P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-27 07:26:11 +01:00
Code Releases Activity
0b0a4b6a51
AMR/articles/datasets.html
github-actions 0b0a4b6a51 cli-147-2196
2024-05-20 19:35:19 +00:00

2277 lines
80 KiB
HTML
Raw Blame History

This file contains invisible Unicode characters

This file contains invisible Unicode characters that are indistinguishable to humans but may be processed differently by a computer. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="AMR">
<title>Data sets for download / own use • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
<!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@msberends">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
<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="">2.1.1.9032</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">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="active nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
<span class="fa fa-question-circle"></span>
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antiviral Drug
</a>
</div>
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-group"></span>
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
</div>
</li>
<li class="nav-item">
<a class="nav-link" href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li class="nav-item">
<a class="nav-link" href="../authors.html">
<span class="fa fa-users"></span>
Authors
</a>
</li>
</ul>
<form class="form-inline my-2 my-lg-0" role="search">
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
</form>
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link" href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
<li class="nav-item">
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
</li>
</ul>
</div>
</div>
</nav><div class="container template-article">
<div class="row">
<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">20 May 2024</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>
</div>
<p>All reference data (about microorganisms, antibiotics, SIR
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, MS Excel, Apache Feather, Apache
Parquet, SPSS, SAS, and Stata. We also provide tab-separated text files
that are machine-readable and suitable for input in any software
program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure
of the data sets look like.</p>
<div class="section level2">
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52 171 rows and 23 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</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>oxygen_tolerance</em>, <em>source</em>, <em>lpsn</em>,
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>,
<em>gbif_parent</em>, <em>gbif_renamed_to</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 14 July 2023 08:49:06 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> (1.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (11.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
Excel workbook</a> (5.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
Feather file</a> (5.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
Parquet file</a> (2.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
transport (XPT) file</a> (48.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (17.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (48.6 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
exceed 100 MB; the file size limit of GitHub.</strong> Their file
structures and compression techniques are very inefficient. Advice? Use
R instead. It’s free and much better in many ways.</p>
<p>The tab-separated text file and Microsoft Excel workbook both contain
all SNOMED codes as comma separated values.</p>
<div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3>
<p>This data set contains the full microbial taxonomy of five kingdoms
from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
and the Global Biodiversity Information Facility (GBIF):</p>
<ul>
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
International Journal of Systematic and Evolutionary Microbiology, 70,
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on December 11th, 2022.</li>
<li>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on January 8th, 2024.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
</li>
</ul>
</div>
<div class="section level3">
<h3 id="example-content">Example content<a class="anchor" aria-label="anchor" href="#example-content"></a>
</h3>
<p>Included (sub)species per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
<th align="center">Kingdom</th>
<th align="center">Number of (sub)species</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">(unknown kingdom)</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1 379</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1 314</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 501</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7 905</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">5 071</td>
</tr>
</tbody>
</table>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table class="table">
<colgroup>
<col width="3%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="4%">
<col width="5%">
<col width="4%">
<col width="5%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="2%">
<col width="6%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="11%">
</colgroup>
<thead><tr class="header">
<th align="center">mo</th>
<th align="center">fullname</th>
<th align="center">status</th>
<th align="center">kingdom</th>
<th align="center">phylum</th>
<th align="center">class</th>
<th align="center">order</th>
<th align="center">family</th>
<th align="center">genus</th>
<th align="center">species</th>
<th align="center">subspecies</th>
<th align="center">rank</th>
<th align="center">ref</th>
<th align="center">oxygen_tolerance</th>
<th align="center">source</th>
<th align="center">lpsn</th>
<th align="center">lpsn_parent</th>
<th align="center">lpsn_renamed_to</th>
<th align="center">gbif</th>
<th align="center">gbif_parent</th>
<th align="center">gbif_renamed_to</th>
<th align="center">prevalence</th>
<th align="center">snomed</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">B_ESCHR</td>
<td align="center">Escherichia</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">genus</td>
<td align="center">Castellani et al., 1919</td>
<td align="center">facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">515602</td>
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">407310004, 407251000, 407281008, …</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_ADCR</td>
<td align="center">Escherichia adecarboxylata</td>
<td align="center">synonym</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">adecarboxylata</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Leclerc, 1962</td>
<td align="center">aerobe</td>
<td align="center">LPSN</td>
<td align="center">776052</td>
<td align="center">515602</td>
<td align="center">777447</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_ALBR</td>
