tl_import: Import taxonomic database tables

In taxadb: A High-Performance Local Taxonomic Database Interface

Import taxonomic database tables

Description

Downloads the requested taxonomic data tables and return a local path to the data in tsv.gz format. Downloads are cached and identified by content hash so that tl_import will not attempt to download the same file multiple times.

Usage

tl_import(
  provider = getOption("tl_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  prov = prov_cache()
)

Arguments

provider	from which provider should the hierarchy be returned? Default is 'itis', which can also be configured using ⁠options(default_taxadb_provider=...")⁠. See ⁠[td_create]⁠ for a list of recognized providers.
schema	One of "dwc" (for Darwin Core data) or "common" (for the Common names table.)
version	Which version of the taxadb provider database should we use? defaults to latest. See tl_import for details.
prov	Address (URL) to provenance record

Details

tl_import parses a schema.org record to determine the correct version to download. If offline, tl_import will attempt to resolve against it's own provenance cache. Users can also examine / parse the prov JSON-LD file directly to determine the provenance of the data products used.

Value

path(s) to the downloaded files in the cache

taxadb documentation built on March 31, 2023, 10:20 p.m.