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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)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)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)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)name2taxid
(scientific or
common name to taxonomy ID); taxid2name
(taxonomy ID to
scientific name); taxid2rank
(taxonomy ID to rank) (#41)
(#42)?taxizedb-package
)
with details on each data source, their update schedules, and
examplesdb_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)downstream()
work for most data sourcessrc_*
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
db_load()
is now defunct. Now just use
db_download*
then src*
for your data source
(see also #43)dplyr
, which now requires dbplyr
package -
also DBI
now imported (#16)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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