NEWS.md

In cboettig/taxadb: A High-Performance Local Taxonomic Database Interface

taxadb 0.2.2

• clean_names now also removes the "spp." epithet

taxadb 0.2.1

• substantial speed improvements to all filter_* and get_* functions
• streamline legacy code in filter_ and get_ functions to better leverage duckdb speed increase
• get_names and get_ids now use the same argument name, provider, to specify the naming provider, rather than db (which was used in taxize::get_ids)

taxadb 0.2.0

• taxadb is now backed by partitioned parquet files, cached locally by contentid
• taxadb is now fully-duckdb based. This deprecates the previous 'pluggable' backend with options to use RSQLite or no database backend. Parquet-backed option means that even initial import is much faster, leaving no need to use any of the inferior backend options.
• mutate_db is deprecated, dplyr::mutate() will work as anticipated.
• metadata/prov archive is now based on schema.org rather than DCAT2
• includes 22.12 release for name providers col, itis, ncbi, ott, and gbif. Other database name providers are currently deprecated (though at least iucn should be restored soon).

taxadb 0.1.6

• bugfix for recent duckdb release. (imported table names are now prefixed with "v" to avoid names that start with numbers)

taxadb 0.1.5

• bugfix for upcoming dbplyr release

taxadb 0.1.4

• bugfix in get_ids() when multiple English common names are accepted for the species.
• export taxadb_dir(), making it easier to purge the DB after duckdb upgrades
• All imports must be used
• Improve testing in db=NULL case.
• Require R.utils, to ensure compressed files can be expanded

taxadb 0.1.3

• more robust testing

taxadb 0.1.2

• avoid erroneous messages when installing providers that lack common names.

taxadb 0.1.1

• introduce tl_import to import taxonomic databases [#79]
• make duckdb the default backend
• bugfix to possible ordering problem in get_names [#78]
• Added a NEWS.md file to track changes to the package.

cboettig/taxadb documentation built on April 17, 2024, 6:34 p.m.