <span class='st'>"nd"</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
- <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>18</span>)),
- <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>set_nd_nq</span>(<span class='no'>table_10</span>, <span class='fl'>0.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; [,1] [,2] [,3] [,4] [,5] [,6]
-#&gt; [1,] 10.00 10.00 0.25 NA NA NA
-#&gt; [2,] 10.00 10.00 0.25 NA NA NA
-#&gt; [3,] 10.00 10.00 10.00 0.25 NA NA
-#&gt; [4,] 0.25 10.00 0.25 NA NA NA
-#&gt; [5,] NA 0.25 NA NA NA NA
-#&gt; [6,] NA NA NA NA NA NA
-#&gt; [7,] NA NA NA NA NA NA</div></pre>
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- <h2>Contents</h2>
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- <li><a href="#arguments">Arguments</a></li>
- <li><a href="#value">Value</a></li>
- <li><a href="#functions">Functions</a></li>
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- <li><a href="#examples">Examples</a></li>
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