taxizedb 0.3.2

MINOR IMPROVEMENTS

For certain databases, the 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)

Replaced readr::read_tsv_chunked with vroom::vroom() to avoid memory limitation for checks on macOS. (#89)

TPL is no longer available so 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)
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)

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)

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

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

db_load() is now defunct. Now just use db_download* then src* for your data source (see also #43)

Fixes to SQL database connection functions for changes in dplyr, which now requires dbplyr package - also DBI now imported (#16)

mirror server hosted at Truenetwork, Russian Federation.