mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 10:46:12 +01:00
dr. M.S. (Matthijs) Berends
45e9546538
Merge branch 'development' of https://github.com/msberends/AMR into development # Conflicts: # docs/articles/AMR.html # docs/articles/AMR_files/figure-html/disk_plots-1.png # docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots-1.png # docs/articles/AMR_files/figure-html/mic_plots-2.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png # docs/articles/AMR_files/figure-html/plot 1-1.png # docs/articles/AMR_files/figure-html/plot 3-1.png # docs/articles/AMR_files/figure-html/plot 4-1.png # docs/articles/AMR_files/figure-html/plot 5-1.png # docs/articles/EUCAST.html # docs/articles/MDR.html # docs/articles/PCA.html # docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png # docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png # docs/articles/SPSS.html # docs/articles/WHONET.html # docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png # docs/articles/benchmarks.html # docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png # docs/articles/datasets.html # docs/articles/resistance_predict.html # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png # docs/articles/welcome_to_AMR.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/AMR-deprecated.html # docs/reference/AMR.html # docs/reference/WHOCC.html # docs/reference/WHONET.html # docs/reference/antibiotics.html # docs/reference/catalogue_of_life.html # docs/reference/catalogue_of_life_version.html # docs/reference/dosage.html # docs/reference/example_isolates.html # docs/reference/example_isolates_unclean.html # docs/reference/g.test.html # docs/reference/intrinsic_resistant.html # docs/reference/microorganisms.codes.html # docs/reference/microorganisms.html # docs/reference/microorganisms.old.html # docs/reference/rsi_translation.html
318 lines
13 KiB
HTML
318 lines
13 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=1.0">
|
||
<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">
|
||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||
<script src="../bootstrap-toc.js"></script><!-- 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">
|
||
<!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||
<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="@univgroningen">
|
||
<!-- 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 data-spy="scroll" data-target="#toc">
|
||
|
||
|
||
<div class="container template-article">
|
||
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||
<div class="container">
|
||
<div class="navbar-header">
|
||
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
|
||
<span class="sr-only">Toggle navigation</span>
|
||
<span class="icon-bar"></span>
|
||
<span class="icon-bar"></span>
|
||
<span class="icon-bar"></span>
|
||
</button>
|
||
<span class="navbar-brand">
|
||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||
<<<<<<< HEAD
|
||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||
=======
|
||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</span>
|
||
</div>
|
||
|
||
<div id="navbar" class="navbar-collapse collapse">
|
||
<ul class="nav navbar-nav">
|
||
<li>
|
||
<a href="../index.html">
|
||
<span class="fa fa-home"></span>
|
||
|
||
Home
|
||
</a>
|
||
</li>
|
||
<li class="dropdown">
|
||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||
<span class="fa fa-question-circle"></span>
|
||
|
||
How to
|
||
|
||
<span class="caret"></span>
|
||
</a>
|
||
<ul class="dropdown-menu" role="menu">
|
||
<li>
|
||
<a href="../articles/AMR.html">
|
||
<span class="fa fa-directions"></span>
|
||
|
||
Conduct AMR analysis
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/resistance_predict.html">
|
||
<span class="fa fa-dice"></span>
|
||
|
||
Predict antimicrobial resistance
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/datasets.html">
|
||
<span class="fa fa-database"></span>
|
||
|
||
Data sets for download / own use
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/PCA.html">
|
||
<span class="fa fa-compress"></span>
|
||
|
||
Conduct principal component analysis for AMR
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/MDR.html">
|
||
<span class="fa fa-skull-crossbones"></span>
|
||
|
||
Determine multi-drug resistance (MDR)
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/WHONET.html">
|
||
<span class="fa fa-globe-americas"></span>
|
||
|
||
Work with WHONET data
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/SPSS.html">
|
||
<span class="fa fa-file-upload"></span>
|
||
|
||
Import data from SPSS/SAS/Stata
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/EUCAST.html">
|
||
<span class="fa fa-exchange-alt"></span>
|
||
|
||
Apply EUCAST rules
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/mo_property.html">
|
||
<span class="fa fa-bug"></span>
|
||
|
||
Get properties of a microorganism
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/ab_property.html">
|
||
<span class="fa fa-capsules"></span>
|
||
|
||
Get properties of an antibiotic
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../articles/benchmarks.html">
|
||
<span class="fa fa-shipping-fast"></span>
|
||
|
||
Other: benchmarks
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<a href="../reference/index.html">
|
||
<span class="fa fa-book-open"></span>
|
||
|
||
Manual
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../authors.html">
|
||
<span class="fa fa-users"></span>
|
||
|
||
Authors
|
||
</a>
|
||
</li>
|
||
<li>
|
||
<a href="../news/index.html">
|
||
<span class="far fa-newspaper"></span>
|
||
|
||
Changelog
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<li>
|
||
<a href="https://github.com/msberends/AMR" class="external-link">
|
||
<span class="fab fa-github"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<!--/.nav-collapse -->
|
||
</div>
|
||
<!--/.container -->
|
||
</div>
|
||
<!--/.navbar -->
|
||
|
||
|
||
|
||
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||
<div class="col-md-9 contents">
|
||
<div class="page-header toc-ignore">
|
||
<h1 data-toc-skip>Welcome to the <code>AMR</code> 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="hidden 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 MDRO’s, 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><code>AMR</code> is a free, open-source and independent R package
|
||
(see <a href="https://msberends.github.io/AMR/#copyright">Copyright</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 antimicrobial resistance
|
||
data analysis, that can therefore empower epidemiological analyses to
|
||
continuously enable surveillance and treatment evaluation in any
|
||
setting.</p>
|
||
<p>After installing this package, R knows ~71,000 distinct microbial
|
||
species and all ~570 antibiotic, antimycotic and antiviral drugs by name
|
||
and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and
|
||
knows all about valid R/SI and MIC values. It supports any data format,
|
||
including WHONET/EARS-Net data.</p>
|
||
<p>The <code>AMR</code> package is available in Danish, Dutch, English,
|
||
French, German, Italian, Portuguese, Russian, Spanish and Swedish.
|
||
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 Catalogue of Life and List
|
||
of Prokaryotic names with Standing in Nomenclature</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 R/SI</li>
|
||
<li>Principal component analysis for AMR</li>
|
||
</ul>
|
||
<p>All reference data sets (about microorganisms, antibiotics, R/SI
|
||
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
||
publicly and freely available. We continually export our data sets to
|
||
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
|
||
files that are machine-readable and suitable for input in any software
|
||
program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
|
||
download links on our website</a>, which is automatically updated with
|
||
every code change.</p>
|
||
<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>. This
|
||
R package 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>) but is actively and durably maintained (see
|
||
<a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>)
|
||
by two public healthcare organisations in the Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||
|
||
</div>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="copyright">
|
||
<p></p>
|
||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
|
||
Erwin E. A. Hassing.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown">
|
||
<p></p>
|
||
<<<<<<< HEAD
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
|
||
2.0.2.</p>
|
||
=======
|
||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|