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 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, using as.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 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
  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, using as.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
#> # A tibble: 500 × 53
#>    `Identification number` `Specimen number` Organism Country         Laboratory
#>    <chr>                               <int> <chr>    <chr>           <chr>     
#>  1 fe41d7bafa                           1748 SPN      Belgium         National …
#>  2 91f175ec37                           1767 eco      The Netherlands National …
#>  3 cc4015056e                           1343 eco      The Netherlands National …
#>  4 e864b692f5                           1894 MAP      Denmark         National …
#>  5 3d051fe345                           1739 PVU      Belgium         National …
#>  6 c80762a08d                           1846 103      The Netherlands National …
#>  7 8022d3727c                           1628 103      Denmark         National …
#>  8 f3dc5f553d                           1493 eco      The Netherlands National …
#>  9 15add38f6c                           1847 eco      France          National …
#> 10 fd41248def                           1458 eco      Germany         National …
#> # ℹ 490 more rows
#> # ℹ 48 more variables: `Last name` <chr>, `First name` <chr>, Sex <chr>,
#> #   Age <dbl>, `Age category` <chr>, `Date of admission` <date>,
#> #   `Specimen date` <date>, `Specimen type` <chr>,
#> #   `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>,
#> #   `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,
#> #   Carbapenemase <lgl>, `MRSA screening test` <lgl>, …