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<img src="../logo.svg" class="logo" alt=""><h1>Age in Years of Individuals</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/age.R" class="external-link"><code>R/age.R</code></a></small>
<div class="d-none name"><code>age.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Calculates age in years based on a reference date, which is the system date at default.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><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" class="external-link">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></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>date(s), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dt>reference</dt>
<dd><p>reference date(s) (default is today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dt>exact</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">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" class="external-link">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></dd>
<dt>na.rm</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed</p></dd>
<dt>...</dt>
<dd><p>arguments passed on to <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>, such as <code>origin</code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> (no decimals) if <code>exact = FALSE</code>, a <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> (with decimals) otherwise</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></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>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># 10 random pre-Y2K birth dates</span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>birth_date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2000-01-01"</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">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></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># add ages</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">$</span><span class="va">age</span> <span class="op">&lt;-</span> <span class="fu">age</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">birth_date</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># add exact ages</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">$</span><span class="va">age_exact</span> <span class="op">&lt;-</span> <span class="fu">age</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">birth_date</span>, exact <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># add age at millenium switch</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">$</span><span class="va">age_at_y2k</span> <span class="op">&lt;-</span> <span class="fu">age</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">birth_date</span>, <span class="st">"2000-01-01"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.24317 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.00546 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.33607 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.04918 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.03552 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.14481 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.51639 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.10109 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.71038 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.56284 13</span>
</code></pre></div>
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