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diff --git a/docs/index.html b/docs/index.html index a724173..4019484 100644 --- a/docs/index.html +++ b/docs/index.html @@ -25,6 +25,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -37,19 +39,13 @@ </button> <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> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> <a href="articles/chemCal.html">Get started</a> </li> <li> @@ -61,7 +57,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <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"><-</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">#> $x</span> +<span class="co">#> [1] 5.407085</span> +<span class="co">#> </span> +<span class="co">#> $y</span> +<span class="co">#> [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">#> $x</span> +<span class="co">#> [1] 2.720388</span> +<span class="co">#> </span> +<span class="co">#> $y</span> +<span class="co">#> [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">#> $x</span> +<span class="co">#> [1] 9.627349</span> +<span class="co">#> </span> +<span class="co">#> $y</span> +<span class="co">#> [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">#> $Prediction</span> +<span class="co">#> [1] 43.93983</span> +<span class="co">#> </span> +<span class="co">#> $`Standard Error`</span> +<span class="co">#> [1] 1.576985</span> +<span class="co">#> </span> +<span class="co">#> $Confidence</span> +<span class="co">#> [1] 3.230307</span> +<span class="co">#> </span> +<span class="co">#> $`Confidence Limits`</span> +<span class="co">#> [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">#> $Prediction</span> +<span class="co">#> [1] 43.93983</span> +<span class="co">#> </span> +<span class="co">#> $`Standard Error`</span> +<span class="co">#> [1] 0.796884</span> +<span class="co">#> </span> +<span class="co">#> $Confidence</span> +<span class="co">#> [1] 1.632343</span> +<span class="co">#> </span> +<span class="co">#> $`Confidence Limits`</span> +<span class="co">#> [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 (>= 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> </div> + +<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> </div> + + </div> </div> <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <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> </div> </footer> @@ -138,5 +235,7 @@ + + </body> </html> |