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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-23 10:32:36 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-31 18:35:09 +0200
commitf4fcef8228ebd5a1a73bc6edc47b5efa259c2e20 (patch)
treef9e0489c8941257b5055783a443f4859212ad4f1 /docs/index.html
parent4c2b22d75cc5102ddc595ea479c46bfdb46c1016 (diff)
Use 'investr' conditionally in tests, updates
Most prominently, a README was added, giving a nice overview for the people visiting the github page, the package page on CRAN, or the online docs at pkgdown.jrwb.de. The maintainer e-mail address was also updated.
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@@ -25,6 +25,8 @@
<![endif]-->
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+
+
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<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -37,19 +39,13 @@
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<span class="navbar-brand">
<a class="navbar-link" href="index.html">chemCal</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.3</span>
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@@ -61,7 +57,7 @@
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- <a href="https://github.com/jranke/chemCal/">
+ <a href="https://github.com/jranke/chemCal/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
@@ -78,58 +74,159 @@
</header><div class="row">
<div class="contents col-md-9">
-<div id="chemcal---calibration-functions-for-analytical-chemistry" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#chemcal---calibration-functions-for-analytical-chemistry" class="anchor"></a>chemCal - Calibration functions for analytical chemistry</h1></div>
+<div class="section level1">
+<div class="page-header"><h1 id="chemcal---calibration-functions-for-analytical-chemistry">chemCal - Calibration functions for analytical chemistry<a class="anchor" aria-label="anchor" href="#chemcal---calibration-functions-for-analytical-chemistry"></a>
+</h1></div>
<!-- badges: start -->
-<p>Static documentation of this R package can be found at <a href="https://pkgdown.jrwb.de/chemCal" class="uri">https://pkgdown.jrwb.de/chemCal</a></p>
+<div class="section level2">
+<h2 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a>
+</h2>
+<p>chemCal is an R package providing some basic functions for conveniently working with linear calibration curves with one explanatory variable.</p>
+</div>
+<div class="section level2">
+<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
+</h2>
+<p>From within <a href="https://r-project.org" class="external-link">R</a>, get the official chemCal release using</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"chemCal"</span><span class="op">)</span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
+</h2>
+<p>chemCal works with univariate linear models of class <code>lm</code>. Working with one of the datasets coming with chemCal, we can produce a calibration plot using the <code>calplot</code> function:</p>
+<div class="section level3">
+<h3 id="plotting-a-calibration">Plotting a calibration<a class="anchor" aria-label="anchor" href="#plotting-a-calibration"></a>
+</h3>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/chemCal/" class="external-link">chemCal</a></span><span class="op">)</span>
+<span class="va">m0</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">massart97ex3</span><span class="op">)</span>
+<span class="fu"><a href="reference/calplot.lm.html">calplot</a></span><span class="op">(</span><span class="va">m0</span><span class="op">)</span></code></pre></div>
+<p><img src="reference/figures/README-calplot-1.png"><!-- --></p>
+</div>
+<div class="section level3">
+<h3 id="lod-and-loq">LOD and LOQ<a class="anchor" aria-label="anchor" href="#lod-and-loq"></a>
+</h3>
+<p>If you use unweighted regression, as in the above example, we can calculate a Limit Of Detection (LOD) from the calibration data.</p>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="reference/lod.html">lod</a></span><span class="op">(</span><span class="va">m0</span><span class="op">)</span>
+<span class="co">#&gt; $x</span>
+<span class="co">#&gt; [1] 5.407085</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $y</span>
+<span class="co">#&gt; [1] 13.63911</span></code></pre></div>
+<p>This is the minimum detectable value (German: Erfassungsgrenze), i.e. the value where the probability that the signal is not detected although the analyte is present is below a specified error tolerance beta (default is 0.05 following the IUPAC recommendation).</p>
+<p>You can also calculate the decision limit (German: Nachweisgrenze), i.e. the value that is significantly different from the blank signal with an error tolerance alpha (default is 0.05, again following IUPAC recommendations) by setting beta to 0.5.</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="reference/lod.html">lod</a></span><span class="op">(</span><span class="va">m0</span>, beta <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span>
+<span class="co">#&gt; $x</span>
+<span class="co">#&gt; [1] 2.720388</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $y</span>
+<span class="co">#&gt; [1] 8.314841</span></code></pre></div>
+<p>Furthermore, you can calculate the Limit Of Quantification (LOQ), being defined as the value where the relative error of the quantification given the calibration model reaches a prespecified value (default is 1/3).</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="reference/loq.html">loq</a></span><span class="op">(</span><span class="va">m0</span><span class="op">)</span>
