taxalight (version 0.1.3)

tl_create: Create a Lightning Memory-Mapped Database (LMDB) for a given provider

Description

Download raw data and store in a local LMDB database. Importing data is a time-consuming step that needs be run only once per machine and will persist through sessions.

Usage

tl_create(
  provider = getOption("tl_default_provider", "itis"),
  version = tl_latest_version(),
  dir = tl_dir(),
  lines = 100000L
)

Arguments

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

lines

number of lines to read in each chunk.

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].

Examples

# NOT RUN {
## example uses "itis_test" for illustration only:

# }
# NOT RUN {
tl_create("itis_test")
# }
# NOT RUN {
# }