A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
example_isolates_unclean
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
AMX:GEN
4 different antibiotics that have to be transformed with as.rsi()
On our website https://msberends.gitlab.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.