<td align="center">Escherichia albertii</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">albertii</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Huys et al., 2003</td>
<td align="center">aerobe</td>
<td align="center">LPSN</td>
<td align="center">776053</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">5427575</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">419388003</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_BLTT</td>
<td align="center">Escherichia blattae</td>
<td align="center">synonym</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">blattae</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Burgess et al., 1973</td>
<td align="center">likely facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776056</td>
<td align="center">515602</td>
<td align="center">788468</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.5</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_COLI</td>
<td align="center">Escherichia coli</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Castellani et al., 1919</td>
<td align="center">facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1095001000112106, 715307006, 737528008, …</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_DYSN</td>
<td align="center">Escherichia dysenteriae</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">dysenteriae</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center"></td>
<td align="center">likely facultative anaerobe</td>
<td align="center">GBIF</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">10862979</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1.5</td>
<td align="center"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="antibiotics-antibiotic-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
</h2>
<p>A data set with 483 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 24 February 2024 14:16:52 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> (44 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>
<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> (73 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> (0.1 MB)<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> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
transport (XPT) file</a> (1.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
DTA file</a> (0.5 MB)</li>
</ul>
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the ATC codes, common abbreviations,
trade names and LOINC codes as comma separated values.</p>
<div class="section level3">
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
</h3>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO
and WHONET, and all compound IDs from PubChem. It also contains all
brand names (synonyms) as found on PubChem and Defined Daily Doses
(DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">ATC/DDD index from
WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this
may not be used for commercial purposes, but is freely available from
the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
<li><a href="https://loinc.org" class="external-link">LOINC (Logical Observation Identifiers
Names and Codes)</a></li>
</ul>
</div>
<div class="section level3">
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
</h3>
<table class="table">
<colgroup>
<col width="1%">
<col width="2%">
<col width="8%">
<col width="7%">
<col width="7%">
<col width="12%">
<col width="17%">
<col width="6%">
<col width="13%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">ab</th>
<th align="center">cid</th>
<th align="center">name</th>
<th align="center">group</th>
<th align="center">atc</th>
<th align="center">atc_group1</th>
<th align="center">atc_group2</th>
<th align="center">abbreviations</th>
<th align="center">synonyms</th>
<th align="center">oral_ddd</th>
<th align="center">oral_units</th>
<th align="center">iv_ddd</th>
<th align="center">iv_units</th>
<th align="center">loinc</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">AMK</td>
<td align="center">37768</td>
<td align="center">Amikacin</td>
<td align="center">Aminoglycosides</td>
<td align="center">D06AX12, J01GB06, S01AA21</td>
<td align="center">Aminoglycoside antibacterials</td>
<td align="center">Other aminoglycosides</td>
<td align="center">ak, ami, amik, …</td>
<td align="center">amicacin, amikacillin, amikacin, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">g</td>
<td align="center">101493-5, 11-7, 12-5, …</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">33613</td>
<td align="center">Amoxicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CA04</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td>
<td align="center">actimoxi, amoclen, amolin, …</td>
<td align="center">1.5</td>
<td align="center">g</td>
<td align="center">3.0</td>
<td align="center">g</td>
<td align="center">101498-4, 15-8, 16-6, …</td>
</tr>
<tr class="odd">
<td align="center">AMC</td>
<td align="center">23665637</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CR02</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Combinations of penicillins, incl. beta-lactamase
inhibitors</td>
<td align="center">a/c, amcl, aml, …</td>
<td align="center">amocla, amoclan, amoclav, …</td>
<td align="center">1.5</td>
<td align="center">g</td>
<td align="center">3.0</td>
<td align="center">g</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="center">AMP</td>
<td align="center">6249</td>
<td align="center">Ampicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CA01, S01AA19</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">am, amp, ampi</td>
<td align="center">acillin, adobacillin, amblosin, …</td>
<td align="center">2.0</td>
<td align="center">g</td>
<td align="center">6.0</td>
<td align="center">g</td>
<td align="center">101477-8, 101478-6, 18864-9, …</td>
</tr>
<tr class="odd">
<td align="center">AZM</td>
<td align="center">447043</td>
<td align="center">Azithromycin</td>
<td align="center">Macrolides/lincosamides</td>
<td align="center">J01FA10, S01AA26</td>
<td align="center">Macrolides, lincosamides and streptogramins</td>
<td align="center">Macrolides</td>
<td align="center">az, azi, azit, …</td>
<td align="center">aritromicina, aruzilina, azasite, …</td>
<td align="center">0.3</td>
<td align="center">g</td>
<td align="center">0.5</td>
<td align="center">g</td>
<td align="center">100043-9, 16420-2, 16421-0, …</td>
</tr>
<tr class="even">
<td align="center">PEN</td>
<td align="center">5904</td>
<td align="center">Benzylpenicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CE01, S01AA14</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">bepe, pen, peni, …</td>
<td align="center">abbocillin, ayercillin, bencilpenicilina, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">3.6</td>
<td align="center">g</td>
<td align="center"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="antivirals-antiviral-drugs">
<code>antivirals</code>: Antiviral Drugs<a class="anchor" aria-label="anchor" href="#antivirals-antiviral-drugs"></a>
