create a local taxonomic database

create a local taxonomic database

Usage

td_create(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  overwrite = NULL,
  lines = NULL,
  dbdir = NULL,
  db = td_connect()
)

Arguments

provider

a list (character vector) of provider(s) to be included in the database. By default, will install itis. See details for a list of recognized provider. available provider automatically.

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.

overwrite

Should we overwrite existing tables? Default is TRUE. Change to "ask" for interactive interface, or TRUE to force overwrite (i.e. updating a local database upon new release.)

lines

number of lines that can be safely read in to memory at once. Leave at default or increase for faster importing if you have plenty of spare RAM.

dbdir

a location on your computer where the database should be installed. Defaults to user data directory given by [tools::R_user_dir()].

db

connection to a database. By default, taxadb will set up its own fast database connection.

Value

path where database has been installed (invisibly)

Details

Authorities currently recognized by taxadb 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

• iucn: IUCN Red List, https://iucnredlist.org

• itis_test: a small subset of ITIS, cached locally with the package for testing purposes only

Examples

# \donttest{
  # \dontshow{
   ## All examples use a temporary directory
   Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))
   options("taxadb_default_provider"="itis_test")

  # }
  ## Install the ITIS database
  td_create()

  ## force re-install:
  td_create( overwrite = TRUE)
#> Warning: deprecated arguments will be removed  from future releases, see function docs

# }