mirror of https://github.com/msberends/AMR.git
343 lines
15 KiB
HTML
343 lines
15 KiB
HTML
<!-- Generated by pkgdown: do not edit by hand -->
|
|
<!DOCTYPE html>
|
|
<html lang="en">
|
|
<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>Age in Years of Individuals — age • AMR (for R)</title>
|
|
|
|
<!-- favicons -->
|
|
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
|
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
|
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
|
|
|
<!-- jquery -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
|
<!-- Bootstrap -->
|
|
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
|
|
|
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
|
|
|
<!-- bootstrap-toc -->
|
|
<link rel="stylesheet" href="../bootstrap-toc.css">
|
|
<script src="../bootstrap-toc.js"></script>
|
|
|
|
<!-- Font Awesome icons -->
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
|
|
|
<!-- clipboard.js -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
|
|
|
<!-- headroom.js -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
|
|
|
<!-- pkgdown -->
|
|
<link href="../pkgdown.css" rel="stylesheet">
|
|
<script src="../pkgdown.js"></script>
|
|
|
|
|
|
|
|
<link href="../extra.css" rel="stylesheet">
|
|
<script src="../extra.js"></script>
|
|
|
|
<meta property="og:title" content="Age in Years of Individuals — age" />
|
|
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
|
|
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<!-- mathjax -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
|
|
|
<!--[if lt IE 9]>
|
|
<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 data-spy="scroll" data-target="#toc">
|
|
|
|
|
|
<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" aria-expanded="false">
|
|
<span class="sr-only">Toggle navigation</span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
</button>
|
|
<span class="navbar-brand">
|
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
|
|
</span>
|
|
</div>
|
|
|
|
<div id="navbar" class="navbar-collapse collapse">
|
|
<ul class="nav navbar-nav">
|
|
<li>
|
|
<a href="../index.html">
|
|
<span class="fa fa-home"></span>
|
|
|
|
Home
|
|
</a>
|
|
</li>
|
|
<li class="dropdown">
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|
<span class="fa fa-question-circle"></span>
|
|
|
|
How to
|
|
|
|
<span class="caret"></span>
|
|
</a>
|
|
<ul class="dropdown-menu" role="menu">
|
|
<li>
|
|
<a href="../articles/AMR.html">
|
|
<span class="fa fa-directions"></span>
|
|
|
|
Conduct AMR analysis
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/resistance_predict.html">
|
|
<span class="fa fa-dice"></span>
|
|
|
|
Predict antimicrobial resistance
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/datasets.html">
|
|
<span class="fa fa-database"></span>
|
|
|
|
Data sets for download / own use
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/PCA.html">
|
|
<span class="fa fa-compress"></span>
|
|
|
|
Conduct principal component analysis for AMR
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/MDR.html">
|
|
<span class="fa fa-skull-crossbones"></span>
|
|
|
|
Determine multi-drug resistance (MDR)
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/WHONET.html">
|
|
<span class="fa fa-globe-americas"></span>
|
|
|
|
Work with WHONET data
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/SPSS.html">
|
|
<span class="fa fa-file-upload"></span>
|
|
|
|
Import data from SPSS/SAS/Stata
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/EUCAST.html">
|
|
<span class="fa fa-exchange-alt"></span>
|
|
|
|
Apply EUCAST rules
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/mo_property.html">
|
|
<span class="fa fa-bug"></span>
|
|
|
|
Get properties of a microorganism
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/ab_property.html">
|
|
<span class="fa fa-capsules"></span>
|
|
|
|
Get properties of an antibiotic
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/benchmarks.html">
|
|
<span class="fa fa-shipping-fast"></span>
|
|
|
|
Other: benchmarks
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/index.html">
|
|
<span class="fa fa-book-open"></span>
|
|
|
|
Manual
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../authors.html">
|
|
<span class="fa fa-users"></span>
|
|
|
|
Authors
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../news/index.html">
|
|
<span class="far fa-newspaper"></span>
|
|
|
|
Changelog
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
<ul class="nav navbar-nav navbar-right">
|
|
<li>
|
|
<a href="https://github.com/msberends/AMR">
|
|
<span class="fab fa-github"></span>
|
|
|
|
Source Code
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../survey.html">
|
|
<span class="fa fa-clipboard-list"></span>
|
|
|
|
Survey
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
|
|
</div><!--/.nav-collapse -->
|
|
</div><!--/.container -->
|
|
</div><!--/.navbar -->
|
|
|
|
|
|
|
|
</header>
|
|
|
|
<div class="row">
|
|
<div class="col-md-9 contents">
|
|
<div class="page-header">
|
|
<h1>Age in Years of Individuals</h1>
|
|
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/age.R'><code>R/age.R</code></a></small>
|
|
<div class="hidden name"><code>age.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
|
|
</div>
|
|
|
|
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
|
|
|
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
|
<table class="ref-arguments">
|
|
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
|
<tr>
|
|
<th>x</th>
|
|
<td><p>date(s), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>reference</th>
|
|
<td><p>reference date(s) (defaults to today), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>exact</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of <a href='https://en.wikipedia.org/wiki/Year-to-date'>year-to-date</a> (YTD) of <code>x</code> by the number of days in the year of <code>reference</code> (either 365 or 366).</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>na.rm</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether missing values should be removed</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>...</th>
|
|
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code>, such as <code>origin</code></p></td>
|
|
</tr>
|
|
</table>
|
|
|
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
|
|
|
<p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a> (no decimals) if <code>exact = FALSE</code>, a <a href='https://rdrr.io/r/base/double.html'>double</a> (with decimals) otherwise</p>
|
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
|
|
|
<p>Ages below 0 will be returned as <code>NA</code> with a warning. Ages above 120 will only give a warning.</p>
|
|
<p>This function vectorises over both <code>x</code> and <code>reference</code>, meaning that either can have a length of 1 while the other argument has a larger length.</p>
|
|
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
|
|
|
|
|
|
|
|
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
|
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
|
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
|
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
|
|
|
|
|
|
|
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
|
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
|
|
|
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>
|
|
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># 10 random birth dates</span>
|
|
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>birth_date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fl'>10</span><span class='op'>)</span> <span class='op'>*</span> <span class='fl'>25000</span><span class='op'>)</span>
|
|
<span class='co'># add ages</span>
|
|
<span class='va'>df</span><span class='op'>$</span><span class='va'>age</span> <span class='op'><-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span><span class='op'>)</span>
|
|
<span class='co'># add exact ages</span>
|
|
<span class='va'>df</span><span class='op'>$</span><span class='va'>age_exact</span> <span class='op'><-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span>, exact <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
|
|
|
<span class='va'>df</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
|
<nav id="toc" data-toggle="toc" class="sticky-top">
|
|
<h2 data-toc-skip>Contents</h2>
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
<footer>
|
|
<div class="copyright">
|
|
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
|
|
</div>
|
|
|
|
<div class="pkgdown">
|
|
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
|
|
</div>
|
|
|
|
</footer>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</body>
|
|
</html>
|
|
|
|
|