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16 files changed, 583 insertions, 277 deletions
diff --git a/docs/authors.html b/docs/authors.html index f4d3c9f..0f55a98 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -18,19 +18,25 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> <script src="jquery.sticky-kit.min.js"></script> <script src="pkgdown.js"></script> - + + +<meta property="og:title" content="Authors" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -74,7 +80,7 @@ <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a> </p> </li> </ul> @@ -90,7 +96,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/index.html b/docs/index.html index b4cc3cf..e33d1ad 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,17 @@ <title>Calibration Functions for Analytical Chemistry • 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]> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Calibration Functions for Analytical Chemistry"> +<meta property="og:description" content="Simple functions for plotting linear + calibration functions and estimating standard errors for measurements + according to the Handbook of Chemometrics and Qualimetrics: Part A + by Massart et al. There are also functions estimating the limit + of detection (LOD) and limit of quantification (LOQ). + The functions work on model objects from - optionally weighted - linear + regression (lm) or robust linear regression ('rlm' from the 'MASS' package)."> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/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]--> @@ -48,7 +57,7 @@ <div class="contents col-md-9"> <div id="chemcal" class="section level1"> <div class="page-header"><h1 class="hasAnchor"> -<a href="#chemcal" class="anchor"> </a>chemCal</h1></div> +<a href="#chemcal" class="anchor"></a>chemCal</h1></div> <p>Static documentation of this R package can be found unter <a href="https://pkgdown.jrwb.de/chemCal" class="uri">https://pkgdown.jrwb.de/chemCal</a></p> </div> @@ -64,14 +73,12 @@ <p>GPL (>= 2)</p> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </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"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li> </ul> -<html><body> <h2>Dev status</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> </ul> -</body></html> </div> </div> @@ -81,7 +88,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index fd7b0ba..181fe63 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -34,13 +34,14 @@ img.icon { float: right; } -/* Section anchors ---------------------------------*/ - -.hasAnchor { - margin-left: -30px; +img { + max-width: 100%; } +/* Section anchors ---------------------------------*/ + a.anchor { + margin-left: -30px; display:inline-block; width: 30px; height: 30px; @@ -56,6 +57,13 @@ a.anchor { visibility: visible; } +@media (max-width: 767px) { + .hasAnchor:hover a.anchor { + visibility: hidden; + } +} + + /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -63,6 +71,17 @@ a.anchor { margin-top: -60px; } +/* Static header placement on mobile devices */ +@media (max-width: 767px) { + .navbar-fixed-top { + position: absolute; + } + .navbar { + padding: 0; + } +} + + /* Sidebar --------------------------*/ #sidebar { @@ -81,33 +100,95 @@ a.anchor { margin-bottom: 0.5em; } +.orcid { + height: 16px; + vertical-align: middle; +} + +/* Reference index & topics ----------------------------------------------- */ + +.ref-index th {font-weight: normal;} +.ref-index h2 {font-size: 20px;} + +.ref-index td {vertical-align: top;} +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-arguments th {text-align: right; padding-right: 10px;} +.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments .name {width: 20%;} +.ref-arguments .desc {width: 80%;} + +/* Nice scrolling for wide elements --------------------------------------- */ + +table { + display: block; + overflow: auto; +} + /* Syntax highlighting ---------------------------------------------------- */ -code { - background-color: #f7f7f7; - color: #333; +pre { + word-wrap: normal; + word-break: normal; + border: 1px solid #eee; } -code a { - color: #375f84; + +pre, code { + background-color: #f8f8f8; + color: #333; } -.warning { color: red; } -.message { font-weight: bolder; } -.error { color: red; font-weight: bolder; } +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} -.fl,.number {color:rgb(21,20,181);} -.fu,.functioncall {color:#264D66 ;} -.ch,.st,.string {color:#375D81 ;} -.kw,.keyword {color:black;} -.argument {color:#264D66 ;} -.co,.comment {color: #777;} -.formalargs {color: #264D66;} -.eqformalargs {color:#264D66;} -.slot {font-style:italic;} -.symbol {color:black ;} -.prompt {color:black ;} +pre .img { + margin: 5px 0; +} -pre img { +pre .img img { background-color: #fff; display: block; + height: auto; +} + +code a, pre a { + color: #375f84; +} + +a.sourceLine:hover { + text-decoration: none; +} + +.fl {color: #1514b5;} +.fu {color: #000000;} /* function */ +.ch,.st {color: #036a07;} /* string */ +.kw {color: #264D66;} /* keyword */ +.co {color: #888888;} /* comment */ + +.message { color: black; font-weight: bolder;} +.error { color: orange; font-weight: bolder;} +.warning { color: #6A0366; font-weight: bolder;} + +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; } diff --git a/docs/pkgdown.js b/docs/pkgdown.js index c8b38c4..64b20df 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,8 +1,94 @@ $(function() { - $("#sidebar").stick_in_parent({offset_top: 40}); + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + $('body').scrollspy({ target: '#sidebar', offset: 60 }); + var cur_path = paths(location.pathname); + $("#navbar ul li a").each(function(index, value) { + if (value.text == "Home") + return; + if (value.getAttribute("href") === "#") + return; + + var path = paths(value.pathname); + if (is_prefix(cur_path, path)) { + // Add class to parent <li>, and enclosing <li> if in dropdown + var menu_anchor = $(value); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); }); + +function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); +} + +function is_prefix(needle, haystack) { + if (needle.length > haystack.lengh) + return(false); + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(false); + } + + return(true); +} + +/* Clipboard --------------------------*/ + +function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); +} + +if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>"; + + $(".examples").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); +} + diff --git a/docs/reference/calplot.lm-1.png b/docs/reference/calplot.lm-1.png Binary files differnew file mode 100644 index 0000000..c90b25f --- /dev/null +++ b/docs/reference/calplot.lm-1.png diff --git a/docs/reference/calplot.lm.html b/docs/reference/calplot.lm.html index 5a33491..910e4ea 100644 --- a/docs/reference/calplot.lm.html +++ b/docs/reference/calplot.lm.html @@ -18,19 +18,29 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Plot calibration graphs from univariate linear models — calplot" /> +<meta property="og:description" content="Produce graphics of calibration data, the fitted model as well + as confidence, and, for unweighted regression, prediction bands." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -77,45 +87,46 @@ as confidence, and, for unweighted regression, prediction bands.</p> - <pre><span class='fu'>calplot</span>(<span class='no'>object</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"auto"</span>), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"auto"</span>), + <pre class="usage"><span class='fu'>calplot</span>(<span class='no'>object</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"auto"</span>), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"auto"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Concentration"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Response"</span>, <span class='kw'>alpha</span><span class='kw'>=</span><span class='fl'>0.05</span>, <span class='kw'>varfunc</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>object</dt> - <dd> - A univariate model object of class <code>lm</code> or + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>A univariate model object of class <code>lm</code> or <code><a href='http://www.rdocumentation.org/packages/MASS/topics/rlm'>rlm</a></code> - with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>. - </dd> - <dt>xlim</dt> - <dd> - The limits of the plot on the x axis. - </dd> - <dt>ylim</dt> - <dd> - The limits of the plot on the y axis. - </dd> - <dt>xlab</dt> - <dd> - The label of the x axis. - </dd> - <dt>ylab</dt> - <dd> - The label of the y axis. - </dd> - <dt>alpha</dt> - <dd> - The error tolerance level for the confidence and prediction bands. Note that this + with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>The limits of the plot on the x axis.</p></td> + </tr> + <tr> + <th>ylim</th> + <td><p>The limits of the plot on the y axis.</p></td> + </tr> + <tr> + <th>xlab</th> + <td><p>The label of the x axis.</p></td> + </tr> + <tr> + <th>ylab</th> + <td><p>The label of the y axis.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The error tolerance level for the confidence and prediction bands. Note that this includes both tails of the Gaussian distribution, unlike the alpha and beta parameters - used in <code><a href='lod.html'>lod</a></code> (see note below). - </dd> - <dt>varfunc</dt> - <dd> - The variance function for generating the weights in the model. - Currently, this argument is ignored (see note below). - </dd> - </dl> + used in <code>lod</code> (see note below).</p></td> + </tr> + <tr> + <th>varfunc</th> + <td><p>The variance function for generating the weights in the model. + Currently, this argument is ignored (see note below).</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -129,16 +140,16 @@ for the data, for which responses should be predicted. Prediction intervals using weights e.g. from a variance function are currently not supported by the internally used function <code>predict.lm</code>, therefore, - <code>calplot</code> does not draw prediction bands for such models.