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diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index a2063d05..3ee21a41 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -1,82 +1,69 @@ <!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, shrink-to-fit=no"><meta name="description" content="This function automates replacing unquantified values in residue time and +<!-- 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, shrink-to-fit=no"><title>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><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 name="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)."><title>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><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 +it automates the proposal of Boesten et al (2015)."><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)."><!-- 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> +it automates the proposal of Boesten et al (2015)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Set non-detects and unquantified values in residue series without replicates</h1> + + <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="d-none name"><code>set_nd_nq.Rd</code></div> </div> @@ -105,7 +92,9 @@ it automates the proposal of Boesten et al (2015).</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>res_raw</dt> + + +<dl><dt id="arg-res-raw">res_raw<a class="anchor" aria-label="anchor" href="#arg-res-raw"></a></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. @@ -115,44 +104,42 @@ 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> +<dt id="arg-lod">lod<a class="anchor" aria-label="anchor" href="#arg-lod"></a></dt> <dd><p>Limit of detection (numeric)</p></dd> -<dt>loq</dt> +<dt id="arg-loq">loq<a class="anchor" aria-label="anchor" href="#arg-loq"></a></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> +<dt id="arg-time-zero-presence">time_zero_presence<a class="anchor" aria-label="anchor" href="#arg-time-zero-presence"></a></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> +<dt id="arg-set-first-sample-nd">set_first_sample_nd<a class="anchor" aria-label="anchor" href="#arg-set-first-sample-nd"></a></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> +<dt id="arg-first-sample-nd-value">first_sample_nd_value<a class="anchor" aria-label="anchor" href="#arg-first-sample-nd-value"></a></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> +<dt id="arg-ignore-below-loq-after-first-nd">ignore_below_loq_after_first_nd<a class="anchor" aria-label="anchor" href="#arg-ignore-below-loq-after-first-nd"></a></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 class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> + <p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> </div> <div class="section level2"> <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></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 class="section level2"> @@ -225,23 +212,23 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |