AMR R Package — Function Reference Index

Abstraction: R package for antimicrobial resistance analysis and microbial taxonomy

Key points:

• Provides taxonomically valid microorganism lookup across 96,982 records and 625 antimicrobial drugs
• Key functions: as.mo() for arbitrary input to valid microbial taxonomy; as.ab() for antibiotic IDs; as.sir() for MIC/disk diffusion SIR interpretation
• Supports EUCAST and CLSI interpretive rules; eucast_rules() and clsi_rules() apply breakpoints automatically
• mdro() and related functions classify multidrug-resistant organisms (MDRO, BRMO, MRGN, MDR-TB)
• antibiogram() / wisca() generate traditional, combination, and syndromic antibiograms with ggplot2 integration
• ab_from_text() and av_from_text() extract drug names and doses from free-text clinical records

Connections: Amr Package · Antimicrobial Resistance · Clinical Data Analysis

Source: https://msberends.github.io/AMR/reference/