</p> - <p>It is possible to compare the <code>calplot</code> prediction bands with the - <code><a href='lod.html'>lod</a></code> values if the <code>lod()</code> alpha and beta parameters are + <code>calplot</code> does not draw prediction bands for such models.</p> +<p>It is possible to compare the <code>calplot</code> prediction bands with the + <code>lod</code> values if the <code>lod()</code> alpha and beta parameters are half the value of the <code>calplot()</code> alpha parameter.</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='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'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex3</span>) -<span class='fu'>calplot</span>(<span class='no'>m</span>)</div><img src='calplot-2.png' alt='' width='540' height='400' /></pre> +<span class='fu'>calplot</span>(<span class='no'>m</span>)</div><div class='img'><img src='calplot.lm-1.png' alt='' width='700' height='432.632880098887' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -156,7 +167,7 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> + <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> @@ -167,7 +178,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/chemCal-package.html b/docs/reference/chemCal-package.html index b720fc9..ee92d84 100644 --- a/docs/reference/chemCal-package.html +++ b/docs/reference/chemCal-package.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — chemCal-package • chemCal</title> +<title>Calibration functions for analytical chemistry — chemCal-package • chemCal</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -19,19 +18,28 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Calibration functions for analytical chemistry — chemCal-package" /> +<meta property="og:description" content="See ../DESCRIPTION" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -70,18 +78,17 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Calibration functions for analytical chemistry</h1> </div> - <p>See <a href = '../DESCRIPTION'>../DESCRIPTION</a></p> + <p>See <a href='../DESCRIPTION'>../DESCRIPTION</a></p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>There is a package vignette located in <a href = '../doc/chemCal.pdf'>../doc/chemCal.pdf</a>.</p> + <p>There is a package vignette located in <a href='../doc/chemCal.pdf'>../doc/chemCal.pdf</a>.</p> </div> @@ -105,7 +112,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/din32645-1.png b/docs/reference/din32645-1.png Binary files differnew file mode 100644 index 0000000..d04e5fe --- /dev/null +++ b/docs/reference/din32645-1.png diff --git a/docs/reference/din32645.html b/docs/reference/din32645.html index 65a9268..5e2bf2d 100644 --- a/docs/reference/din32645.html +++ b/docs/reference/din32645.html @@ -18,19 +18,28 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Calibration data from DIN 32645 — din32645" /> +<meta property="og:description" content="Sample dataset to test the package." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -76,7 +85,7 @@ <p>Sample dataset to test the package.</p> - <pre><span class='fu'>data</span>(<span class='no'>din32645</span>)</pre> + <pre class="usage"><span class='fu'>data</span>(<span class='no'>din32645</span>)</pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -85,10 +94,10 @@ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>DIN 32645 (equivalent to ISO 11843), Beuth Verlag, Berlin, 1994</p> - <p>Dintest. Plugin for MS Excel for evaluations of calibration data. Written +<p>Dintest. Plugin for MS Excel for evaluations of calibration data. Written by Georg Schmitt, University of Heidelberg. Formerly available from the Website of the University of Heidelberg.</p> - <p>Currie, L. A. (1997) Nomenclature in evaluation of analytical methods including +<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> @@ -96,9 +105,9 @@ <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'>din32645</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'>data</span> <span class='kw'>=</span> <span class='no'>din32645</span>) -<span class='fu'><a href='calplot.html'>calplot</a></span>(<span class='no'>m</span>)</div><img src='din32645-2.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>calplot</span>(<span class='no'>m</span>)</div><div class='img'><img src='din32645-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'> <span class='co'>## Prediction of x with confidence interval</span> -(<span class='no'>prediction</span> <span class='kw'><-</span> <span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m</span>, <span class='fl'>3500</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#> $Prediction +(<span class='no'>prediction</span> <span class='kw'><-</span> <span class='fu'>inverse.predict</span>(<span class='no'>m</span>, <span class='fl'>3500</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#> $Prediction #> [1] 0.1054792 #> #> $`Standard Error` @@ -114,7 +123,7 @@ <span class='co'># was collected from Procontrol 3.1 (isomehr GmbH) in this case</span> <span class='fu'>round</span>(<span