ropensci/taxizedb: taxizedb v0.2.0

Published August 13, 2020 | Version v0.2.0

Software Open

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)

Files

Name	Size	Download all
ropensci/taxizedb-v0.2.0.zip md5:5c94455f647957a9189f7dd2cb011260	72.5 kB	Preview Download