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Data Set with Previously Accepted Taxonomic Names

Source: R/data.R
microorganisms.old.Rd

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().

Usage

microorganisms.old

Format

A [tibbletibble::tibble with 14,338 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

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().

See also

as.mo() mo_property() microorganisms

Examples

microorganisms.old
#> # A tibble: 14,338 × 4
#>    fullname                   fullname_new                 ref           preva…¹
#>    <chr>                      <chr>                        <chr>           <dbl>
#>  1 Abaphospora petrucciana    Nectria petrucciana          Kirschst, 19…       2
#>  2 Abathostoma stercoris      Echinocyclidium stercoris    Berger in Co…       3
#>  3 Abbottina tannerbankensis  Nonion tannerbankensis       McCulloch, 1…       3
#>  4 Abditodentrix rhomboidalis Tortoplectella rhomboidalis  Millett, 1899       3
#>  5 Abiotrophia adiacens       Granulicatella adiacens      Kawamura et …       2
#>  6 Abiotrophia balaenopterae  Granulicatella balaenopterae Lawson et al…       2
#>  7 Abiotrophia elegans        Granulicatella elegans       Roggenkamp e…       2
#>  8 Absidia blakesleeana       Lichtheimia blakesleeana     Lendn, 1924         3
#>  9 Absidia butleri            Gongronella butleri          Lendn, 1926         3
#> 10 Absidia corymbifera        Lichtheimia corymbifera      Sacc et al.,…       3
#> # … with 14,328 more rows, and abbreviated variable name ¹​prevalence