WHONET {AMR} | R Documentation |
Data Set with 500 Isolates - WHONET Example
Description
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 antimicrobial results are from our example_isolates data set. All patient names were created using online surname generators and are only in place for practice purposes.
Usage
WHONET
Format
A tibble 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, usingas.mo()
. -
Country
Country of origin -
Laboratory
Name of laboratory -
Last name
Fictitious last name of patient -
First name
Fictitious initial of patient -
Sex
Fictitious gender of patient -
Age
Fictitious age of patient -
Age category
Age group, can also be looked up usingage_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 usingmo_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
28 different antimicrobials. You can lookup the abbreviations in the antimicrobials data set, or use e.g.ab_name("AMP")
to get the official name immediately. Before analysis, you should transform this to a valid antimicrobial class, usingas.sir()
.
Download Our Reference Data
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit our website for direct download links, or explore the actual files in our GitHub repository.
Examples
WHONET