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| author | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-14 07:19:15 +0100 |
|---|---|---|
| committer | Johannes Ranke <johannes.ranke@jrwb.de> | 2025-02-14 07:19:15 +0100 |
| commit | b0f08271d1dae8ffaf57f557c27eba1314ece1d5 (patch) | |
| tree | 98da899d455d6945849d6f4b4e98adfb98dc8b2b /docs/reference/set_nd_nq.html | |
| parent | 7dc59c522d0639f6473463340e518e2e8074e364 (diff) | |
| parent | 55d9c2331e468efd364472555dbfae84603a4f73 (diff) | |
Merge branch 'main' into dev
Diffstat (limited to 'docs/reference/set_nd_nq.html')
| -rw-r--r-- | docs/reference/set_nd_nq.html | 237 |
1 files changed, 95 insertions, 142 deletions
diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 249a7600..3ee21a41 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -1,118 +1,74 @@ <!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 +<!-- 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)."><!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</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 class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</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> +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)."></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <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> + + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item dropdown"> + <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> </ul></li> -<li> - 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<div class="ref-description"> + <div class="ref-description section level2"> <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 @@ -120,7 +76,8 @@ 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="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <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> @@ -133,9 +90,11 @@ it automates the proposal of Boesten et al (2015).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>res_raw</dt> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<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. @@ -145,48 +104,46 @@ 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 id="value"> - <h2>Value</h2> - - -<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> + <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> </div> - <div id="functions"> - <h2>Functions</h2> - + <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 id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></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 @@ -197,8 +154,8 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi 18 December 2014, p. 251</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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> @@ -255,27 +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> - </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> + </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="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <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> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer></div> + </footer></div> + - - </body></html> |