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Changelog

Source: NEWS.md

taxadb 0.2.2

  • clean_names now also removes the “spp.” epithet

taxadb 0.2.1

CRAN release: 2023-03-08

  • 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

CRAN release: 2023-02-14

  • 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

CRAN release: 2022-09-14

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

taxadb 0.1.5

CRAN release: 2022-05-03

  • bugfix for upcoming dbplyr release

taxadb 0.1.4

CRAN release: 2022-03-05

  • 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

CRAN release: 2021-04-27

  • more robust testing

taxadb 0.1.2

CRAN release: 2021-03-15

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

taxadb 0.1.1

CRAN release: 2021-02-25

  • 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.