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A data set containing species groups and microbiological complexes, which are used in the clinical breakpoints table.

Usage

microorganisms.groups

Format

A tibble with 521 observations and 4 variables:

  • mo_group
    ID of the species group / microbiological complex

  • mo
    ID of the microorganism belonging in the species group / microbiological complex

  • mo_group_name
    Name of the species group / microbiological complex, as retrieved with mo_name()

  • mo_name
    Name of the microorganism belonging in the species group / microbiological complex, as retrieved with mo_name()

Details

Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

Examples

microorganisms.groups
#> # A tibble: 521 × 4
#>    mo_group       mo           mo_group_name                   mo_name          
#>    <mo>           <mo>         <chr>                           <chr>            
#>  1 B_ACNTB_BMNN-C B_ACNTB_BMNN Acinetobacter baumannii complex Acinetobacter ba…
#>  2 B_ACNTB_BMNN-C B_ACNTB_CLCC Acinetobacter baumannii complex Acinetobacter ca…
#>  3 B_ACNTB_BMNN-C B_ACNTB_LCTC Acinetobacter baumannii complex Acinetobacter di…
#>  4 B_ACNTB_BMNN-C B_ACNTB_NSCM Acinetobacter baumannii complex Acinetobacter no…
#>  5 B_ACNTB_BMNN-C B_ACNTB_PITT Acinetobacter baumannii complex Acinetobacter pi…
#>  6 B_ACNTB_BMNN-C B_ACNTB_SFRT Acinetobacter baumannii complex Acinetobacter se…
#>  7 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex    Bacteroides frag…
#>  8 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex    Bacteroides ovat…
#>  9 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex    Bacteroides thet…
#> 10 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex    Bacteroides vulg…
#> # ℹ 511 more rows

# these are all species in the Bacteroides fragilis group, as per WHONET:
microorganisms.groups[microorganisms.groups$mo_group == "B_BCTRD_FRGL-C", ]
#> # A tibble: 5 × 4
#>   mo_group       mo           mo_group_name                mo_name              
#>   <mo>           <mo>         <chr>                        <chr>                
#> 1 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides fragilis 
#> 2 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovatus   
#> 3 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thetaiot…
#> 4 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex Bacteroides vulgatus 
#> 5 B_BCTRD_FRGL-C B_PRBCT_DSTS Bacteroides fragilis complex Parabacteroides dist…