# The <code>AMR</code> Package — AMR • AMR (for R)
Welcome to the AMR package.

# The `AMR` Package

`AMR.Rd`

Welcome to the `AMR` package.

## Details

`AMR` is 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. It supports any table format, including WHONET/EARS-Net data.

We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.

This package can be used for:

- Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life

- Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines

- Calculating antimicrobial resistance

- Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)

- Calculating empirical susceptibility of both mono therapy and combination therapy

- Predicting future antimicrobial resistance using regression models

- Getting properties for any microorganism (like Gram stain, species, genus or family)

- Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)

- Plotting antimicrobial resistance

- Determining first isolates to be used for AMR analysis

- Applying EUCAST expert rules

- Descriptive statistics: frequency tables, kurtosis and skewness

## Authors

Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1]

[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - https://www.rug.nl https://www.umcg.nl
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - https://www.certe.nl

## Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

## Contact us

For suggestions, comments or questions, please contact us at:

Matthijs S. Berends
m.s.berends [at] umcg [dot] nl
Department of Medical Microbiology, University of Groningen
University Medical Center Groningen
Post Office Box 30001
9700 RB Groningen

If you have found a bug, please file a new issue at:
https://gitlab.com/msberends/AMR/issues