tl {taxalight}

taxalight query: rapidly look up scientific names from a local database

Description

taxalight query: rapidly look up scientific names from a local database

Usage

tl(
  x,
  provider = getOption("tl_default_provider", "itis"),
  version = tl_latest_version(),
  dir = tl_dir()
)

Arguments

x

character vector of either scientific names or taxonomic identifiers (with prefix). Can mix and match too.

provider

Abbreviation for a known naming provider. Provider data should first be imported with ⁠[tl_create]⁠. Note: setting provider to "itis_test" is for testing purposes only, use "itis" for the full ITIS data. See details

version

version of the authority to use (e.g. four-digit year)

dir

storage location for the LMDB databases

Details

Naming providers currently recognized by taxalight are:

• itis: Integrated Taxonomic Information System, https://www.itis.gov/

• ncbi: National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/taxonomy

• col: Catalogue of Life, http://www.catalogueoflife.org/

• gbif: Global Biodiversity Information Facility, https://www.gbif.org/

• ott: OpenTree Taxonomy: https://github.com/OpenTreeOfLife/reference-taxonomy

• itis_test: a small subset of ITIS, cached locally for testing purposes only.

The default provider is itis, which can be reconfigured by setting tl_default_provider in ⁠[options]⁠.

Value

a data.frame in Darwin Core format with rows matching the acceptedNameUsageID or scientificName requested.

See Also

tl_create

Examples

 # slow initial import
sp <- c("Dendrocygna autumnalis", "Dendrocygna bicolor")
id <- c("ITIS:180092", "ITIS:179913")

## example uses "itis_test" provider for illustration only:
tl(sp, "itis_test")
tl(id, "itis_test")