A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read the tutorial on our website.
example_isolatesA 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()
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.
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.