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.
Format
A [tibbletibble::tibble with 5,604 observations and 2 variables:
code
Commonly used code of a microorganismmo
ID of the microorganism in the microorganisms data set
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, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.
Catalogue of Life
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.
Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with catalogue_of_life_version().
Examples
microorganisms.codes
#> # A tibble: 5,604 × 2
#> code mo
#> <chr> <mo>
#> 1 _FAM_A- B_GRAMN
#> 2 _FAM_A+ B_GRAMP
#> 3 _FAM_AC B_GRAMP
#> 4 _FAM_AE B_GRAMN
#> 5 _FAM_AN B_GRAMN
#> 6 _FAM_AO B_GRAMP
#> 7 _FAM_AP UNKNOWN
#> 8 _FAM_AS F_FUNGUS
#> 9 _FAM_AT UNKNOWN
#> 10 _FAM_AV UNKNOWN
#> # … with 5,594 more rows