mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 21:26:12 +01:00
323 lines
17 KiB
HTML
323 lines
17 KiB
HTML
<!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>Welcome to the `AMR` package • 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-5.2.2/bootstrap.min.css" rel="stylesheet">
|
|
<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></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="Welcome to the `AMR` package">
|
|
<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"><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="">2.0.0.9023</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="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 & dplyr/tidyverse
|
|
</a>
|
|
<a class="dropdown-item" href="../articles/other_pkg.html">
|
|
<span class="fa fa-layer-group"></span>
|
|
|
|
AMR & data.table
|
|
</a>
|
|
<a class="dropdown-item" href="../articles/other_pkg.html">
|
|
<span class="fa fa-layer-group"></span>
|
|
|
|
AMR & tidymodels
|
|
</a>
|
|
<a class="dropdown-item" href="../articles/other_pkg.html">
|
|
<span class="fa fa-layer-group"></span>
|
|
|
|
AMR & 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>Welcome to the `AMR` package</h1>
|
|
|
|
|
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
|
|
<div class="d-none name"><code>welcome_to_AMR.Rmd</code></div>
|
|
</div>
|
|
|
|
|
|
|
|
<p>Note: to keep the package size as small as possible, we only included
|
|
this vignette on CRAN. You can read more vignettes on our website about
|
|
how to conduct AMR data analysis, determine MDROs, find explanation of
|
|
EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
|
|
<hr>
|
|
<p>The <code>AMR</code> package is a <a href="https://msberends.github.io/AMR/#copyright">free and
|
|
open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero
|
|
dependencies</a> to simplify the analysis and prediction of
|
|
Antimicrobial Resistance (AMR) and to work with microbial and
|
|
antimicrobial data and properties, by using evidence-based methods.
|
|
<strong>Our aim is to provide a standard</strong> for clean and
|
|
reproducible AMR data analysis, that can therefore empower
|
|
epidemiological analyses to continuously enable surveillance and
|
|
treatment evaluation in any setting. <a href="https://msberends.github.io/AMR/authors.html">Many different
|
|
researchers</a> from around the globe are continually helping us to make
|
|
this a successful and durable project!</p>
|
|
<p>This work was published in the Journal of Statistical Software
|
|
(Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI
|
|
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
|
|
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
|
|
10.33612/diss.192486375</a>).</p>
|
|
<p>After installing this package, R knows ~52 000 distinct microbial
|
|
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
|
|
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
|
|
CT), and knows all about valid SIR and MIC values. The integral
|
|
breakpoint guidelines from CLSI and EUCAST are included from the last 10
|
|
years. It supports and can read any data format, including WHONET
|
|
data.</p>
|
|
<p>With the help of contributors from all corners of the world, the
|
|
<code>AMR</code> package is available in English, Czech, Chinese,
|
|
Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese,
|
|
Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish,
|
|
Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial
|
|
microorganism names are provided in these languages.</p>
|
|
<p>This package is fully independent of any other R package and works on
|
|
Windows, macOS and Linux with all versions of R since R-3.0 (April
|
|
2013). <strong>It was designed to work in any setting, including those
|
|
with very limited resources</strong>. Since its first public release in
|
|
early 2018, this package has been downloaded from more than 175
|
|
countries.</p>
|
|
<p>This package can be used for:</p>
|
|
<ul>
|
|
<li>Reference for the taxonomy of microorganisms, since the package
|
|
contains all microbial (sub)species from the List of Prokaryotic names
|
|
with Standing in Nomenclature (LPSN) and the Global Biodiversity
|
|
Information Facility (GBIF)</li>
|
|
<li>Interpreting raw MIC and disk diffusion values, based on the latest
|
|
CLSI or EUCAST guidelines</li>
|
|
<li>Retrieving antimicrobial drug names, doses and forms of
|
|
administration from clinical health care records</li>
|
|
<li>Determining first isolates to be used for AMR data analysis</li>
|
|
<li>Calculating antimicrobial resistance</li>
|
|
<li>Determining multi-drug resistance (MDR) / multi-drug resistant
|
|
organisms (MDRO)</li>
|
|
<li>Calculating (empirical) susceptibility of both mono therapy and
|
|
combination therapies</li>
|
|
<li>Predicting future antimicrobial resistance using regression
|
|
models</li>
|
|
<li>Getting properties for any microorganism (like Gram stain, species,
|
|
genus or family)</li>
|
|
<li>Getting properties for any antibiotic (like name, code of
|
|
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
|
|
<li>Plotting antimicrobial resistance</li>
|
|
<li>Applying EUCAST expert rules</li>
|
|
<li>Getting SNOMED codes of a microorganism, or getting properties of a
|
|
microorganism based on a SNOMED code</li>
|
|
<li>Getting LOINC codes of an antibiotic, or getting properties of an
|
|
antibiotic based on a LOINC code</li>
|
|
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
|
|
translate MIC values and disk diffusion diameters to SIR</li>
|
|
<li>Principal component analysis for AMR</li>
|
|
</ul>
|
|
<p>All reference data sets (about microorganisms, antibiotics, SIR
|
|
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
|
publicly and freely available. We continually export our data sets to
|
|
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
|
|
files that are machine-readable and suitable for input in any software
|
|
program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
|
|
download links on our website</a>, which is automatically updated with
|
|
every code change.</p>
|
|
<p>This R package was created for both routine data analysis and
|
|
academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
|
|
with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
|
|
Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>, and
|
|
is being <a href="https://msberends.github.io/AMR/news/">actively and
|
|
durably maintained</a> by two public healthcare organisations in the
|
|
Netherlands.</p>
|
|
<hr>
|
|
<p><small> This AMR package for R is free, open-source software and
|
|
licensed under the <a href="https://msberends.github.io/AMR/LICENSE-text.html">GNU General
|
|
Public License v2.0 (GPL-2)</a>. These requirements are consequently
|
|
legally binding: modifications must be released under the same license
|
|
when distributing the package, changes made to the code must be
|
|
documented, source code must be made available when the package is
|
|
distributed, and a copy of the license and copyright notice must be
|
|
included with the package. </small></p>
|
|
</main>
|
|
</div>
|
|
|
|
|
|
|
|
<footer><div class="pkgdown-footer-left">
|
|
<p></p>
|
|
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
|
</div>
|
|
|
|
<div class="pkgdown-footer-right">
|
|
<p></p>
|
|
<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>
|