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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 2,000 Example Isolates</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>example_isolates.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">example_isolates</span></span></code></pre></div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 2,000 observations and 49 variables:</p><ul><li><p><code>date</code><br> date of receipt at the laboratory</p></li>
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<li><p><code>hospital_id</code><br> ID of the hospital, from A to D</p></li>
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<li><p><code>ward_icu</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is an intensive care unit</p></li>
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<li><p><code>ward_clinical</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is a regular clinical ward</p></li>
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<li><p><code>ward_outpatient</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is an outpatient clinic</p></li>
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<li><p><code>age</code><br> age of the patient</p></li>
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<li><p><code>gender</code><br> gender of the patient</p></li>
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<li><p><code>patient_id</code><br> ID of the patient</p></li>
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<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li>
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<li><p><code>PEN:RIF</code><br> 40 different antibiotics with class <code><a href="as.rsi.html">rsi</a></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>); these column names occur in the <a href="antibiotics.html">antibiotics</a> data set and can be translated with <code><a href="ab_property.html">ab_name()</a></code></p></li>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 6 × 49</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>, and …</span></span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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