Data set with 500 isolates - WHONET example

This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our septic_patients data set.

WHONET

Format

A data.frame with 500 observations and 53 variables:

Identification number: ID of the sample
Specimen number: ID of the specimen
Organism: Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using as.mo.
Country: Country of origin
Laboratory: Name of laboratory
Last name: Last name of patient
First name: Initial of patient
Sex: Gender of patient
Age: Age of patient
Age category: Age group, can also be looked up using age_groups
Date of admission: Date of hospital admission
Specimen date: Date when specimen was received at laboratory
Specimen type: Specimen type or group
Specimen type (Numeric): Translation of "Specimen type"
Reason: Reason of request with Differential Diagnosis
Isolate number: ID of isolate
Organism type: Type of microorganism, can also be looked up using mo_type
Serotype: Serotype of microorganism
Beta-lactamase: Microorganism produces beta-lactamase?
ESBL: Microorganism produces extended spectrum beta-lactamase?
Carbapenemase: Microorganism produces carbapenemase?
MRSA screening test: Microorganism is possible MRSA?
Inducible clindamycin resistance: Clindamycin can be induced?
Comment: Other comments
Date of data entry: Date this data was entered in WHONET
AMP_ND10:CIP_EE: 27 different antibiotics. You can lookup the abbreviatons in the antibiotics data set, or use e.g. atc_name("AMP") to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using as.rsi.

Data set with 500 isolates - WHONET example

Format

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