A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo().

microorganisms.old

Format

A data.frame with 12,708 observations and 4 variables:

  • fullname
    Old full taxonomic name of the microorganism

  • fullname_new
    New full taxonomic name of the microorganism

  • ref
    Author(s) and year of concerning scientific publication

  • prevalence
    Prevalence of the microorganism, see as.mo()

Source

Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).

Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786

Catalogue of Life


This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.

Click here for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with catalogue_of_life_version().

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

See also