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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-06 17:00:48 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-06 17:00:48 +0100 |
| commit | 73e650114af77582238abf5273e63005e0b2287e (patch) | |
| tree | e0effa0124a713738c850aa47acc54d1b82318d8 /docs/reference/massart97ex3.html | |
| parent | fcb3332b7b186639cce940696057a2b6dd2c5cca (diff) | |
Static documentation now built by pkgdown::build_site()
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| -rw-r--r-- | docs/reference/massart97ex3.html | 188 |
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diff --git a/docs/reference/massart97ex3.html b/docs/reference/massart97ex3.html new file mode 100644 index 0000000..2ec8f6f --- /dev/null +++ b/docs/reference/massart97ex3.html @@ -0,0 +1,188 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <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>Calibration data from Massart et al. (1997), example 3 — massart97ex3 • chemCal</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> + <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"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">chemCal</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> +<li> + <a href="../articles/index.html">Articles</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calibration data from Massart et al. (1997), example 3</h1> + </div> + + + <p>Sample dataset from p. 188 to test the package.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A dataframe containing 6 levels of x values with 5 + observations of y for each level.</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</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 8.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>massart97ex3</span>) +<span class='fu'>attach</span>(<span class='no'>massart97ex3</span>)</div><div class='output co'>#> <span class='message'>The following objects are masked from massart97ex3 (pos = 3):</span> +#> <span class='message'></span> +#> <span class='message'> x, y</span></div><div class='input'><span class='no'>yx</span> <span class='kw'><-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>) +<span class='no'>ybar</span> <span class='kw'><-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>) +<span class='no'>s</span> <span class='kw'><-</span> <span class='fu'>round</span>(<span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>sd</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>) +<span class='no'>w</span> <span class='kw'><-</span> <span class='fu'>round</span>(<span class='fl'>1</span> / (<span class='no'>s</span>^<span class='fl'>2</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>) +<span class='no'>weights</span> <span class='kw'><-</span> <span class='no'>w</span>[<span class='fu'>factor</span>(<span class='no'>x</span>)] +<span class='no'>m</span> <span class='kw'><-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>w</span> <span class='kw'>=</span> <span class='no'>weights</span>) +<span class='fu'><a href='calplot.html'>calplot</a></span>(<span class='no'>m</span>)</div><div class='output co'>#> <span class='warning'>Warning: Assuming constant prediction variance even though model fit is weighted</span></div><img src='massart97ex3-5.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># The following concords with the book p. 200</span> +<span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m</span>, <span class='fl'>15</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>1.67</span>) <span class='co'># 5.9 +- 2.5</span></div><div class='output co'>#> $Prediction +#> [1] 5.865367 +#> +#> $`Standard Error` +#> [1] 0.8926109 +#> +#> $Confidence +#> [1] 2.478285 +#> +#> $`Confidence Limits` +#> [1] 3.387082 8.343652 +#> </div><div class='input'><span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m</span>, <span class='fl'>90</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>0.145</span>) <span class='co'># 44.1 +- 7.9</span></div><div class='output co'>#> $Prediction +#> [1] 44.06025 +#> +#> $`Standard Error` +#> [1] 2.829162 +#> +#> $Confidence +#> [1] 7.855012 +#> +#> $`Confidence Limits` +#> [1] 36.20523 51.91526 +#> </div><div class='input'> +<span class='co'># The LOD is only calculated for models from unweighted regression</span> +<span class='co'># with this version of chemCal</span> +<span class='no'>m0</span> <span class='kw'><-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>) +<span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m0</span>)</div><div class='output co'>#> $x +#> [1] 5.407085 +#> +#> $y +#> 1 +#> 13.63911 +#> </div><div class='input'> +<span class='co'># Limit of quantification from unweighted regression</span> +<span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m0</span>)</div><div class='output co'>#> $x +#> [1] 13.97764 +#> +#> $y +#> 1 +#> 30.6235 +#> </div><div class='input'> +<span class='co'># For calculating the limit of quantification from a model from weighted</span> +<span class='co'># regression, we need to supply weights, internally used for inverse.predict</span> +<span class='co'># If we are not using a variance function, we can use the weight from</span> +<span class='co'># the above example as a first approximation (x = 15 is close to our</span> +<span class='co'># loq approx 14 from above).</span> +<span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m</span>, <span class='kw'>w.loq</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)</div><div class='output co'>#> $x +#> [1] 7.346195 +#> +#> $y +#> 1 +#> 17.90777 +#> </div><div class='input'><span class='co'># The weight for the loq should therefore be derived at x = 7.3 instead</span> +<span class='co'># of 15, but the graphical procedure of Massart (p. 201) to derive the </span> +<span class='co'># variances on which the weights are based is quite inaccurate anyway. </span></div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> |