</h2>
<p>A data set with 120 rows and 11 columns, containing the following
column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
<em>atc_group</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>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 20 October 2023 12:51:48 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> (6 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">tab-separated
text file</a> (17 kB)<br>
</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> (16 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> (16 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> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xpt" class="external-link">SAS
transport (XPT) file</a> (73 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> (32 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> (78 kB)</li>
</ul>
<p>The tab-separated text file and Microsoft Excel workbook, and SAS,
SPSS and Stata files all contain the trade names and LOINC codes as
comma separated values.</p>
<div class="section level3">
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
</h3>
<p>This data set contains all ATC codes gathered from WHO and all
compound IDs from PubChem. It also contains all brand names (synonyms)
as found on PubChem and Defined Daily Doses (DDDs) for oral and
parenteral administration.</p>
<ul>
<li>
<a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">ATC/DDD index from
WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this
may not be used for commercial purposes, but is freely available from
the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
<li><a href="https://loinc.org" class="external-link">LOINC (Logical Observation Identifiers
Names and Codes)</a></li>
</ul>
</div>
<div class="section level3">
<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
</h3>
<table class="table">
<colgroup>
<col width="2%">
<col width="8%">
<col width="3%">
<col width="4%">
<col width="28%">
<col width="23%">
<col width="4%">
<col width="4%">
<col width="3%">
<col width="4%">
<col width="13%">
</colgroup>
<thead><tr class="header">
<th align="center">av</th>
<th align="center">name</th>
<th align="center">atc</th>
<th align="center">cid</th>
<th align="center">atc_group</th>
<th align="center">synonyms</th>
<th align="center">oral_ddd</th>
<th align="center">oral_units</th>
<th align="center">iv_ddd</th>
<th align="center">iv_units</th>
<th align="center">loinc</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">ABA</td>
<td align="center">Abacavir</td>
<td align="center">J05AF06</td>
<td align="center">441300</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase
inhibitors</td>
<td align="center">abacavir sulfate, avacavir, ziagen</td>
<td align="center">0.6</td>
<td align="center">g</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">29113-8, 30273-7, 30287-7, …</td>
</tr>
<tr class="even">
<td align="center">ACI</td>
<td align="center">Aciclovir</td>
<td align="center">J05AB01</td>
<td align="center">135398513</td>
<td align="center">Nucleosides and nucleotides excl. reverse
transcriptase inhibitors</td>
<td align="center">acicloftal, aciclovier, aciclovirum, …</td>
<td align="center">4.0</td>
<td align="center">g</td>
<td align="center">4</td>
<td align="center">g</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">ADD</td>
<td align="center">Adefovir dipivoxil</td>
<td align="center">J05AF08</td>
<td align="center">60871</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase
inhibitors</td>
<td align="center">adefovir di, adefovir di ester, adefovir dipivoxyl,
…</td>
<td align="center">10.0</td>
<td align="center">mg</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="center">AME</td>
<td align="center">Amenamevir</td>
<td align="center">J05AX26</td>
<td align="center">11397521</td>
<td align="center">Other antivirals</td>
<td align="center">amenalief</td>
<td align="center">0.4</td>
<td align="center">g</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="center">AMP</td>
<td align="center">Amprenavir</td>
<td align="center">J05AE05</td>
<td align="center">65016</td>
<td align="center">Protease inhibitors</td>
<td align="center">agenerase, carbamate, prozei</td>
<td align="center">1.2</td>
<td align="center">g</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">29114-6, 30296-8, 30297-6, …</td>
</tr>
<tr class="even">
<td align="center">ASU</td>
<td align="center">Asunaprevir</td>
<td align="center">J05AP06</td>
<td align="center">16076883</td>
<td align="center">Antivirals for treatment of HCV infections</td>
<td align="center">sunvepra, sunvepratrade</td>
<td align="center">0.2</td>
<td align="center">g</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir">
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 29 883 rows and 13 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</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>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 24 February 2024 14:16:52 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.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/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (61 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (2.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (91 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (8.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (4.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (8.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
(2011-2023).</p>
<p>Clinical breakpoints in this package were validated through and
imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop
Windows application developed and supported by the WHO Collaborating
Centre for Surveillance of Antimicrobial Resistance. More can be read on
<a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET
and this <code>AMR</code> package have been in contact about sharing
their work. We highly appreciate their development on the WHONET
software.</p>
<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and
public use of this <code>AMR</code> package (and consequently the use of
their breakpoints) in June 2023, when future development of distributing
clinical breakpoints was discussed in a meeting between CLSI, EUCAST,
the WHO, and developers of WHONET and the <code>AMR</code> package.</p>
<p><strong>NOTE:</strong> this <code>AMR</code> package (and the WHONET
software as well) contains internal methods to apply the guidelines,
which is rather complex. For example, some breakpoints must be applied
on certain species groups (which are in case of this package available
through the <code>microorganisms.groups</code> data set). It is
important that this is considered when using the breakpoints for own
use.</p>
</div>
<div class="section level3">
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
</h3>
<table class="table">
<colgroup>
<col width="6%">
<col width="3%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="7%">
