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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-31 19:21:03 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-31 19:59:10 +0200
commit08465d77a6ca5a9656ac86047c6008f1e7f3e9c7 (patch)
treef27a775e146748881eb6526ed57298f4bdc40c2f /docs/reference/lod.html
parentf4fcef8228ebd5a1a73bc6edc47b5efa259c2e20 (diff)
Fix URLs in README, convert to roxygenv0.2.3
- The roxygen conversion was done using Rd2roxygen - Also edit _pkgdown.yml to group the reference - Use markdown bullet lists for lod and loq docs
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@@ -1,12 +1,12 @@
<!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>Estimate a limit of detection (LOD) — lod • chemCal</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="Estimate a limit of detection (LOD) — lod"><meta property="og:description" content="The decision limit (German: Nachweisgrenze) is defined as the signal or
- analyte concentration that is significantly different from the blank signal
- with a first order error alpha (one-sided significance test).
- The detection limit, or more precise, the minimum detectable value
- (German: Erfassungsgrenze), is then defined as the signal or analyte
- concentration where the probability that the signal is not detected although
- the analyte is present (type II or false negative error), is beta (also a
- one-sided significance test)."><!-- 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]>
+analyte concentration that is significantly different from the blank signal
+with a first order error alpha (one-sided significance test). The detection
+limit, or more precise, the minimum detectable value (German:
+Erfassungsgrenze), is then defined as the signal or analyte concentration
+where the probability that the signal is not detected although the analyte
+is present (type II or false negative error), is beta (also a one-sided
+significance test)."><!-- 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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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -54,76 +54,81 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Estimate a limit of detection (LOD)</h1>
-
+ <small class="dont-index">Source: <a href="https://github.com/jranke/chemCal/blob/HEAD/R/lod.R" class="external-link"><code>R/lod.R</code></a></small>
<div class="hidden name"><code>lod.Rd</code></div>
</div>
<div class="ref-description">
<p>The decision limit (German: Nachweisgrenze) is defined as the signal or
- analyte concentration that is significantly different from the blank signal
- with a first order error alpha (one-sided significance test).
- The detection limit, or more precise, the minimum detectable value
- (German: Erfassungsgrenze), is then defined as the signal or analyte
- concentration where the probability that the signal is not detected although
- the analyte is present (type II or false negative error), is beta (also a
- one-sided significance test).</p>
+analyte concentration that is significantly different from the blank signal
+with a first order error alpha (one-sided significance test). The detection
+limit, or more precise, the minimum detectable value (German:
+Erfassungsgrenze), is then defined as the signal or analyte concentration
+where the probability that the signal is not detected although the analyte
+is present (type II or false negative error), is beta (also a one-sided
+significance test).</p>
</div>
<div id="ref-usage">
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">lod</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, beta <span class="op">=</span> <span class="fl">0.05</span>, method <span class="op">=</span> <span class="st">"default"</span>, tol <span class="op">=</span> <span class="st">"default"</span><span class="op">)</span></code></pre></div>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">lod</span><span class="op">(</span>
+ <span class="va">object</span>,
+ <span class="va">...</span>,
+ alpha <span class="op">=</span> <span class="fl">0.05</span>,
+ beta <span class="op">=</span> <span class="fl">0.05</span>,
+ method <span class="op">=</span> <span class="st">"default"</span>,
+ tol <span class="op">=</span> <span class="st">"default"</span>
+<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>object</dt>
-<dd><p>A univariate model object of class <code><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></code> or
- <code><a href="https://rdrr.io/pkg/MASS/man/rlm.html" class="external-link">rlm</a></code>
- with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>,
- optionally from a weighted regression.</p></dd>
+<dd><p>A univariate model object of class <code><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></code> or
+<code><a href="https://rdrr.io/pkg/MASS/man/rlm.html" class="external-link">rlm</a></code> with model formula <code>y ~ x</code> or <code>y ~ x -
+1</code>, optionally from a weighted regression.</p></dd>
<dt>...</dt>
-<dd><p>Placeholder for further arguments that might be needed by
- future implementations.</p></dd>
+<dd><p>Placeholder for further arguments that might be needed by
+future implementations.</p></dd>
<dt>alpha</dt>
<dd><p>The error tolerance for the decision limit (critical value).</p></dd>
<dt>beta</dt>
<dd><p>The error tolerance beta for the detection limit.</p></dd>
<dt>method</dt>
-<dd><p>The “default” method uses a prediction interval at the LOD
- for the estimation of the LOD, which obviously requires
- iteration. This is described for example in Massart, p. 432 ff.
