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Data Set with 2 000 Example Isolates

Source: R/data.R
example_isolates.Rd

A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website.

Usage

example_isolates

Format

A tibble with 2 000 observations and 46 variables:

  • date
    Date of receipt at the laboratory

  • patient
    ID of the patient

  • age
    Age of the patient

  • gender
    Gender of the patient, either "F" or "M"

  • ward
    Ward type where the patient was admitted, either "Clinical", "ICU", or "Outpatient"

  • mo
    ID of microorganism created with as.mo(), see also the microorganisms data set

  • PEN:RIF
    40 different antimicrobials with class sir (see as.sir()); these column names occur in the antimicrobials data set and can be translated with set_ab_names() or ab_name()

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

example_isolates
#> # A tibble: 2,000 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI   R     NA    NA    NA 
#>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI   R     NA    NA    NA 
#>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
#>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
#>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
#>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
#>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS   R     NA    S     R  
#>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS   R     NA    S     R  
#>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
#> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR   R     NA    S     NA 
#> # ℹ 1,990 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …