A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.



A data.frame with 3,000 observations and 8 variables:

  • patient_id
    ID of the patient

  • date
    date of receipt at the laboratory

  • hospital
    ID of the hospital, from A to C

  • bacteria
    info about microorganism that can be transformed with as.mo(), see also microorganisms

    4 different antibiotics that have to be transformed with as.rsi()

Reference Data Publicly Available

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.

Read more on Our Website!

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.