tl {taxalight} | R Documentation |
taxalight query: rapidly look up scientific names from a local database
tl(
x,
provider = getOption("tl_default_provider", "itis"),
version = tl_latest_version(),
dir = tl_dir()
)
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 |
version |
version of the authority to use (e.g. four-digit year) |
dir |
storage location for the LMDB databases |
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]
.
a data.frame in Darwin Core format with rows matching the acceptedNameUsageID or scientificName requested.
# 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")