<col width="14%">
<col width="6%">
<col width="2%">
<col width="15%">
<col width="8%">
<col width="8%">
<col width="7%">
<col width="7%">
<col width="3%">
</colgroup>
<thead><tr class="header">
<th align="center">guideline</th>
<th align="center">type</th>
<th align="center">host</th>
<th align="center">method</th>
<th align="center">site</th>
<th align="center">mo</th>
<th align="center">mo_name</th>
<th align="center">rank_index</th>
<th align="center">ab</th>
<th align="center">ab_name</th>
<th align="center">ref_tbl</th>
<th align="center">disk_dose</th>
<th align="center">breakpoint_S</th>
<th align="center">breakpoint_R</th>
<th align="center">uti</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
<td align="center">A. xylosoxidans</td>
<td align="center">10ug</td>
<td align="center">26.000</td>
<td align="center">20.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">1.000</td>
<td align="center">4.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center">1.25ug/23.75ug</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">0.125</td>
<td align="center">0.125</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center">30ug/6ug</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">B_ACHRMB_XYLS</td>
<td align="center">Achromobacter xylosoxidans</td>
<td align="center">2</td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">4.000</td>
<td align="center">4.000</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="intrinsic_resistant-intrinsic-bacterial-resistance">
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134 634 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 16 December 2022 15:10:43 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>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
text file</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
Feather file</a> (1.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache
Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xpt" class="external-link">SAS
transport (XPT) file</a> (9.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
SPSS Statistics data file</a> (7.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
DTA file</a> (9.5 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of
all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">‘EUCAST
Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
v3.3</a> (2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
</h3>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<table class="table">
<thead><tr class="header">
<th align="center">microorganism</th>
<th align="center">antibiotic</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Acetylmidecamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Acetylspiramycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin/clavulanic acid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Ampicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Ampicillin/sulbactam</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Avoparcin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Azithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Benzylpenicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cadazolid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefadroxil</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalexin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefalotin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefoxitin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clindamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cycloserine</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dalbavancin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Dirithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Erythromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Flurithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Fusidic acid</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Gamithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Josamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Kitasamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Lincomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Linezolid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Meleumycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Midecamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Miocamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Nafithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Norvancomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oleandomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oritavancin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pirlimycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Primycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pristinamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Quinupristin/dalfopristin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Ramoplanin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Rifampicin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Rokitamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Roxithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Solithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Spiramycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tedizolid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telavancin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Thiacetazone</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tildipirosin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tilmicosin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Troleandomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tulathromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tylosin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tylvalosin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="dosage-dosage-guidelines-from-eucast">
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
</h2>
<p>A data set with 503 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 22 June 2023 13:10:59 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>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated
text file</a> (43 kB)<br>
</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> (25 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> (21 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> (9 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xpt" class="external-link">SAS
transport (XPT) file</a> (0.1 MB)<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> (64 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> (0.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
</h3>
<p>EUCAST breakpoints used in this package are based on the dosages in
this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href=""></a> (), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
</h3>
<table class="table">
<colgroup>
<col width="4%">
<col width="10%">
<col width="15%">
<col width="10%">
<col width="9%">
<col width="13%">
<col width="5%">
