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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="d-none name"><code>WHONET.Rd</code></div>
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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://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</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="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>
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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">WHONET</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identification number Specimen number Organism Country</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 fe41d7bafa 1748 SPN Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 91f175ec37 1767 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 cc4015056e 1343 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 e864b692f5 1894 MAP Denmark</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 3d051fe345 1739 PVU Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 c80762a08d 1846 103 The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> Laboratory Last name First name Sex Age</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 National Laboratory of Belgium Abel B. F 68</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 National Laboratory of The Netherlands Delacroix F. M 89</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 National Laboratory of The Netherlands Steensen F. M 85</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 National Laboratory of Denmark Beyersdorf L. M 62</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 National Laboratory of Belgium Hummel W. M 86</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 National Laboratory of The Netherlands Eikenboom J. F 53</span>
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<span class="r-out co"><span class="r-pr">#></span> Age category Date of admission Specimen date Specimen type</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 55-74 2005-01-12 2005-01-30 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 75+ 2006-07-30 2006-08-16 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 75+ 2014-03-05 2014-03-14 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 55-74 2014-10-22 2014-11-01 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 75+ 2016-10-28 2016-11-17 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 25-54 2017-12-21 2018-01-02 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> Specimen type (Numeric) Reason Isolate number Organism type Serotype</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 2 Unknown 1748 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 2 2 Unknown 1767 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 3 2 Unknown 1343 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 4 2 Unknown 1894 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 Unknown 1739 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 Unknown 1846 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> Beta-lactamase ESBL Carbapenemase MRSA screening test</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> Inducible clindamycin resistance Comment Date of data entry AMP_ND10 AMC_ED20</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE 2005-01-30 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE 2006-08-16 <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE 2014-03-14 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE 2014-11-01 R <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE 2016-11-17 R R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE 2018-01-02 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP_ED30 FEP_ED30 CTX_ED5 FOX_ED30 CAZ_ED10 CRO_ED30 CIP_ED5 AMK_ED30</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 S <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 S <NA> <NA> <NA> <NA> <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S <NA> S R S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S <NA> S S S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> GEN_ED10 TOB_ED10 SXT_ED1.2 IPM_ND10 PEN_ND1 AMP_ND2 AMC_ND2 CHL_ND30 VAN_ED5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 R R S <NA> S S S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 S <NA> R <NA> R <NA> S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> <NA> <NA> S S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 R R <NA> <NA> R R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S S R I R R R <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S S S S R S S <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA_ED1 ERY_ED15 CLI_ED2 TCY_ED30 RIF_ED5 PEN_EE AMP_EE CRO_EE CIP_EE</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 <NA> S <NA> S <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> S S S <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> S <NA> <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> S <NA> <NA> R R <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 <NA> R <NA> R R R R S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 <NA> R <NA> <NA> R R S S S</span>
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</code></pre></div>
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