P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 13:41:49 +02:00
Code Releases Activity

support veterinary MIC/disk translation

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
parent 74ea6c8c60
commit 7be4dabbc0
69 changed files with 34521 additions and 30207 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
man/AMR.Rd
View File

@ -2,8 +2,8 @@
% Please edit documentation in R/aa_amr-package.R
\docType{package}
\name{AMR}
\alias{AMR}
\alias{AMR-package}
\alias{AMR}
\title{The \code{AMR} Package}
\source{
To cite AMR in publications use:
@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~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 clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated January 2024) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~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 clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, 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.
}
@ -55,7 +55,6 @@ Useful links:
Authors:
\itemize{
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Dennis Souverein (\href{https://orcid.org/0000-0003-0455-0336}{ORCID}) [contributor]
\item Erwin E. A. Hassing [contributor]
}
@ -70,14 +69,18 @@ Other contributors:
\item Eric H. L. C. M. Hazenberg [contributor]
\item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
\item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Bart C. Meijer [contributor]
\item Dmytro Mykhailenko [contributor]
\item Anton Mymrikov [contributor]
\item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
\item Matthew Saab [contributor]
\item Jonas Salm [contributor]
\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
\item Rogier P. Schade [contributor]
\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
\item Jason Stull (\href{https://orcid.org/0000-0002-9028-8153}{ORCID}) [contributor]
\item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
\item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
}