example_isolates.RdAn anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This data.frame 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:
datedate of receipt at the laboratory
hospital_idID of the hospital, from A to D
ward_iculogical to determine if ward is an intensive care unit
ward_clinicallogical to determine if ward is a regular clinical ward
ward_outpatientlogical to determine if ward is an outpatient clinic
ageage of the patient
gendergender of the patient
patient_idID of the patient, first 10 characters of an SHA hash containing irretrievable information
moID of microorganism created with as.mo, see also microorganisms
PEN:RIF40 different antibiotics with class rsi (see as.rsi); these column names occur in antibiotics data set and can be translated with ab_name
On our website https://msberends.gitlab.io/AMR you can find a 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.