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(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
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docs/reference/example_isolates.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set with 2,000 blood culture isolates from septic patients — example_isolates • AMR (for R)</title>
<title>Data set with 2,000 blood culture isolates — example_isolates • AMR (for R)</title>
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 2,000 blood culture isolates from septic patients — example_isolates" />
<meta property="og:title" content="Data set with 2,000 blood culture isolates — example_isolates" />
<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. This data.frame can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
<meta property="og:description" content="An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This data.frame can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9075</span>
</span>
</div>
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<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 2,000 blood culture isolates from septic patients</h1>
<h1>Data set with 2,000 blood culture isolates</h1>
<div class="hidden name"><code>example_isolates.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. This <code>data.frame</code> can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
<p>An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This <code>data.frame</code> can be used to practice AMR analysis. For examples, please read <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
</div>
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<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='ab_property.html'>ab_name</a></code></p></dd>
<dt><code>PEN:RIF</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='ab_property.html'>ab_name</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>