NEWS.md
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)