You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Go to file
dr. M.S. (Matthijs) Berends 7108454ba5
(v0.7.1.9055) algorithm improvements
4 years ago
R (v0.7.1.9055) algorithm improvements 4 years ago
data (v0.7.1.9055) algorithm improvements 4 years ago
data-raw (v0.7.1.9055) algorithm improvements 4 years ago
docs (v0.7.1.9055) algorithm improvements 4 years ago
inst/rstudio (v0.6.1.9050) support staged install 4 years ago
man (v0.7.1.9055) algorithm improvements 4 years ago
pkgdown (v0.7.1.9030) eucast_rules() fix 4 years ago
tests (v0.7.1.9055) algorithm improvements 4 years ago
vignettes (v0.7.1.9035) cephalosporins and unit tests 4 years ago
.Rbuildignore (v0.6.1.9050) support staged install 4 years ago
.gitignore (v0.7.1.9033) 5000 new fungi 4 years ago
.gitlab-ci.R new EUCAST rules algorithm 4 years ago
.gitlab-ci.yml (v0.7.1.9037) CI and global env fix 4 years ago
DESCRIPTION (v0.7.1.9055) algorithm improvements 4 years ago
LICENSE (v0.7.1.9027) tibble printing 4 years ago
NAMESPACE (v0.7.1.9036) preserve ab/mo classes in subsetting 4 years ago (v0.7.1.9055) algorithm improvements 4 years ago new git flow to repository 4 years ago
_pkgdown.yml (v0.7.1.9015) Remove freq() 4 years ago
appveyor.yml (v0.7.1.9020) CI fix 2 4 years ago
codecov.yml (v0.7.1.9021) CI fix for resistance_predict 4 years ago new git flow to repository 4 years ago (v0.7.1.9031) include_unknown for first_isolate() 4 years ago (v0.7.1.9019) CI fix 4 years ago (v0.6.1.9053) prerelease fixes 4 years ago (v0.7.1.9003) website update 4 years ago (v0.7.1.9055) algorithm improvements 4 years ago

% AMR (for R)

AMR (for R)

Not a developer? Then please visit our website to read about this package.

It contains documentation about all of the included functions and also a comprehensive tutorial about how to conduct AMR analysis.

Development source

NOTE: the original source code is on GitLab (, so you can report a bug at There is a mirror repository on GitHub ( As the mirror process is automated by GitLab, both repositories always contain the latest changes.

This is the development source of AMR, a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.


Matthijs S. Berends 1,2,a,
Christian F. Luz 1,a,
Erwin E.A. Hassing2,
Corinna Glasner 1,b,
Alex W. Friedrich 1,b,
Bhanu N.M. Sinha 1,b

1 Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands -

2 Certe Medical Diagnostics & Advice, Groningen, the Netherlands -

a Thesis dissertant

b Thesis advisor

How to get this package

All stable versions of this package are published on CRAN, the official R network with a peer-reviewed submission process.

Install from CRAN

CRAN_Badge CRAN_Downloads

(Note: Downloads measured only by, this excludes e.g. the official

  • RStudio favicon Install using RStudio (recommended):

    • Click on Tools and then Install Packages...
    • Type in AMR and press Install
  • R favicon Install in R directly:

    • install.packages("AMR")

Install from Zenodo


This package was also published on Zenodo (stable releases only):

Install from GitLab

This is the latest development version. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green:

Development Test Result Reference
All functions checked on Linux pipeline status GitLab CI [ref 1]
All functions checked on Windows AppVeyor_Build Appveyor Systems Inc. [ref 2]
Percentage of syntax lines checked Code_Coverage Code_Coverage Codecov LLC [ref 3]

If so, try it with:


This R package is licensed under the GNU General Public License (GPL) v2.0. In a nutshell, this means that this package:

  • May be used for commercial purposes

  • May be used for private purposes

  • May not be used for patent purposes

  • May be modified, although:

    • Modifications must be released under the same license when distributing the package
    • Changes made to the code must be documented
  • May be distributed, although:

    • Source code must be made available when the package is distributed
    • A copy of the license and copyright notice must be included with the package.
  • Comes with a LIMITATION of liability

  • Comes with NO warranty