A High-Performance Taxonomic Database Interface

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Documentation for package ‘taxadb’ version 0.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

available_providers	Name providers available for a given version
available_versions	Versions of the taxadb data available
build_col	Rebuild the Catalogue of Life snapshot
build_dir	Where build inputs and outputs are kept
build_fishbase	Rebuild the FishBase or SeaLifeBase snapshot
build_gbif	Rebuild the GBIF backbone snapshot
build_itis	Rebuild the ITIS snapshot
build_ncbi	Rebuild the NCBI Taxonomy snapshot
build_ott	Rebuild the Open Tree Taxonomy snapshot
clean_names	Clean taxonomic names
common_contains	common name starts with
common_starts_with	common name starts with
filter_by	Creates a data frame with column name given by 'by', and values given by the vector 'x', and then uses this table to do a filtering join, joining on the 'by' column to return all rows matching the 'x' values (scientificNames, taxonIDs, etc).
filter_common	Look up taxonomic information by common name
filter_id	Return a taxonomic table matching the requested ids
filter_name	Look up taxonomic information by scientific name
filter_rank	Get all members (descendants) of a given rank level
fuzzy_filter	Match names that start or contain a specified text string
get_ids	get_ids
get_names	get_names
latest_version	The most recent taxadb snapshot version
list_snapshots	List the taxonomic snapshots available from the taxadb repository
name_contains	return all taxa in which scientific name contains the text provided
name_starts_with	scientific name starts with
taxadb_dir	Show the local taxadb directory
taxadb_providers	Providers taxadb can rebuild
taxadb_provider_info	Describe the taxonomic name providers
taxadb_repo	The taxadb data repository
taxadb_uri	Locate the Parquet files backing a taxadb table
taxa_tbl	Return a reference to a given table in the taxadb database
td_build	Rebuild taxadb snapshots from the providers
td_connect	Connect to the taxadb database
td_create	Create a local taxadb database
td_disconnect	Disconnect from the taxadb database.
td_download	Install a local copy of a taxadb snapshot
td_manifest	Describe a built snapshot
td_validate	Check a taxadb table against the taxadb Darwin Core rules
td_write_metadata	Write the metadata published with a snapshot