An 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

Format

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, first 10 characters of an SHA hash containing irretrievable information

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 antibiotics data set and can be translated with ab_name

Read more on our website!

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.