P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 16:27:57 +02:00
Code Releases Activity

Built site for AMR: 1.8.1.9045@e7af5fc

Browse Source
This commit is contained in:
github-actions
2022-08-28 20:45:38 +00:00
parent 44b99f8875
commit a62a35d91d
107 changed files with 3425 additions and 2733 deletions
Download Patch File Download Diff File Expand all files Collapse all files

536
articles/datasets.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -161,7 +161,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">26 August 2022</h4>
<h4 data-toc-skip class="date">28 August 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -177,7 +177,7 @@
</h2>
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.3 MB)<br>
@ -403,7 +403,7 @@
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">original R Data Structure (RDS) file</a> (0.2 MB)<br>
@ -473,18 +473,18 @@
</h2>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated text file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated text file</a> (0.2 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft Excel workbook</a> (65 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft Excel workbook</a> (66 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache Feather file</a> (98 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache Feather file</a> (97 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache Parquet file</a> (76 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.parquet" class="external-link">Apache Parquet file</a> (74 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS data file</a> (1.8 MB)<br>
</li>
@ -646,7 +646,7 @@
</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@ -655,13 +655,13 @@
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache Feather file</a> (13 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache Feather file</a> (12 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache Parquet file</a> (11 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.parquet" class="external-link">Apache Parquet file</a> (10 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS data file</a> (80 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM SPSS Statistics data file</a> (68 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM SPSS Statistics data file</a> (27 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata DTA file</a> (67 kB)</li>
</ul>
@ -778,7 +778,7 @@
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@ -789,7 +789,7 @@
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.feather" class="external-link">Apache Feather file</a> (0.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.parquet" class="external-link">Apache Parquet file</a> (99 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS data file</a> (4 MB)<br>
</li>
@ -937,7 +937,7 @@
</h2>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@ -1209,7 +1209,7 @@
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 26 August 2022 21:26:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@ -1218,13 +1218,13 @@
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft Excel workbook</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache Feather file</a> (12 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache Feather file</a> (11 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache Parquet file</a> (8 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache Parquet file</a> (7 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS data file</a> (52 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM SPSS Statistics data file</a> (45 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM SPSS Statistics data file</a> (23 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata DTA file</a> (44 kB)</li>
</ul>
@ -1319,6 +1319,502 @@
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="example_isolates-example-data-for-practice">
<code>example_isolates</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates-example-data-for-practice"></a>
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
<div class="section level3">
<h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
</h3>
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
</div>
<div class="section level3">
<h3 id="example-content-7">Example content<a class="anchor" aria-label="anchor" href="#example-content-7"></a>
</h3>
<table class="table">
<colgroup>
<col width="4%">
<col width="3%">
<col width="1%">
<col width="3%">
<col width="3%">
<col width="5%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
<col width="1%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
<th align="center">patient</th>
<th align="center">age</th>
<th align="center">gender</th>
<th align="center">ward</th>
<th align="center">mo</th>
<th align="center">PEN</th>
<th align="center">OXA</th>
<th align="center">FLC</th>
<th align="center">AMX</th>
<th align="center">AMC</th>
<th align="center">AMP</th>
<th align="center">TZP</th>
<th align="center">CZO</th>
<th align="center">FEP</th>
<th align="center">CXM</th>
<th align="center">FOX</th>
<th align="center">CTX</th>
<th align="center">CAZ</th>
<th align="center">CRO</th>
<th align="center">GEN</th>
<th align="center">TOB</th>
<th align="center">AMK</th>
<th align="center">KAN</th>
<th align="center">TMP</th>
<th align="center">SXT</th>
<th align="center">NIT</th>
<th align="center">FOS</th>
<th align="center">LNZ</th>
<th align="center">CIP</th>
<th align="center">MFX</th>
<th align="center">VAN</th>
<th align="center">TEC</th>
<th align="center">TCY</th>
<th align="center">TGC</th>
<th align="center">DOX</th>
<th align="center">ERY</th>
<th align="center">CLI</th>
<th align="center">AZM</th>
<th align="center">IPM</th>
<th align="center">MEM</th>
<th align="center">MTR</th>
<th align="center">CHL</th>
<th align="center">COL</th>
<th align="center">MUP</th>
<th align="center">RIF</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2002-01-02</td>
<td align="center">A77334</td>
<td align="center">65</td>
<td align="center">F</td>
<td align="center">Clinical</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
</tr>
<tr class="even">
<td align="center">2002-01-03</td>
<td align="center">A77334</td>
<td align="center">65</td>
<td align="center">F</td>
<td align="center">Clinical</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2002-01-07</td>
<td align="center">067927</td>
<td align="center">45</td>
<td align="center">F</td>
<td align="center">ICU</td>
<td align="center">B_STPHY_EPDR</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="center">2002-01-07</td>
<td align="center">067927</td>
<td align="center">45</td>
<td align="center">F</td>
<td align="center">ICU</td>
<td align="center">B_STPHY_EPDR</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">2002-01-13</td>
<td align="center">067927</td>
<td align="center">45</td>
<td align="center">F</td>
<td align="center">ICU</td>
<td align="center">B_STPHY_EPDR</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="center">2002-01-13</td>
<td align="center">067927</td>
<td align="center">45</td>
<td align="center">F</td>
<td align="center">ICU</td>
<td align="center">B_STPHY_EPDR</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">R</td>
<td align="center"></td>
<td align="center"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="example_isolates_unclean-example-data-for-practice">
<code>example_isolates_unclean</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-example-data-for-practice"></a>
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
<p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 August 2022 20:39:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
</h3>
<p>This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.</p>
</div>
<div class="section level3">
<h3 id="example-content-8">Example content<a class="anchor" aria-label="anchor" href="#example-content-8"></a>
</h3>
<table class="table">
<thead><tr class="header">
<th align="center">patient_id</th>
<th align="center">hospital</th>
<th align="center">date</th>
<th align="center">bacteria</th>
<th align="center">AMX</th>
<th align="center">AMC</th>
<th align="center">CIP</th>
<th align="center">GEN</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">J3</td>
<td align="center">A</td>
<td align="center">2012-11-21</td>
<td align="center">E. coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">R7</td>
<td align="center">A</td>
<td align="center">2018-04-03</td>
<td align="center">K. pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="center">P3</td>
<td align="center">A</td>
<td align="center">2014-09-19</td>
<td align="center">E. coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">P10</td>
<td align="center">A</td>
<td align="center">2015-12-10</td>
<td align="center">E. coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="center">B7</td>
<td align="center">A</td>
<td align="center">2015-03-02</td>
<td align="center">E. coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">W3</td>
<td align="center">A</td>
<td align="center">2018-03-31</td>
<td align="center">S. aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside>