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