taxizedb 0.2.2
BUG FIXES
taxizedb 0.2.0
NEW FEATURES
- gains 3 new data sources: NCBI taxonomy, World Flora Online, Wikidata (#18) (#49) (#37)
- gains ports of
taxize functions to taxizedb (NCBI & ITIS supported): children, classification, downstream. beware when both taxize and taxizedb loaded in the same R session to namespace calls to these three functions (#19) (#25) (#44) (#48)
- gains mapping functions:
name2taxid (scientific or common name to taxonomy ID); taxid2name (taxonomy ID to scientific name); taxid2rank (taxonomy ID to rank) (#41) (#42)
- intro vignette added (#17)
- GBIF and COL data sources are not updated daily in the repos https://github.com/ropenscilabs/gbif-backbone-sql and https://github.com/ropenscilabs/col-sql/ via GithHub Actions. See those repos for details (#26)
- update package level manual file (
?taxizedb-package) with details on each data source, their update schedules, and examples
- all data sources now use SQLite as the database storage engine. passwords/ports/usernames/etc are no longer needed! note that some
db_download* functions download already created SQLite databases, whereas for other data sources the database is built locally on your machine from other data formats downloaded (see also #36, #46)
- a copy of the taxonomic ranks information from taxize package was ported over for internal use to be able to make
downstream() work for most data sources
MINOR IMPROVEMENTS
- remove check for whether SQLite is installed (#5 #29)
- all
src_* functions now only have two paramters: path and .... where path by default figures out the path for you using the function db_path(), and ... allows the user to pass on parameters to DBI::dbConnect
DEFUNCT
db_load() is now defunct. Now just use db_download* then src* for your data source (see also #43)
taxizedb 0.1.4
BUG FIXES
- Fixes to SQL database connection functions for changes in
dplyr, which now requires dbplyr package - also DBI now imported (#16)
taxizedb 0.1.0
NEW FEATURES