mirror of https://github.com/msberends/AMR.git
235 lines
15 KiB
HTML
235 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>Split ages into age groups — age_groups • AMR</title>
|
|||
|
|
|
|||
|
|
<!-- jquery -->
|
|||
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
|||
|
|
<!-- Bootstrap -->
|
|||
|
|
|
|||
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
|
|||
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
|||
|
|
|
|||
|
|
<!-- Font Awesome icons -->
|
|||
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
|
|||
|
|
|
|||
|
|
<!-- clipboard.js -->
|
|||
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
|||
|
|
|
|||
|
|
<!-- sticky kit -->
|
|||
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
|
|||
|
|
|
|||
|
|
<!-- pkgdown -->
|
|||
|
|
<link href="../pkgdown.css" rel="stylesheet">
|
|||
|
|
<script src="../pkgdown.js"></script>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<meta property="og:title" content="Split ages into age groups — age_groups" />
|
|||
|
|
|
|||
|
|
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
|
|||
|
|
<meta name="twitter:card" content="summary" />
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<!-- 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>
|
|||
|
|
<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</a>
|
|||
|
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9007</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 fa-lg"></span>
|
|||
|
|
|
|||
|
|
</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="../articles/AMR.html">Get started</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="../reference/index.html">Reference</a>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|||
|
|
Articles
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="../articles/freq.html">Creating Frequency Tables</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="../news/index.html">Changelog</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
|
|||
|
|
<ul class="nav navbar-nav navbar-right">
|
|||
|
|
|
|||
|
|
</ul>
|
|||
|
|
|
|||
|
|
</div><!--/.nav-collapse -->
|
|||
|
|
</div><!--/.container -->
|
|||
|
|
</div><!--/.navbar -->
|
|||
|
|
|
|||
|
|
|
|||
|
|
</header>
|
|||
|
|
|
|||
|
|
<div class="row">
|
|||
|
|
<div class="col-md-9 contents">
|
|||
|
|
<div class="page-header">
|
|||
|
|
<h1>Split ages into age groups</h1>
|
|||
|
|
|
|||
|
|
<div class="hidden name"><code>age_groups.Rd</code></div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div class="ref-description">
|
|||
|
|
|
|||
|
|
<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<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>
|
|||
|
|
|
|||
|
|
<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>age, e.g. calculated with <code><a href='age.html'>age</a></code></p></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr>
|
|||
|
|
<th>split_at</th>
|
|||
|
|
<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>
|
|||
|
|
</tr>
|
|||
|
|
</table>
|
|||
|
|
|
|||
|
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
|||
|
|
|
|||
|
|
<p>Ordered <code><a href='https://www.rdocumentation.org/packages/base/topics/factor'>factor</a></code></p>
|
|||
|
|
|
|||
|
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
|||
|
|
|
|||
|
|
<p>To split ages, the input can be:</p><ul>
|
|||
|
|
<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+.
|
|||
|
|
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>
|
|||
|
|
<li><p>A character:</p><ul>
|
|||
|
|
<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>
|
|||
|
|
<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>
|
|||
|
|
<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>
|
|||
|
|
<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>
|
|||
|
|
</ul></li>
|
|||
|
|
</ul>
|
|||
|
|
|
|||
|
|
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
|||
|
|
|
|||
|
|
<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>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|||
|
|
<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>)
|
|||
|
|
|
|||
|
|
<span class='co'># split into 0-49 and 50+</span>
|
|||
|
|
<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
|
|||
|
|
#> Levels: 0-49 < 50+</div><div class='input'>
|
|||
|
|
<span class='co'># split into 0-19, 20-49 and 50+</span>
|
|||
|
|
<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
|
|||
|
|
#> Levels: 0-19 < 20-49 < 50+</div><div class='input'>
|
|||
|
|
<span class='co'># split into groups of ten years</span>
|
|||
|
|
<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
|
|||
|
|
#> 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
|
|||
|
|
#> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+</div><div class='input'>
|
|||
|
|
<span class='co'># split into groups of five years</span>
|
|||
|
|
<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
|
|||
|
|
#> 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
|
|||
|
|
#> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+</div><div class='input'>
|
|||
|
|
<span class='co'># split specifically for children</span>
|
|||
|
|
<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+
|
|||
|
|
#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+</div><div class='input'><span class='co'># same:</span>
|
|||
|
|
<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+
|
|||
|
|
#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-16 < 17+</div><div class='input'>
|
|||
|
|
<span class='co'># resistance of ciprofloxacine per age group</span>
|
|||
|
|
<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>
|
|||
|
|
#> <span class='message'>Attaching package: ‘dplyr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:testthat’:</span>
|
|||
|
|
#> <span class='message'></span>
|
|||
|
|
#> <span class='message'> matches</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:stats’:</span>
|
|||
|
|
#> <span class='message'></span>
|
|||
|
|
#> <span class='message'> filter, lag</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:base’:</span>
|
|||
|
|
#> <span class='message'></span>
|
|||
|
|
#> <span class='message'> intersect, setdiff, setequal, union</span></div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
|||
|
|
<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>
|
|||
|
|
<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>,
|
|||
|
|
<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>
|
|||
|
|
<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>
|
|||
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
|
|||
|
|
<span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
|||
|
|
<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>
|
|||
|
|
</div>
|
|||
|
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
|||
|
|
<h2>Contents</h2>
|
|||
|
|
<ul class="nav nav-pills nav-stacked">
|
|||
|
|
<li><a href="#arguments">Arguments</a></li>
|
|||
|
|
|
|||
|
|
<li><a href="#value">Value</a></li>
|
|||
|
|
|
|||
|
|
<li><a href="#details">Details</a></li>
|
|||
|
|
|
|||
|
|
<li><a href="#see-also">See also</a></li>
|
|||
|
|
|
|||
|
|
<li><a href="#examples">Examples</a></li>
|
|||
|
|
</ul>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<footer>
|
|||
|
|
<div class="copyright">
|
|||
|
|
<p>Developed by Matthijs S. Berends, Christian F. Luz.</p>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div class="pkgdown">
|
|||
|
|
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
|||
|
|
</div>
|
|||
|
|
</footer>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
</body>
|
|||
|
|
</html>
|
|||
|
|
|