mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 15:26:11 +01:00
234 lines
16 KiB
HTML
234 lines
16 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>Data set with 2000 blood culture isolates of septic patients — septic_patients • 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="Data set with 2000 blood culture isolates of septic patients — septic_patients" />
|
|
|
|
<meta property="og:description" content="An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This data.frame can be used to practice AMR analysis. For examples, press F1." />
|
|
<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>Data set with 2000 blood culture isolates of septic patients</h1>
|
|
|
|
<div class="hidden name"><code>septic_patients.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
|
|
<p>An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This <code>data.frame</code> can be used to practice AMR analysis. For examples, press F1.</p>
|
|
|
|
</div>
|
|
|
|
<pre class="usage"><span class='no'>septic_patients</span></pre>
|
|
|
|
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
|
|
|
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,000 observations and 49 variables:</p><dl class='dl-horizontal'>
|
|
<dt><code>date</code></dt><dd><p>date of receipt at the laboratory</p></dd>
|
|
<dt><code>hospital_id</code></dt><dd><p>ID of the hospital, from A to D</p></dd>
|
|
<dt><code>ward_icu</code></dt><dd><p>logical to determine if ward is an intensive care unit</p></dd>
|
|
<dt><code>ward_clinical</code></dt><dd><p>logical to determine if ward is a regular clinical ward</p></dd>
|
|
<dt><code>ward_outpatient</code></dt><dd><p>logical to determine if ward is an outpatient clinic</p></dd>
|
|
<dt><code>age</code></dt><dd><p>age of the patient</p></dd>
|
|
<dt><code>gender</code></dt><dd><p>gender of the patient</p></dd>
|
|
<dt><code>patient_id</code></dt><dd><p>ID of the patient, first 10 characters of an SHA hash containing irretrievable information</p></dd>
|
|
<dt><code>mo</code></dt><dd><p>ID of microorganism created with <code><a href='as.mo.html'>as.mo</a></code>, see also <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
|
|
<dt><code>peni:rifa</code></dt><dd><p>40 different antibiotics with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>); these column names occur in <code><a href='antibiotics.html'>antibiotics</a></code> data set and can be translated with <code><a href='abname.html'>abname</a></code></p></dd>
|
|
</dl>
|
|
|
|
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<pre class="examples"><div class='input'><span class='co'># ----------- #</span>
|
|
<span class='co'># PREPARATION #</span>
|
|
<span class='co'># ----------- #</span>
|
|
|
|
<span class='co'># Save this example data set to an object, so we can edit it:</span>
|
|
<span class='no'>my_data</span> <span class='kw'><-</span> <span class='no'>septic_patients</span>
|
|
|
|
<span class='co'># load the dplyr package to make data science A LOT easier</span>
|
|
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
|
|
|
<span class='co'># Add first isolates to our data set:</span>
|
|
<span class='no'>my_data</span> <span class='kw'><-</span> <span class='no'>my_data</span> <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolates</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>my_data</span>, <span class='st'>"date"</span>, <span class='st'>"patient_id"</span>, <span class='st'>"mo"</span>))</div><div class='output co'>#> <span class='message'>=> Found <span style='font-weight: bold;'>1,315 first isolates</span><span> (65.8% of total)</span></div><div class='input'>
|
|
<span class='co'># -------- #</span>
|
|
<span class='co'># ANALYSIS #</span>
|
|
<span class='co'># -------- #</span>
|
|
|
|
<span class='co'># 1. Get the amoxicillin resistance percentages (p)</span>
|
|
<span class='co'># and numbers (n) of E. coli, divided by hospital:</span>
|
|
|
|
<span class='no'>my_data</span> <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>guess_mo</a></span>(<span class='st'>"E. coli"</span>),
|
|
<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amox</span>),
|
|
<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amox</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 19 results available (minimum set to 30).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 4 x 3</span><span>
|
|
#> hospital_id n p
|
|
#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
|
|
#> </span><span style='color: #BCBCBC;'>1</span><span> A 19 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>2</span><span> B 65 0.477
|
|
#> </span><span style='color: #BCBCBC;'>3</span><span> C 35 0.543
|
|
#> </span><span style='color: #BCBCBC;'>4</span><span> D 93 0.495</div><div class='input'>
|
|
|
|
<span class='co'># 2. Get the amoxicillin/clavulanic acid resistance</span>
|
|
<span class='co'># percentages of E. coli, trend over the years:</span>
|
|
|
|
<span class='no'>my_data</span> <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>guess_mo</a></span>(<span class='st'>"E. coli"</span>),
|
|
<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</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'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
|
|
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amcl</span>),
|
|
<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amcl</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>20</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 15 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 16 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 18 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 10 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 16 x 3</span><span>
|
|
#> year n p
|
|
#> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 1</span><span> 2002 13 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 2</span><span> 2003 14 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 3</span><span> 2004 13 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 4</span><span> 2005 15 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 5</span><span> 2006 16 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 6</span><span> 2007 17 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 7</span><span> 2008 17 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 8</span><span> 2009 18 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'> 9</span><span> 2010 13 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>10</span><span> 2011 21 0.095</span><span style='text-decoration: underline;'>2</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>11</span><span> 2012 10 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>12</span><span> 2013 13 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>13</span><span> 2014 20 0.2
|
|
#> </span><span style='color: #BCBCBC;'>14</span><span> 2015 13 </span><span style='color: #BB0000;'>NA</span><span>
|
|
#> </span><span style='color: #BCBCBC;'>15</span><span> 2016 21 0.190
|
|
#> </span><span style='color: #BCBCBC;'>16</span><span> 2017 20 0.4 </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="#format">Format</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>
|
|
|