A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website.
example_isolates
A data.frame with 2,000 observations and 49 variables:
date
date of receipt at the laboratory
hospital_id
ID of the hospital, from A to D
ward_icu
logical to determine if ward is an intensive care unit
ward_clinical
logical to determine if ward is a regular clinical ward
ward_outpatient
logical to determine if ward is an outpatient clinic
age
age of the patient
gender
gender of the patient
patient_id
ID of the patient
mo
ID of microorganism created with as.mo(), see also microorganisms
PEN:RIF
40 different antibiotics with class rsi (see as.rsi()); these column names occur in the antibiotics data set and can be translated with ab_name()
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.