td_connect: Connect to the taxadb database

In taxadb: A High-Performance Local Taxonomic Database Interface

Connect to the taxadb database

Description

Connect to the taxadb database

Usage

td_connect(dbdir = NULL, driver = NULL, read_only = NULL)

Arguments

dbdir	Path to the database. no longer needed
driver	deprecated, ignored. driver will always be duckdb.
read_only	deprecated, driver is always read-only.

Details

This function provides a default database connection for taxadb. Note that you can use taxadb with any DBI-compatible database connection by passing the connection object directly to taxadb functions using the db argument. td_connect() exists only to provide reasonable automatic defaults based on what is available on your system.

For performance reasons, this function will also cache and restore the existing database connection, making repeated calls to td_connect() much faster and more failsafe than repeated calls to DBI::dbConnect

Value

Returns a DBI connection to the default duckdb database

Examples

## OPTIONAL: you can first set an alternative home location,
## such as a temporary directory:
Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))

## Connect to the database:
db <- td_connect()

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