AMR/reference/age_groups.html

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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Split Ages into Age Groups</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_groups.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</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_groups</span><span class="op">(</span><span class="va">x</span>, split_at <span class="op">=</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">12</span>, <span class="fl">25</span>, <span class="fl">55</span>, <span class="fl">75</span><span class="op">)</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</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>age, e.g. calculated with <code><a href="age.html">age()</a></code></p></dd>


<dt>split_at</dt>
<dd><p>values to split <code>x</code> at - the default is age groups 0-11, 12-24, 25-54, 55-74 and 75+. See <em>Details</em>.</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>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>


<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></p>


    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>To split ages, the input for the <code>split_at</code> argument can be:</p><ul><li><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector. A value of e.g. <code>c(10, 20)</code> will split <code>x</code> on 0-9, 10-19 and 20+. A value of only <code>50</code> will split <code>x</code> on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
<li><p>A character:</p><ul><li><p><code>"children"</code> or <code>"kids"</code>, equivalent of: <code>c(0, 1, 2, 4, 6, 13, 18)</code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code>c(65, 75, 85)</code>. This will split on 0-64, 65-74, 75-84, 85+.</p></li>
<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, ..., 95-99, 100+.</p></li>
<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, ..., 90-99, 100+.</p></li>
</ul></li>
</ul></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 determine ages, based on one or more reference dates, use the <code><a href="age.html">age()</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="va">ages</span> <span class="op">&lt;-</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">3</span>, <span class="fl">8</span>, <span class="fl">16</span>, <span class="fl">54</span>, <span class="fl">31</span>, <span class="fl">76</span>, <span class="fl">101</span>, <span class="fl">43</span>, <span class="fl">21</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># split into 0-49 and 50+</span></span></span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, <span class="fl">50</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-49 0-49 0-49 50+  0-49 50+  50+  0-49 0-49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: 0-49 &lt; 50+</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># split into 0-19, 20-49 and 50+</span></span></span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</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">20</span>, <span class="fl">50</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-19  0-19  0-19  50+   20-49 50+   50+   20-49 20-49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: 0-19 &lt; 20-49 &lt; 50+</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># split into groups of ten years</span></span></span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span> <span class="op">*</span> <span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 Levels: 0-9 &lt; 10-19 &lt; 20-29 &lt; 30-39 &lt; 40-49 &lt; 50-59 &lt; 60-69 &lt; ... &lt; 100+</span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, split_at <span class="op">=</span> <span class="st">"tens"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 Levels: 0-9 &lt; 10-19 &lt; 20-29 &lt; 30-39 &lt; 40-49 &lt; 50-59 &lt; 60-69 &lt; ... &lt; 100+</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># split into groups of five years</span></span></span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">20</span> <span class="op">*</span> <span class="fl">5</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 Levels: 0-4 &lt; 5-9 &lt; 10-14 &lt; 15-19 &lt; 20-24 &lt; 25-29 &lt; 30-34 &lt; ... &lt; 100+</span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, split_at <span class="op">=</span> <span class="st">"fives"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 Levels: 0-4 &lt; 5-9 &lt; 10-14 &lt; 15-19 &lt; 20-24 &lt; 25-29 &lt; 30-34 &lt; ... &lt; 100+</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># split specifically for children</span></span></span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</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">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">6</span>, <span class="fl">13</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: 0 &lt; 1 &lt; 2-3 &lt; 4-5 &lt; 6-12 &lt; 13-17 &lt; 18+</span>
<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, <span class="st">"children"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: 0 &lt; 1 &lt; 2-3 &lt; 4-5 &lt; 6-12 &lt; 13-17 &lt; 18+</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># resistance of ciprofloxacin per age group</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>    <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>age_group <span class="op">=</span> <span class="fu">age_groups</span><span class="op">(</span><span class="va">age</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span>    <span class="fu"><a href="ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>      x <span class="op">=</span> <span class="st">"age_group"</span>,</span></span>
<span class="r-in"><span>      minimum <span class="op">=</span> <span class="fl">0</span>,</span></span>
<span class="r-in"><span>      x.title <span class="op">=</span> <span class="st">"Age Group"</span>,</span></span>
<span class="r-in"><span>      title <span class="op">=</span> <span class="st">"Ciprofloxacin resistance per age group"</span></span></span>
<span class="r-in"><span>    <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: ggplot2</span>
<span class="r-plt img"><img src="age_groups-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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