Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values.
rsi_translation
A data.frame with 18,650 observations and 10 variables:
guideline
Name of the guideline
method
Either "MIC" or "DISK"
site
Body site, e.g. "Oral" or "Respiratory"
mo
Microbial ID, see as.mo()
ab
Antibiotic ID, see as.ab()
ref_tbl
Info about where the guideline rule can be found
disk_dose
Dose of the used disk diffusion method
breakpoint_S
Lowest MIC value or highest number of millimetres that leads to "S"
breakpoint_R
Highest MIC value or lowest number of millimetres that leads to "R"
uti
A logical value (TRUE/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 analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!