| beesTaxonomy {BeeBDC} | R Documentation |
Download a nearly complete taxonomy of bees globally
Description
Downloads the taxonomic information for the bees of the world. Source of taxonomy is listed under "source" but are mostly derived from the Discover Life website. The data will be sourced from the BeeBDC article's Figshare.
Note that sometimes the download might not work without restarting R. In this case, you could
alternatively download the dataset from the URL below and then read it in using
base::readRDS("filePath.Rda").
Usage
beesTaxonomy(
URL = "https://open.flinders.edu.au/ndownloader/files/47089969",
...
)
Arguments
URL |
A character vector to the FigShare location of the dataset. The default will be to the most-recent version. |
... |
Extra variables that can be passed to |
Details
Column details
flags Flags or comments about the taxon name.
taxonomic_status Taxonomic status. Values are "accepted" or "synonym"
source Source of the name.
accid The id of the accepted taxon name or "0" if taxonomic_status == accepted.
id The id number for the taxon name.
kingdom The biological kingdom the taxon belongs to. For bees, kingdom == Animalia.
phylum The biological phylum the taxon belongs to. For bees, phylum == Arthropoda.
class The biological class the taxon belongs to. For bees, class == Insecta.
order The biological order the taxon belongs to. For bees, order == Hymenoptera.
family The family of bee which the species belongs to.
subfamily The subfamily of bee which the species belongs to.
tribe The tribe of bee which the species belongs to.
subtribe The subtribe of bee which the species belongs to.
validName The valid scientific name as it should occur in the 'scientificName" column in a Darwin Core file.
canonical The scientificName without the scientificNameAuthority.
canonical_withFlags The scientificName without the scientificNameAuthority and with Discover Life taxonomy flags.
genus The genus the bee species belongs to.
subgenus The subgenus the bee species belongs to.
species The specific epithet for the bee species.
infraspecies The infraspecific epithet for the bee addressed.
authorship The author who described the bee species.
taxon_rank Rank for the bee taxon addressed in the entry.
notes Additional notes about the name/taxon.
Value
A downloaded beesTaxonomy.Rda file in the tempdir() and the same tibble returned to
the environment.
References
This dataset was created using the Discover Life taxonomy. Dataset is from the publication: Dorey, J.B., Fischer, E.E., Chesshire, P.R., Nava-Bolaños, A., O’Reilly, R.L., Bossert, S., Collins, S.M., Lichtenberg, E.M., Tucker, E., Smith-Pardo, A., Falcon-Brindis, A., Guevara, D.A., Ribeiro, B.R., de Pedro, D., Hung, J.K.-L., Parys, K.A., McCabe, L.M., Rogan, M.S., Minckley, R.L., Velzco, S.J.E., Griswold, T., Zarrillo, T.A., Jetz, W., Sica, Y.V., Orr, M.C., Guzman, L.M., Ascher, J., Hughes, A.C. & Cobb, N.S. (2023) A globally synthesised and flagged bee occurrence dataset and cleaning workflow. Scientific Data, 10, 1–17. https://www.doi.org/10.1038/S41597-023-02626-W The taxonomy data are mostly compiled from Discover Life data, www.discoverlife.org: Ascher, J.S. & Pickering, J. (2020) Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila). http://www.discoverlife.org/mp/20q?guide=Apoidea_species
See Also
taxadbToBeeBDC() to download any other taxonomy (of any taxa or of bees)
and harmoniseR() for the
taxon-cleaning function where these taxonomies are implemented. It may also be worth seeing
beesChecklist().
Examples
## Not run:
beesTaxonomy <- BeeBDC::beesTaxonomy()
## End(Not run)