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(v0.7.1.9075) new microorganism codes
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<title>Data set with 2,000 blood culture isolates — example_isolates • AMR (for R)</title>
(v0.7.1.9063) septic_patients -> example_isolates
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<meta property="og:title" content="Data set with 2,000 blood culture isolates — example_isolates" />
(v0.7.1.9063) septic_patients -> example_isolates
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(v0.7.1.9075) new microorganism codes
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<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." />
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9076</span>
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(v0.7.1.9075) new microorganism codes
2019-09-18 15:46:09 +02:00
<h1>Data set with 2,000 blood culture isolates</h1>
(v0.7.1.9063) septic_patients -> example_isolates
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<div class="hidden name"><code>example_isolates.Rd</code></div>
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(v0.7.1.9075) new microorganism codes
2019-09-18 15:46:09 +02:00
<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>
(v0.7.1.9063) septic_patients -> example_isolates
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<pre class="usage"><span class='no'>example_isolates</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>
(v0.7.1.9075) new microorganism codes
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<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>
(v0.7.1.9063) septic_patients -> example_isolates
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</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>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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