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# Data Set with 6 029 Common Microorganism Codes

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

A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with `set_mo_source()`. They will all be searched when using `as.mo()` and consequently all the `mo_*` functions.

## Usage

    microorganisms.codes

## Format

A tibble with 6 029 observations and 2 variables:

- `code`
  Commonly used code of a microorganism. This is a unique identifier.

- `mo`
  ID of the microorganism in the microorganisms data set

## 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.codes
    #> # A tibble: 6,029 × 2
    #>    code  mo
    #>    <chr> <mo>
    #>  1 1011  B_GRAMP
    #>  2 1012  B_GRAMP
    #>  3 1013  B_GRAMN
    #>  4 1014  B_GRAMN
    #>  5 1015  F_YEAST
    #>  6 103   B_ESCHR_COLI
    #>  7 104   B_SLMNL_ENTR_ENTR
    #>  8 1100  B_STRPT
    #>  9 1101  B_STRPT_VIRI
    #> 10 1102  B_STRPT_HAEM
    #> # ℹ 6,019 more rows

    # 'ECO' or 'eco' is the WHONET code for E. coli:
    microorganisms.codes[microorganisms.codes$code == "ECO", ]
    #> # A tibble: 1 × 2
    #>   code  mo
    #>   <chr> <mo>
    #> 1 ECO   B_ESCHR_COLI

    # and therefore, 'eco' will be understood as E. coli in this package:
    mo_info("eco")
    #> $mo
    #> [1] "B_ESCHR_COLI"
    #>
    #> $rank
    #> [1] "species"
    #>
    #> $domain
    #> [1] "Bacteria"
    #>
    #> $kingdom
    #> [1] "Pseudomonadati"
    #>
    #> $phylum
    #> [1] "Pseudomonadota"
    #>
    #> $class
    #> [1] "Gammaproteobacteria"
    #>
    #> $order
    #> [1] "Enterobacterales"
    #>
    #> $family
    #> [1] "Enterobacteriaceae"
    #>
    #> $genus
    #> [1] "Escherichia"
    #>
    #> $species
    #> [1] "coli"
    #>
    #> $subspecies
    #> [1] ""
    #>
    #> $status
    #> [1] "accepted"
    #>
    #> $synonyms
    #> NULL
    #>
    #> $gramstain
    #> [1] "Gram-negative"
    #>
    #> $morphology
    #> [1] "Rods"
    #>
    #> $oxygen_tolerance
    #> [1] "facultative anaerobe"
    #>
    #> $url
    #> [1] "https://lpsn.dsmz.de/species/escherichia-coli"
    #>
    #> $ref
    #> [1] "Castellani et al., 1919"
    #>
    #> $snomed
    #>  [1] "1095001000112106" "715307006"        "737528008"        "416989002"
    #>  [5] "116397003"        "414097009"        "414098004"        "414099007"
    #>  [9] "414100004"        "116395006"        "735270003"        "116396007"
    #> [13] "83285000"         "116394005"        "112283007"        "710886005"
    #> [17] "710887001"        "710888006"        "710889003"        "414132004"
    #> [21] "721892009"        "416812001"        "416740004"        "417216001"
    #> [25] "457541006"        "710253004"        "416530004"        "417189006"
    #> [29] "409800005"        "713925008"        "444771000124108"  "838549008"
    #>
    #> $lpsn
    #> [1] "776057"
    #>
    #> $mycobank
    #> [1] NA
    #>
    #> $gbif
    #> [1] "NT3L7"
    #>
    #> $group_members
    #> character(0)
    #>

    # works for all AMR functions:
    mo_is_intrinsic_resistant("eco", ab = "vancomycin")
    #> [1] TRUE