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diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html new file mode 100644 index 00000000..26a28339 --- /dev/null +++ b/docs/dev/reference/set_nd_nq.html @@ -0,0 +1,258 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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 and unquantified values in residue series without replicates — set_nd_nq • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" 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" 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 and unquantified values in residue series without replicates — set_nd_nq"><meta property="og:description" content="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)."><meta name="robots" content="noindex"><!-- 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 data-spy="scroll" data-target="#toc"> + + + <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">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </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 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 & 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"><-</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">#></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"><-</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">#></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">#></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"><-</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">#></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">#></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"><-</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">#></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">#></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"><-</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">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 1.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 1.00 0.25 NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 1.00 10.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] 0.25 1.00 1.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA 0.25 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> +<span class="r-in"><span><span class="va">table_10</span> <span class="op"><-</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">#></span> [,1] [,2] [,3] [,4] [,5] [,6]</span> +<span class="r-out co"><span class="r-pr">#></span> [1,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [2,] 10.00 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [3,] 10.00 10.00 10.00 0.25 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [4,] 0.25 10.00 0.25 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [5,] NA 0.25 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [6,] NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</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></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + |