db_download_*() function
downloaded a preprocessed SQLite database from the cloud, where it was
updated automatically e.g. daily. However, cloud access occasionally
broke. To provide robust functionaility. db_download_*()
was updated to download raw data and convert it to SQLite locally, on
demand, for all databases. (#81)readr::read_tsv_chunked with
vroom::vroom() to avoid memory limitation for checks on
macOS. (#89)db_download_tpl() will
fail. However, if the database was downloaded earlier, it can still be
queried using taxizedb functions. (#87)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::dbConnectdb_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)
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