beesChecklist {BeeBDC}

Download a country-level checklist of bees from Discover Life

Description

Download the table contains taxonomic and country information for the bees of the world based on data collated on Discover Life. 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").

See beesTaxonomy() for further context.

Usage

beesChecklist(
  URL =
    "https://figshare.com/ndownloader/files/42320598?private_link=bce1f92848c2ced313ee",
  ...
)

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 utils::download.file()

Value

A downloaded beesChecklist.Rda file in the outPath and the same tibble returned to the environment.

**Column details **

validName The valid scientificName as it should occur in the scientificName column.

DiscoverLife_name The full country name as it occurs on Discover Life.

rNaturalEarth_name Country name from rnaturalearth's name_long.

shortName A short version of the country name.

DiscoverLife_ISO The ISO country name as it occurs on Discover Life.

Alpha-2 Alpha-2 from rnaturalearth.

Alpha-3 Alpha-3 from rnaturalearth.

official Official country name = "yes" or only a Discover Life name = "no".

Source A text strign denoting the source or author of the name-country pair.

matchCertainty Quality of the name's match to the Discover Life checklist.

canonical The valid species name without scientificNameAuthority.

canonical_withFlags The validName without the scientificNameAuthority but with Discover Life flags.

family Bee family.

subfamily Bee subfamily.

genus Bee genus.

subgenus Bee subgenus.

infraspecies Bee infraSpecificEpithet.

species Bee specificEpithet.

scientificNameAuthorship Bee scientificNameAuthorship.

taxon_rank Rank of the taxon name.

Notes Discover Life country name notes.

References

This dataset was created using the Discover Life checklist and 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 checklist 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

Examples

## Not run: 
beesChecklist <- BeeBDC::beesChecklist()

## End(Not run)