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# Data Set with 530 Microorganisms In Species Groups

Source: `R/data.R`
`microorganisms.groups.Rd`

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

## Usage

    microorganisms.groups

## Format

A tibble with 530 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()`

## 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.

## See also

`as.mo()` microorganisms

## Examples

    microorganisms.groups
    #> # A tibble: 530 × 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 520 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…