A small test taxonomy file for package tests. This dataset was built by filtering the taxonomy data from the three test datasets, beesFlagged, beesRaw, bees3sp.
Usage
data("testTaxonomy", package = "BeeBDC")Format
An object of class "tibble"
- 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.
References
This dataset is a subset of the beesTaxonomy file described in: 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
Examples
beesRaw <- BeeBDC::testTaxonomy
head(testTaxonomy)
#> # A tibble: 6 × 24
#> flags taxonomic_status source accid id kingdom phylum class order family
#> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
#> 1 NA accepted Discover… 0 2288 Animal… Arthr… Inse… Hyme… Andre…
#> 2 NA accepted Discover… 0 4305 Animal… Arthr… Inse… Hyme… Andre…
#> 3 NA accepted Discover… 0 4765 Animal… Arthr… Inse… Hyme… Andre…
#> 4 NA accepted Discover… 0 4783 Animal… Arthr… Inse… Hyme… Andre…
#> 5 NA accepted Discover… 0 5059 Animal… Arthr… Inse… Hyme… Andre…
#> 6 NA accepted Discover… 0 5264 Animal… Arthr… Inse… Hyme… Andre…
#> # ℹ 14 more variables: subfamily <chr>, tribe <chr>, subtribe <chr>,
#> # validName <chr>, canonical <chr>, canonical_withFlags <chr>, genus <chr>,
#> # subgenus <chr>, species <chr>, infraspecies <chr>, authorship <chr>,
#> # taxon_rank <chr>, valid <lgl>, notes <chr>