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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 Isolates - WHONET Example</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="ref-description section level2">
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<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
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</div>
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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">WHONET</span></span></code></pre></div>
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</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://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 500 observations and 53 variables:</p><ul><li><p><code>Identification number</code><br> ID of the sample</p></li>
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<li><p><code>Specimen number</code><br> ID of the specimen</p></li>
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<li><p><code>Organism</code><br> Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href="as.mo.html">as.mo()</a></code>.</p></li>
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<li><p><code>Country</code><br> Country of origin</p></li>
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<li><p><code>Laboratory</code><br> Name of laboratory</p></li>
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<li><p><code>Last name</code><br> Fictitious last name of patient</p></li>
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<li><p><code>First name</code><br> Fictitious initial of patient</p></li>
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<li><p><code>Sex</code><br> Fictitious gender of patient</p></li>
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<li><p><code>Age</code><br> Fictitious age of patient</p></li>
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<li><p><code>Age category</code><br> Age group, can also be looked up using <code><a href="age_groups.html">age_groups()</a></code></p></li>
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<li><p><code>Date of admission</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> of hospital admission</p></li>
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<li><p><code>Specimen date</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> when specimen was received at laboratory</p></li>
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<li><p><code>Specimen type</code><br> Specimen type or group</p></li>
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<li><p><code>Specimen type (Numeric)</code><br> Translation of <code>"Specimen type"</code></p></li>
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<li><p><code>Reason</code><br> Reason of request with Differential Diagnosis</p></li>
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<li><p><code>Isolate number</code><br> ID of isolate</p></li>
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<li><p><code>Organism type</code><br> Type of microorganism, can also be looked up using <code><a href="mo_property.html">mo_type()</a></code></p></li>
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<li><p><code>Serotype</code><br> Serotype of microorganism</p></li>
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<li><p><code>Beta-lactamase</code><br> Microorganism produces beta-lactamase?</p></li>
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<li><p><code>ESBL</code><br> Microorganism produces extended spectrum beta-lactamase?</p></li>
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<li><p><code>Carbapenemase</code><br> Microorganism produces carbapenemase?</p></li>
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<li><p><code>MRSA screening test</code><br> Microorganism is possible MRSA?</p></li>
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<li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li>
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<li><p><code>Comment</code><br> Other comments</p></li>
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<li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li>
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<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.rsi.html">as.rsi()</a></code>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</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="va">WHONET</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 500 × 53</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex Age Age c…⁷</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></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;"><chr></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;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> fe41d7ba… <span style="text-decoration: underline;">1</span>748 SPN Belgium Nation… Abel B. F 68 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 91f175ec… <span style="text-decoration: underline;">1</span>767 eco The Ne… Nation… Delacr… F. M 89 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> cc401505… <span style="text-decoration: underline;">1</span>343 eco The Ne… Nation… Steens… F. M 85 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> e864b692… <span style="text-decoration: underline;">1</span>894 MAP Denmark Nation… Beyers… L. M 62 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3d051fe3… <span style="text-decoration: underline;">1</span>739 PVU Belgium Nation… Hummel W. M 86 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> c80762a0… <span style="text-decoration: underline;">1</span>846 103 The Ne… Nation… Eikenb… J. F 53 25-54 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 8022d372… <span style="text-decoration: underline;">1</span>628 103 Denmark Nation… Leclerc S. F 77 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> f3dc5f55… <span style="text-decoration: underline;">1</span>493 eco The Ne… Nation… Delacr… W. M 53 25-54 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 15add38f… <span style="text-decoration: underline;">1</span>847 eco France Nation… Van La… S. F 63 55-74 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> fd41248d… <span style="text-decoration: underline;">1</span>458 eco Germany Nation… Moulin O. F 75 75+ </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 490 more rows, 43 more variables: `Date of admission` <date>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen date` <date>, `Specimen type` <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Carbapenemase <lgl>, `MRSA screening test` <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Inducible clindamycin resistance` <lgl>, Comment <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Date of data entry` <date>, AMP_ND10 <rsi>, AMC_ED20 <rsi>, …</span></span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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