class='no'>prediction</span>$<span class='no'>Confidence</span>,<span class='fl'>5</span>)</div><div class='output co'>#> [1] 0.07434</div><div class='input'> <span class='co'>## Critical value:</span> -(<span class='no'>crit</span> <span class='kw'><-</span> <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>))</div><div class='output co'>#> $x +(<span class='no'>crit</span> <span class='kw'><-</span> <span class='fu'>lod</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>))</div><div class='output co'>#> $x #> [1] 0.0698127 #> #> $y @@ -129,12 +138,12 @@ <span class='co'># In German, the smallest detectable value is the "Erfassungsgrenze", and we</span> <span class='co'># should get 0.14 according to DIN, which we achieve by using the method </span> <span class='co'># described in it:</span> -<span class='no'>lod.din</span> <span class='kw'><-</span> <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"din"</span>) +<span class='no'>lod.din</span> <span class='kw'><-</span> <span class='fu'>lod</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"din"</span>) <span class='fu'>round</span>(<span class='no'>lod.din</span>$<span class='no'>x</span>, <span class='fl'>2</span>)</div><div class='output co'>#> [1] 0.14</div><div class='input'> <span class='co'>## Limit of quantification</span> <span class='co'># This accords to the test data coming with the test data from Dintest again, </span> <span class='co'># except for the last digits of the value cited for Procontrol 3.1 (0.2121)</span> -(<span class='no'>loq</span> <span class='kw'><-</span> <span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#> $x +(<span class='no'>loq</span> <span class='kw'><-</span> <span class='fu'>loq</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#> $x #> [1] 0.2119575 #> #> $y @@ -143,7 +152,7 @@ #> </div><div class='input'><span class='fu'>round</span>(<span class='no'>loq</span>$<span class='no'>x</span>,<span class='fl'>4</span>)</div><div class='output co'>#> [1] 0.212</div><div class='input'> <span class='co'># A similar value is obtained using the approximation </span> <span class='co'># LQ = 3.04 * LC (Currie 1999, p. 120)</span> -<span class='fl'>3.04</span> * <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>,<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)$<span class='no'>x</span></div><div class='output co'>#> [1] 0.2122306</div></pre> +<span class='fl'>3.04</span> * <span class='fu'>lod</span>(<span class='no'>m</span>,<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)$<span class='no'>x</span></div><div class='output co'>#> [1] 0.2122306</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -165,7 +174,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/index.html b/docs/reference/index.html index c0f2661..9b514f2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,19 +18,25 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Function reference" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -69,56 +75,78 @@ <div class="row"> <div class="col-md-9"> <div class="page-header"> - <h1>Function reference</h1> - <h4>version 0.1-37.9001</h4> + <h1> + Reference + <small>version 0.1-37.9001</small> + </h1> </div> <div class="contents"> - <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> - <p class="section-desc"></p> - - - <p><a href="calplot.lm.html">Plot calibration graphs from univariate linear models</a></p> - <ul> - <li><code><a href="calplot.lm.html">calplot</a></code></li><li><code><a href="calplot.lm.html">calplot.default</a></code></li><li><code><a href="calplot.lm.html">calplot.lm</a></code></li> - </ul> - - <p><a href="chemCal-package.html"> -</a></p> - <ul> - <li><code><a href="chemCal-package.html">chemCal-package</a></code></li> - </ul> - - <p><a href="din32645.html">Calibration data from DIN 32645</a></p> - <ul> - <li><code><a href="din32645.html">din32645</a></code></li> - </ul> - - <p><a href="inverse.predict.html">Predict x from y for a linear calibration</a></p> - <ul> - <li><code><a href="inverse.predict.html">inverse.predict</a></code></li><li><code><a href="inverse.predict.html">inverse.predict.lm</a></code></li><li><code><a href="inverse.predict.html">inverse.predict.rlm</a></code></li><li><code><a href="inverse.predict.html">inverse.predict.default</a></code></li> - </ul> - - <p><a href="lod.html">Estimate a limit of detection (LOD)</a></p> - <ul> - <li><code><a href="lod.html">lod</a></code></li><li><code><a href="lod.html">lod.lm</a></code></li><li><code><a href="lod.html">lod.rlm</a></code></li><li><code><a href="lod.html">lod.default</a></code></li> - </ul> - - <p><a href="loq.html">Estimate a limit of quantification (LOQ)</a></p> - <ul> - <li><code><a href="loq.html">loq</a></code></li><li><code><a href="loq.html">loq.lm</a></code></li><li><code><a href="loq.html">loq.rlm</a></code></li><li><code><a href="loq.html">loq.default</a></code></li> - </ul> - - <p><a href="massart97ex1.html">Calibration data from Massart et al. (1997), example 1</a></p> - <ul> - <li><code><a href="massart97ex1.html">massart97ex1</a></code></li> - </ul> - - <p><a href="massart97ex3.html">Calibration data from Massart et al. (1997), example 3</a></p> - <ul> - <li><code><a href="massart97ex3.html">massart97ex3</a></code></li> - </ul> - + <table class="ref-index"> + + <colgroup> + <col class="alias" /> + <col class="title" /> + </colgroup> + + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + <!-- --> + <td> + <p><code><a href="calplot.lm.html">calplot</a></code> </p> + </td> + <td><p>Plot calibration graphs from univariate linear models</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="chemCal-package.html">chemCal-package</a></code> </p> + </td> + <td><p>Calibration functions for analytical chemistry</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="din32645.html">data</a></code> </p> + </td> + <td><p>Calibration data from DIN 32645</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="inverse.predict.html">inverse.predict</a></code> </p> + </td> + <td><p>Predict x from y for a linear calibration</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="lod.html">lod</a></code> </p> + </td> + <td><p>Estimate a limit of detection (LOD)</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="loq.html">loq</a></code> </p> + </td> + <td><p>Estimate a limit of quantification (LOQ)</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="massart97ex1.html">data</a></code> </p> + </td> + <td><p>Calibration data from Massart et al. (1997), example 1</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="massart97ex3.html">data</a></code> </p> + </td> + <td><p>Calibration data from Massart et al. (1997), example 3</p></td> + </tr> + </tbody> + </table> </div> </div> @@ -136,7 +164,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/inverse.predict.html b/docs/reference/inverse.predict.html index af05986..32f8f44 100644 --- a/docs/reference/inverse.predict.html +++ b/docs/reference/inverse.predict.html @@ -18,19 +18,37 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Predict x from y for a linear calibration — inverse.predict" /> +<meta property="og:description" content="This function predicts x values using a univariate linear model that has been + generated for the purpose of calibrating a measurement method. Prediction + intervals are given at the specified confidence level. + The calculation method was taken from Massart et al. (1997). In particular, + Equations 8.26 and 8.28 were combined in order to yield a general treatment + of inverse prediction for univariate linear models, taking into account + weights that have been used to create the linear model, and at the same + time providing the possibility to specify a precision in sample measurements + differing from the precision in standard samples used for the calibration. + This is elaborated in the package vignette." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -85,43 +103,44 @@ This is elaborated in the package vignette.</p> - <pre>inverse.predict(object, newdata, …, + <pre class="usage">inverse.predict(object, newdata, …, ws, alpha=0.05, var.s = "auto")</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>object</dt> - <dd> - A univariate model object of class <code>lm</code> or + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>A univariate model object of class <code>lm</code> or <code><a href='http://www.rdocumentation.org/packages/MASS/topics/rlm'>rlm</a></code> - with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>. - </dd> - <dt>newdata</dt> - <dd> - A vector of observed y values for one sample. - </dd> - <dt>…</dt> - <dd> - Placeholder for further arguments that might be needed by - future implementations. - </dd> - <dt>ws</dt> - <dd> - The weight attributed to the sample. This argument is obligatory - if <code>object</code> has weights. - </dd> - <dt>alpha</dt> - <dd> - The error tolerance level for the confidence interval to be reported. - </dd> - <dt>var.s</dt> - <dd> - The estimated variance of the sample measurements. The default is to take + with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>.</p></td> + </tr> + <tr> + <th>newdata</th> + <td><p>A vector of observed y values for one sample.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>Placeholder for further arguments that might be needed by + future implementations.</p></td> + </tr> + <tr> + <th>ws</th> + <td><p>The weight attributed to the sample. This argument is obligatory + if <code>object</code> has weights.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The error tolerance level for the confidence interval to be reported.</p></td> + </tr> + <tr> + <th>var.s</th> + <td><p>The estimated variance of the sample measurements. The default is to take the residual standard error from the calibration and to adjust it using <code>ws</code>, if applicable. This means that <code>var.s</code> - overrides <code>ws</code>. - </dd> - </dl> + overrides <code>ws</code>.