taxizedb 0.3.0
NEW FEATURES
db_download()
gains new parameter overwrite
(logical): used to state that you want to overwrite an existing database on disk. before this you would have to manually delete an older database file (#34)
- new function added
taxa_at()
for getting taxa at specific scientific ranks. For example, your known taxon is the family Lachnospiraceae with NCBI identifier of 186803. You want information on the phylum which the Lachnospiraceae family is in. This function can do that for you. (#51)
BUG FIXES
- fixed problem in internal function
txdb_rr()
: in older verions of R (e.g., 3.6) we were creating a data.frame in this function without settings stringsAsFactors=FALSE
, resulting in different behavior in R v3 vs. R v4 given the change in stringsAsFactors
behavior in R v4 onward (#54)
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