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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:54:20 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-17 14:56:25 +0100
commite5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 (patch)
tree18740ef050a68d1a6fe91f1bd2fdfdd97ac6448b /docs/reference/set_nd_nq.html
parent90354f5cd9e095f9ef98424689a2716770b248d4 (diff)
Complete update of online docs for v1.2.0
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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)."><!-- 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]>
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+ <div class="page-header">
+ <h1>Set non-detects and unquantified values in residue series without replicates</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/set_nd_nq.R" class="external-link"><code>R/set_nd_nq.R</code></a></small>
+ <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>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">res_raw</span>, <span class="va">lod</span>, loq <span class="op">=</span> <span class="cn">NA</span>, time_zero_presence <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">set_nd_nq_focus</span><span class="op">(</span></span>
+<span> <span class="va">res_raw</span>,</span>
+<span> <span class="va">lod</span>,</span>
+<span> loq <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span> set_first_sample_nd <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> first_sample_nd_value <span class="op">=</span> <span class="fl">0</span>,</span>
+<span> ignore_below_loq_after_first_nd <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>res_raw</dt>
+<dd><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></dd>
+
+
+<dt>lod</dt>
+<dd><p>Limit of detection (numeric)</p></dd>
+
+
+<dt>loq</dt>
+<dd><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to
+stop after the first non-detection is to be applied</p></dd>
+
+
+<dt>time_zero_presence</dt>
+<dd><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></dd>
+
+
+<dt>set_first_sample_nd</dt>
+<dd><p>Should the first sample be set to "first_sample_nd_value"
+in case it is a non-detection?</p></dd>
+
+
+<dt>first_sample_nd_value</dt>
+<dd><p>Value to be used for the first sample if it is a non-detection</p></dd>
+
+
+<dt>ignore_below_loq_after_first_nd</dt>
+<dd><p>Should we ignore values below the LOQ after the first
+non-detection that occurs after the quantified values?</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p>
+ </div>
+ <div id="functions">
+ <h2>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></div>
+ <div id="references">
+ <h2>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>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># FOCUS (2014) p. 75/76 and 131/132</span></span></span>
+<span class="r-in"><span><span class="va">parent_1</span> <span class="op">&lt;-</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">.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="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_1</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">parent_2</span> <span class="op">&lt;-</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">.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="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">parent_3</span> <span class="op">&lt;-</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">.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="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span>
+<span class="r-in"><span><span class="va">metabolite</span> <span class="op">&lt;-</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">"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="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span>, <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [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</span>
+<span class="r-in"><span><span class="co">#</span></span></span>
+<span class="r-in"><span><span class="co"># Boesten et al. (2015), p. 57/58</span></span></span>
+<span class="r-in"><span><span class="va">table_8</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span>
+<span class="r-in"><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">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nq"</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">2</span><span class="op">)</span>,</span></span>
+<span class="r-in"><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></span>
+<span class="r-in"><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" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><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" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_8</span>, <span class="fl">0.5</span>, <span class="fl">1.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [,1] [,2] [,3] [,4] [,5] [,6]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 10.00 10.00 0.25 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 10.00 10.00 1.00 1.00 0.25 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [3,] 10.00 10.00 10.00 1.00 0.25 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [4,] 1.00 10.00 1.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5,] 0.25 1.00 1.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6,] NA 0.25 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [7,] NA NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">table_10</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span>
+<span class="r-in"><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">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><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" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="st">"nd"</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_10</span>, <span class="fl">0.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [,1] [,2] [,3] [,4] [,5] [,6]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 10.00 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 10.00 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [3,] 10.00 10.00 10.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [4,] 0.25 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5,] NA 0.25 NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6,] NA NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [7,] NA NA NA NA NA NA</span>
+</code></pre></div>
+ </div>
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