Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use
as.rsi() to transform MICs or disks measurements to R/SI values.
A data.frame with 22,000 observations and 10 variables:
Name of the guideline
Either "DISK" or "MIC"
Body site, e.g. "Oral" or "Respiratory"
Microbial ID, see
Antibiotic ID, see
Info about where the guideline rule can be found
Dose of the used disk diffusion method
Lowest MIC value or highest number of millimetres that leads to "S"
Highest MIC value or lowest number of millimetres that leads to "R"
A logical value (
FALSE) to indicate whether the rule applies to a urinary tract infection (UTI)
The repository of this
AMR package contains a file comprising this exact data set: https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This file allows for machine reading EUCAST and CLSI guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this
AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.