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<h1>Split ages into age groups</h1>
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<div class="hidden name"><code>age_groups.Rd</code></div>
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<div class="ref-description">
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<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
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<pre class="usage"><span class='fu'>age_groups</span>(<span class='no'>x</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>))</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>age, e.g. calculated with <code><a href='age.html'>age</a></code></p></td>
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</tr>
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<tr>
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<th>split_at</th>
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<td><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 26-54, 55-74 and 75+. See Details.</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Ordered <code><a href='https://www.rdocumentation.org/packages/base/topics/factor'>factor</a></code></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>To split ages, the input can be:</p><ul>
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<li><p>A numeric vector. A vector of <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
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The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).</p></li>
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<li><p>A character:</p><ul>
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<li><p><code>"children"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
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<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(65, 75, 85, 95)</a></code>. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.</p></li>
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<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.</p></li>
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<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, 20-29 and so forth.</p></li>
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</ul></li>
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</ul>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='age.html'>age</a></code> to determine ages based on one or more reference dates</p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='no'>ages</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)
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<span class='co'># split into 0-49 and 50+</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)</div><div class='output co'>#> [1] 0-49 0-49 0-49 50+ 0-49 50+ 50+ 0-49 0-49
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#> Levels: 0-49 < 50+</div><div class='input'>
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<span class='co'># split into 0-19, 20-49 and 50+</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))</div><div class='output co'>#> [1] 0-19 0-19 0-19 50+ 20-49 50+ 50+ 20-49 20-49
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#> Levels: 0-19 < 20-49 < 50+</div><div class='input'>
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<span class='co'># split into groups of ten years</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)</div><div class='output co'>#> [1] 0-9 0-9 10-19 50-59 30-39 70-79 100+ 40-49 20-29
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#> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+</div><div class='input'><span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)</div><div class='output co'>#> [1] 0-9 0-9 10-19 50-59 30-39 70-79 100+ 40-49 20-29
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#> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+</div><div class='input'>
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<span class='co'># split into groups of five years</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)</div><div class='output co'>#> [1] 0-4 5-9 15-19 50-54 30-34 75-79 100+ 40-44 20-24
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#> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+</div><div class='input'><span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)</div><div class='output co'>#> [1] 0-4 5-9 15-19 50-54 30-34 75-79 100+ 40-44 20-24
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#> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+</div><div class='input'>
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<span class='co'># split specifically for children</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)</div><div class='output co'>#> [1] 2-3 6-12 13-17 18+ 18+ 18+ 18+ 18+ 18+
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#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+</div><div class='input'><span class='co'># same:</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>17</span>))</div><div class='output co'>#> [1] 2-3 6-12 13-16 17+ 17+ 17+ 17+ 17+ 17+
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#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-16 < 17+</div><div class='input'>
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<span class='co'># resistance of ciprofloxacine per age group</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)</div><div class='output co'>#> <span class='message'></span>
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#> <span class='message'>Attaching package: ‘dplyr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:testthat’:</span>
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#> <span class='message'></span>
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#> <span class='message'> matches</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:stats’:</span>
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#> <span class='message'></span>
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#> <span class='message'> filter, lag</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:base’:</span>
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#> <span class='message'></span>
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#> <span class='message'> intersect, setdiff, setequal, union</span></div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
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<span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>date</span><span style='color: #0000BB;'>` as input for `col_date`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>patient_id</span><span style='color: #0000BB;'>` as input for `col_patient_id`.</span><span></span></div><div class='output co'>#> <span class='message'>=> Found </span><span style='font-weight: bold;'>1,315 first isolates</span><span> (65.8% of total)</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 3 rows containing missing values (geom_bar).</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 3 rows containing missing values (geom_text).</span></div><div class='img'><img src='age_groups-1.png' alt='' width='700' height='433' /></div></span></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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