AMR: An R Package for Working with Antimicrobial Resistance Data
Dublin Core
Title
AMR: An R Package for Working with Antimicrobial Resistance Data
Subject
antimicrobial resistance, data analysis, R, software, epidemiology
Description
Antimicrobial resistance is an increasing threat to global health. Evidence for this
trend is generated in microbiological laboratories through testing microorganisms for resistance against antimicrobial agents. International standards and guidelines are in place
for this process as well as for reporting data on (inter-)national levels. However, there is a
gap in the availability of standardized and reproducible tools for working with laboratory
data to produce the required reports. It is known that extensive efforts in data cleaning
and validation are required when working with data from laboratory information systems.
Furthermore, the global spread and relevance of antimicrobial resistance demands to incorporate international reference data in the analysis process.
In this paper, we introduce the AMR package for R that aims at closing this gap
by providing tools to simplify antimicrobial resistance data cleaning and analysis, while
incorporating international guidelines and scientifically reliable reference data. The AMR
package enables standardized and reproducible antimicrobial resistance analyses, including the application of evidence-based rules, determination of first isolates, translation of
various codes for microorganisms and antimicrobial agents, determination of (multi-drug)
resistant microorganisms, and calculation of antimicrobial resistance, prevalence and future trends. The AMR package works independently of any laboratory information system
and provides several functions to integrate into international workflows (e.g., WHONET
software provided by the World Health Organization)
trend is generated in microbiological laboratories through testing microorganisms for resistance against antimicrobial agents. International standards and guidelines are in place
for this process as well as for reporting data on (inter-)national levels. However, there is a
gap in the availability of standardized and reproducible tools for working with laboratory
data to produce the required reports. It is known that extensive efforts in data cleaning
and validation are required when working with data from laboratory information systems.
Furthermore, the global spread and relevance of antimicrobial resistance demands to incorporate international reference data in the analysis process.
In this paper, we introduce the AMR package for R that aims at closing this gap
by providing tools to simplify antimicrobial resistance data cleaning and analysis, while
incorporating international guidelines and scientifically reliable reference data. The AMR
package enables standardized and reproducible antimicrobial resistance analyses, including the application of evidence-based rules, determination of first isolates, translation of
various codes for microorganisms and antimicrobial agents, determination of (multi-drug)
resistant microorganisms, and calculation of antimicrobial resistance, prevalence and future trends. The AMR package works independently of any laboratory information system
and provides several functions to integrate into international workflows (e.g., WHONET
software provided by the World Health Organization)
Creator
Matthijs S. Berends
Source
https://www.jstatsoft.org/article/view/v104i03
Publisher
University of Groningen
Date
September 2022
Contributor
Fajar bagus W
Format
PDF
Language
English
Type
Text
Files
Collection
Citation
Matthijs S. Berends, “AMR: An R Package for Working with Antimicrobial Resistance Data,” Repository Horizon University Indonesia, accessed April 4, 2025, https://repository.horizon.ac.id/items/show/8273.