- The “din” method uses the prediction interval at
- x = 0 as an approximation.</p></dd>
+<dd><p>The “default” method uses a prediction interval at the
+LOD for the estimation of the LOD, which obviously requires iteration. This
+is described for example in Massart, p. 432 ff. The “din” method
+uses the prediction interval at x = 0 as an approximation.</p></dd>
<dt>tol</dt>
<dd><p>When the “default” method is used, the default tolerance
- for the LOD on the x scale is the value of the smallest non-zero standard
- divided by 1000. Can be set to a numeric value to override this.</p></dd>
+for the LOD on the x scale is the value of the smallest non-zero standard
+divided by 1000. Can be set to a numeric value to override this.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
- <p>A list containig the corresponding x and y values of the estimated limit of
- detection of a model used for calibration.</p>
+ <p>A list containig the corresponding x and y values of the estimated
+limit of detection of a model used for calibration.</p>
</div>
<div id="note">
<h2>Note</h2>
- <p>- The default values for alpha and beta are the ones recommended by IUPAC.
- - The estimation of the LOD in terms of the analyte amount/concentration
- xD from the LOD in the signal domain SD is done by simply inverting the
- calibration function (i.e. assuming a known calibration function).
- - The calculation of a LOD from weighted calibration models requires
- a weights argument for the internally used <code><a href="https://rdrr.io/r/stats/predict.lm.html" class="external-link">predict.lm</a></code>
- function, which is currently not supported in R.</p>
+ <p>* The default values for alpha and beta are the ones recommended by IUPAC.
+* The estimation of the LOD in terms of the analyte amount/concentration xD
+from the LOD in the signal domain SD is done by simply inverting the
+calibration function (i.e. assuming a known calibration function).
+* The calculation of a LOD from weighted calibration models requires a
+weights argument for the internally used <code><a href="https://rdrr.io/r/stats/predict.lm.html" class="external-link">predict.lm</a></code>
+function, which is currently not supported in R.</p>
</div>
<div id="references">
<h2>References</h2>
- <p>Massart, L.M, Vandenginste, B.G.M., Buydens, L.M.C., De Jong, S., Lewi, P.J.,
- Smeyers-Verbeke, J. (1997) Handbook of Chemometrics and Qualimetrics: Part A,
- Chapter 13.7.8</p>
+ <p>Massart, L.M, Vandenginste, B.G.M., Buydens, L.M.C., De Jong,
+S., Lewi, P.J., Smeyers-Verbeke, J. (1997) Handbook of Chemometrics and
+Qualimetrics: Part A, Chapter 13.7.8</p>
<p>J. Inczedy, T. Lengyel, and A.M. Ure (2002) International Union of Pure and
- Applied Chemistry Compendium of Analytical Nomenclature: Definitive Rules.
- Web edition.</p>
-<p>Currie, L. A. (1997) Nomenclature in evaluation of analytical methods including
- detection and quantification capabilities (IUPAC Recommendations 1995).
- Analytica Chimica Acta 391, 105 - 126.</p>
+Applied Chemistry Compendium of Analytical Nomenclature: Definitive Rules.
+Web edition.</p>
+<p>Currie, L. A. (1997) Nomenclature in evaluation of analytical methods
+including detection and quantification capabilities (IUPAC Recommendations
+1995). Analytica Chimica Acta 391, 105 - 126.</p>
</div>
<div id="see-also">
<h2>See also</h2>
@@ -132,7 +137,8 @@
<div id="ref-examples">
<h2>Examples</h2>
- <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="va">x</span>, data <span class="op">=</span> <span class="va">din32645</span><span class="op">)</span></span>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
+<span class="r-in"><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="va">x</span>, data <span class="op">=</span> <span class="va">din32645</span><span class="op">)</span></span>
<span class="r-in"><span class="fu">lod</span><span class="op">(</span><span class="va">m</span><span class="op">)</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $x</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.08655484</span>
@@ -150,6 +156,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> $y</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3155.393</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"></span>
</code></pre></div>
</div>
</div>

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