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -201,7 +220,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/lod.html b/docs/reference/lod.html index b9c30e6..13ce70a 100644 --- a/docs/reference/lod.html +++ b/docs/reference/lod.html @@ -18,19 +18,35 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <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)." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -83,45 +99,46 @@ one-sided significance test).</p> - <pre>lod(object, …, alpha = 0.05, beta = 0.05, method = "default", tol = "default")</pre> + <pre class="usage">lod(object, …, alpha = 0.05, beta = 0.05, method = "default", tol = "default")</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>object</dt> - <dd> - A univariate model object of class <code>lm</code> or + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>A univariate model object of class <code>lm</code> or <code><a href='http://www.rdocumentation.org/packages/MASS/topics/rlm'>rlm</a></code> with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>, - optionally from a weighted regression. - </dd> - <dt>…</dt> - <dd> - Placeholder for further arguments that might be needed by - future implementations. - </dd> - <dt>alpha</dt> - <dd> - The error tolerance for the decision limit (critical value). - </dd> - <dt>beta</dt> - <dd> - The error tolerance beta for the detection limit. - </dd> - <dt>method</dt> - <dd> - The “default” method uses a prediction interval at the LOD + optionally from a weighted regression.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>Placeholder for further arguments that might be needed by + future implementations.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The error tolerance for the decision limit (critical value).</p></td> + </tr> + <tr> + <th>beta</th> + <td><p>The error tolerance beta for the detection limit.</p></td> + </tr> + <tr> + <th>method</th> + <td><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. - </dd> - <dt>tol</dt> - <dd> - When the “default” method is used, the default tolerance + x = 0 as an approximation.</p></td> + </tr> + <tr> + <th>tol</th> + <td><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. - </dd> - </dl> + divided by 1000. Can be set to a numeric value to override this.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -143,16 +160,16 @@ <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 +<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 +<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> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Examples for <code><a href='din32645.html'>din32645</a></code></p> + <p>Examples for <code>din32645</code></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -200,7 +217,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/loq.html b/docs/reference/loq.html index ad7fa86..2fb01a8 100644 --- a/docs/reference/loq.html +++ b/docs/reference/loq.html @@ -18,19 +18,34 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Estimate a limit of quantification (LOQ) — loq" /> +<meta property="og:description" content="The limit of quantification is the x value, where the relative error + of the quantification given the calibration model reaches a prespecified + value 1/k. Thus, it is the solution of the equation + $$L = k c(L)$$ + where c(L) is half of the length of the confidence interval at the limit L + (DIN 32645, equivalent to ISO 11843). c(L) is internally estimated by + inverse.predict, and L is obtained by iteration." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -79,62 +94,63 @@ $$L = k c(L)$$ where c(L) is half of the length of the confidence interval at the limit L (DIN 32645, equivalent to ISO 11843). c(L) is internally estimated by - <code><a href='inverse.predict.html'>inverse.predict</a></code>, and L is obtained by iteration.</p> + <code>inverse.predict</code>, and L is obtained by iteration.</p> - <pre>loq(object, …, alpha = 0.05, k = 3, n = 1, w.loq = "auto", + <pre class="usage">loq(object, …, alpha = 0.05, k = 3, n = 1, w.loq = "auto", var.loq = "auto", tol = "default")</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>object</dt> - <dd> - A univariate model object of class <code>lm</code> or + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>A univariate model object of class <code>lm</code> or <code><a href='http://www.rdocumentation.org/packages/MASS/topics/rlm'>rlm</a></code> with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>, optionally from a weighted regression. If weights are specified in the model, either <code>w.loq</code> or <code>var.loq</code> have to - be specified. - </dd> - <dt>alpha</dt> - <dd> - The error tolerance for the prediction of x values in the calculation. - </dd> - <dt>…</dt> - <dd> - Placeholder for further arguments that might be needed by - future implementations. - </dd> - <dt>k</dt> - <dd> - The inverse of the maximum relative error tolerated at the - desired LOQ. - </dd> - <dt>n</dt> - <dd> - The number of replicate measurements for which the LOQ should be - specified. - </dd> - <dt>w.loq</dt> - <dd> - The weight that should be attributed to the LOQ. Defaults + be specified.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The error tolerance for the prediction of x values in the calculation.