+<span class="co">#&gt; $x</span>
+<span class="co">#&gt; [1] 9.627349</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $y</span>
+<span class="co">#&gt; [1] 22.00246</span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="confidence-intervals-for-measured-values">Confidence intervals for measured values<a class="anchor" aria-label="anchor" href="#confidence-intervals-for-measured-values"></a>
+</h3>
+<p>Finally, you can get a confidence interval for the values measured using the calibration curve, i.e. for the inverse predictions using the function <code>inverse.predict</code>.</p>
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="reference/inverse.predict.html">inverse.predict</a></span><span class="op">(</span><span class="va">m0</span>, <span class="fl">90</span><span class="op">)</span>
+<span class="co">#&gt; $Prediction</span>
+<span class="co">#&gt; [1] 43.93983</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $`Standard Error`</span>
+<span class="co">#&gt; [1] 1.576985</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $Confidence</span>
+<span class="co">#&gt; [1] 3.230307</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $`Confidence Limits`</span>
+<span class="co">#&gt; [1] 40.70952 47.17014</span></code></pre></div>
+<p>If you have replicate measurements of the same sample, you can also give a vector of numbers.</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="reference/inverse.predict.html">inverse.predict</a></span><span class="op">(</span><span class="va">m0</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">91</span>, <span class="fl">89</span>, <span class="fl">87</span>, <span class="fl">93</span>, <span class="fl">90</span><span class="op">)</span><span class="op">)</span>
+<span class="co">#&gt; $Prediction</span>
+<span class="co">#&gt; [1] 43.93983</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $`Standard Error`</span>
+<span class="co">#&gt; [1] 0.796884</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $Confidence</span>
+<span class="co">#&gt; [1] 1.632343</span>
+<span class="co">#&gt; </span>
+<span class="co">#&gt; $`Confidence Limits`</span>
+<span class="co">#&gt; [1] 42.30749 45.57217</span></code></pre></div>
+</div>
+</div>
+<div class="section level2">
+<h2 id="reference">Reference<a class="anchor" aria-label="anchor" href="#reference"></a>
+</h2>
+<p>You can use the R help system to view documentation, or you can have a look at the <a href="https://pkgdown.jrwb.de/chemCal" class="external-link">online documentation</a>.</p>
+</div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div class="links">
-<h2>Links</h2>
+<h2 data-toc-skip>Links</h2>
<ul class="list-unstyled">
-<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=chemCal">https://​cloud.r-project.org/​package=chemCal</a>
-</li>
-<li>Browse source code at <br><a href="https://github.com/jranke/chemCal/">https://​github.com/​jranke/​chemCal/​</a>
-</li>
-<li>Report a bug at <br><a href="https://github.com/jranke/chemCal/issues">https://​github.com/​jranke/​chemCal/​issues</a>
-</li>
+<li><a href="https://cloud.r-project.org/package=chemCal" class="external-link">View on CRAN</a></li>
+<li><a href="https://github.com/jranke/chemCal/" class="external-link">Browse source code</a></li>
+<li><a href="https://github.com/jranke/chemCal/issues" class="external-link">Report a bug</a></li>
</ul>
</div>
+
<div class="license">
-<h2>License</h2>
+<h2 data-toc-skip>License</h2>
<ul class="list-unstyled">
<li>GPL (&gt;= 2)</li>
</ul>
</div>
-<div class="developers">
-<h2>Developers</h2>
+
+
+<div class="citation">
+<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li><a href="authors.html#citation">Citing chemCal</a></li>
</ul>
</div>
- <div class="dev-status">
-<h2>Dev status</h2>
+<div class="developers">
+<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
-<li><a href="https://cran.r-project.org/package=chemCal"><img src="https://www.r-pkg.org/badges/version/chemCal"></a></li>
-<li><a href="https://travis-ci.com/jranke/chemCal"><img src="https://travis-ci.com/jranke/chemCal.svg?branch=master" alt="Build Status"></a></li>
-<li><a href="https://codecov.io/github/jranke/chemCal"><img src="https://codecov.io/github/jranke/chemCal/branch/master/graphs/badge.svg" alt="codecov"></a></li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
</ul>
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+
+<div class="dev-status">
+<h2 data-toc-skip>Dev status</h2>
+<ul class="list-unstyled">
+<li><a href="https://cran.r-project.org/package=chemCal" class="external-link"><img src="https://www.r-pkg.org/badges/version/chemCal"></a></li>
+<li><a href="https://app.travis-ci.com/github/jranke/chemCal" class="external-link"><img src="https://travis-ci.com/jranke/chemCal.svg?branch=master" alt="Build Status"></a></li>
+<li><a href="https://codecov.io/github/jranke/chemCal" class="external-link"><img src="https://codecov.io/github/jranke/chemCal/branch/master/graphs/badge.svg" alt="codecov"></a></li>
+</ul>
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+
+ </div>
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<footer><div class="copyright">
- <p>Developed by Johannes Ranke.</p>
+ <p></p>
+<p>Developed by Johannes Ranke.</p>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+ <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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@@ -138,5 +235,7 @@
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