AMR (for R)

NOTE: the original source code is on GitLab (https://gitlab.com/msberends/AMR), so you can report a bug at https://gitlab.com/msberends/AMR/issues. There is a mirror repository on GitHub (https://github.com/msberends/AMR). As the mirror process is automated by GitLab, both repositories always contain the latest changes.

Development source

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.

Not a developer? Then our website https://msberends.gitlab.io/AMR is probably a better place 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.

Authors

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 - rug.nl umcg.nl
² Certe Medical Diagnostics & Advice, Groningen, the Netherlands - certe.nl
^a R package author and 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

(Note: Downloads measured only by cran.rstudio.com, this excludes e.g. the official cran.r-project.org)

• Install using RStudio (recommended):

  • Click on Tools and then Install Packages...
  • Type in AMR and press Install

• Install in R directly:

  • install.packages("AMR")

Install from Zenodo

This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355

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		GitLab CI [ref 1]
All functions checked on Windows		Appveyor Systems Inc. [ref 2]
Percentage of syntax lines checked		Codecov LLC [ref 3]

If so, try it with:

install.packages("devtools") 
devtools::install_gitlab("msberends/AMR")

Copyright

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