<col width="16%">
<col width="13%">
</colgroup>
<thead><tr class="header">
<th align="center">ab</th>
<th align="center">name</th>
<th align="center">type</th>
<th align="center">dose</th>
<th align="center">dose_times</th>
<th align="center">administration</th>
<th align="center">notes</th>
<th align="center">original_txt</th>
<th align="center">eucast_version</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">AMK</td>
<td align="center">Amikacin</td>
<td align="center">standard_dosage</td>
<td align="center">25-30 mg/kg</td>
<td align="center">1</td>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">25-30 mg/kg x 1 iv</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">Amoxicillin</td>
<td align="center">high_dosage</td>
<td align="center">2 g</td>
<td align="center">6</td>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">2 g x 6 iv</td>
<td align="center">13</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
<td align="center">Amoxicillin</td>
<td align="center">standard_dosage</td>
<td align="center">1 g</td>
<td align="center">3</td>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">1 g x 3-4 iv</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">Amoxicillin</td>
<td align="center">high_dosage</td>
<td align="center">0.75-1 g</td>
<td align="center">3</td>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.75-1 g x 3 oral</td>
<td align="center">13</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
<td align="center">Amoxicillin</td>
<td align="center">standard_dosage</td>
<td align="center">0.5 g</td>
<td align="center">3</td>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">Amoxicillin</td>
<td align="center">uncomplicated_uti</td>
<td align="center">0.5 g</td>
<td align="center">3</td>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">13</td>
</tr>
</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 21 January 2023 22:47:20 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-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></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-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></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 27 August 2022 18:49:37 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-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 style="width:100%;" class="table">
<colgroup>
<col width="17%">
<col width="14%">
<col width="17%">
<col width="21%">
<col width="7%">
<col width="7%">
<col width="7%">
<col width="7%">
</colgroup>
<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>
<div class="section level2">
<h2 id="microorganisms-groups-species-groups-and-microbiological-complexes">
<code>microorganisms.groups</code>: Species Groups and
Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
</h2>
<p>A data set with 521 rows and 4 columns, containing the following
column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<em>mo_name</em>.</p>
<p>This data set is in R available as
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 14 July 2023 08:49:06 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.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.groups.rds" class="external-link">original
R Data Structure (RDS) file</a> (6 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
text file</a> (49 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
Excel workbook</a> (20 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
Feather file</a> (19 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
Parquet file</a> (13 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
SPSS Statistics data file</a> (64 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
DTA file</a> (81 kB)</li>
</ul>
<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 species groups and microbiological complexes,
which are used in the <code>clinical_breakpoints</code> data set.</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">
<colgroup>
<col width="17%">
<col width="15%">
<col width="35%">
<col width="31%">
</colgroup>
<thead><tr class="header">
<th align="center">mo_group</th>
<th align="center">mo</th>
<th align="center">mo_group_name</th>
<th align="center">mo_name</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_BMNN</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter baumannii</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_CLCC</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter calcoaceticus</td>
</tr>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_DJKS</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter dijkshoorniae</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_NSCM</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter nosocomialis</td>
</tr>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_PITT</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter pittii</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_SFRT</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter seifertii</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2>
<p>A data set with 4 957 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.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.codes.rds" class="external-link">original
R Data Structure (RDS) file</a> (22 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xlsx" class="external-link">Microsoft
Excel workbook</a> (91 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (85 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (57 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.dta" class="external-link">Stata
DTA file</a> (0.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-9">Source<a class="anchor" aria-label="anchor" href="#source-9"></a>
</h3>
<p>This data set contains commonly used codes for microorganisms, from
laboratory systems and <a href="https://whonet.org" class="external-link">WHONET</a>.</p>
</div>
<div class="section level3">
<h3 id="example-content-9">Example content<a class="anchor" aria-label="anchor" href="#example-content-9"></a>
</h3>
<table class="table">
<thead><tr class="header">
<th align="center">code</th>
<th align="center">mo</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">1011</td>
<td align="center">B_GRAMP</td>
</tr>
<tr class="even">
<td align="center">1012</td>
<td align="center">B_GRAMP</td>
</tr>
<tr class="odd">
<td align="center">1013</td>
<td align="center">B_GRAMN</td>
</tr>
<tr class="even">
<td align="center">1014</td>
<td align="center">B_GRAMN</td>
</tr>
<tr class="odd">
<td align="center">1015</td>
<td align="center">F_YEAST</td>
</tr>
<tr class="even">
<td align="center">103</td>
<td align="center">B_ESCHR_COLI</td>
</tr>
</tbody>
</table>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside>
</div>
<footer><div class="pkgdown-footer-left">
<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>
</div>
<div class="pkgdown-footer-right">
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div>
</footer>
</div>
</body>
</html>
View Git Blame Copy Permalink