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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. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read the tutorial on our website.

Usage

example_isolates

Format

A 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()

Reference Data Publicly Available

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.

Examples

head(example_isolates)
#> # A tibble: 6 × 49
#>   date       hospita…¹ ward_…² ward_…³ ward_…⁴   age gender patie…⁵ mo          
#>   <date>     <fct>     <lgl>   <lgl>   <lgl>   <dbl> <chr>  <chr>   <mo>        
#> 1 2002-01-02 D         FALSE   TRUE    FALSE      65 F      A77334  B_ESCHR_COLI
#> 2 2002-01-03 D         FALSE   TRUE    FALSE      65 F      A77334  B_ESCHR_COLI
#> 3 2002-01-07 B         TRUE    FALSE   FALSE      45 F      067927  B_STPHY_EPDR
#> 4 2002-01-07 B         TRUE    FALSE   FALSE      45 F      067927  B_STPHY_EPDR
#> 5 2002-01-13 B         TRUE    FALSE   FALSE      45 F      067927  B_STPHY_EPDR
#> 6 2002-01-13 B         TRUE    FALSE   FALSE      45 F      067927  B_STPHY_EPDR
#> # … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,
#> #   AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,
#> #   FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,
#> #   AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>,
#> #   LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>,
#> #   TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>,
#> #   MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>, and …