</p></td> + </tr> + <tr> + <th>…</th> + <td><p>Placeholder for further arguments that might be needed by + future implementations.</p></td> + </tr> + <tr> + <th>k</th> + <td><p>The inverse of the maximum relative error tolerated at the + desired LOQ.</p></td> + </tr> + <tr> + <th>n</th> + <td><p>The number of replicate measurements for which the LOQ should be + specified.</p></td> + </tr> + <tr> + <th>w.loq</th> + <td><p>The weight that should be attributed to the LOQ. Defaults to one for unweighted regression, and to the mean of the weights - for weighted regression. See <code><a href='massart97ex3.html'>massart97ex3</a></code> for + for weighted regression. See <code>massart97ex3</code> for an example how to take advantage of knowledge about the - variance function. - </dd> - <dt>var.loq</dt> - <dd> - The approximate variance at the LOQ. The default value is - calculated from the model. - </dd> - <dt>tol</dt> - <dd> - The default tolerance for the LOQ on the x scale is the value of the + variance function.</p></td> + </tr> + <tr> + <th>var.loq</th> + <td><p>The approximate variance at the LOQ. The default value is + calculated from the model.</p></td> + </tr> + <tr> + <th>tol</th> + <td><p>The default tolerance for the LOQ 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. - </dd> - </dl> + numeric value to override this.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -149,7 +165,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Examples for <code><a href='din32645.html'>din32645</a></code></p> + <p>Examples for <code>din32645</code></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -195,7 +211,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/massart97ex1.html b/docs/reference/massart97ex1.html index e84c01b..637d524 100644 --- a/docs/reference/massart97ex1.html +++ b/docs/reference/massart97ex1.html @@ -18,19 +18,28 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Calibration data from Massart et al. (1997), example 1 — massart97ex1" /> +<meta property="og:description" content="Sample dataset from p. 175 to test the package." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -76,7 +85,7 @@ <p>Sample dataset from p. 175 to test the package.</p> - <pre><span class='fu'>data</span>(<span class='no'>massart97ex1</span>)</pre> + <pre class="usage"><span class='fu'>data</span>(<span class='no'>massart97ex1</span>)</pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -108,7 +117,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/massart97ex3-1.png b/docs/reference/massart97ex3-1.png Binary files differnew file mode 100644 index 0000000..88668fa --- /dev/null +++ b/docs/reference/massart97ex3-1.png diff --git a/docs/reference/massart97ex3.html b/docs/reference/massart97ex3.html index 2946139..d737fc5 100644 --- a/docs/reference/massart97ex3.html +++ b/docs/reference/massart97ex3.html @@ -18,19 +18,28 @@ <!-- 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"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Calibration data from Massart et al. (1997), example 3 — massart97ex3" /> +<meta property="og:description" content="Sample dataset from p. 188 to test the package." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -76,7 +85,7 @@ <p>Sample dataset from p. 188 to test the package.</p> - <pre><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)</pre> + <pre class="usage"><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)</pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -100,9 +109,9 @@ <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='fu'>calplot</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><div class='img'><img src='massart97ex3-1.png' alt='' width='700' height='432.632880098887' /></div><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 +<span class='fu'>inverse.predict</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` @@ -113,7 +122,7 @@ #> #> $`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 +#> </div><div class='input'><span class='fu'>inverse.predict</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` @@ -128,7 +137,7 @@ <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 +<span class='fu'>lod</span>(<span class='no'>m0</span>)</div><div class='output co'>#> $x #> [1] 5.407085 #> #> $y @@ -136,7 +145,7 @@ #> 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 +<span class='fu'>loq</span>(<span class='no'>m0</span>)</div><div class='output co'>#> $x #> [1] 13.97764 #> #> $y @@ -148,15 +157,16 @@ <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 +<span class='fu'>loq</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='input'># The weight for the loq should therefore be derived at x = 7.3 instead +# of 15, but the graphical procedure of Massart (p. 201) to derive the +# variances on which the weights are based is quite inaccurate anyway. +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -178,7 +188,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a 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