Package: taxizedb 0.3.1

Tamás Stirling

taxizedb: Tools for Working with 'Taxonomic' Databases

Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.

Authors:Scott Chamberlain [aut], Zebulun Arendsee [aut], Tamás Stirling [ctb, cre]

taxizedb_0.3.1.tar.gz
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taxizedb.pdf |taxizedb.html
taxizedb/json (API)
NEWS

# Install taxizedb in R:
install.packages('taxizedb', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/taxizedb/issues

On CRAN:

itistaxizetaxonomic-databasestaxonomy

31 exports 30 stars 2.80 score 44 dependencies 1 dependents 329 downloads

Last updated 17 days agofrom:bc00b7bff4350f1c33f870da50254cd701167a0f (via master)

Exports:%>%childrenclassificationdb_download_coldb_download_gbifdb_download_itisdb_download_ncbidb_download_tpldb_download_wfodb_download_wikidatadb_load_coldb_load_gbifdb_load_itisdb_load_ncbidb_load_tpldb_load_wikidatadb_pathdownstreamname2taxidsql_collectsrc_colsrc_gbifsrc_itissrc_ncbisrc_tplsrc_wfosrc_wikidatataxa_attaxid2nametaxid2ranktdb_cache

Dependencies:bitbit64blobcachemclicliprcpp11crayoncurldata.tableDBIdbplyrdigestdplyrfansifastmapgenericsgluehmshoardrlifecyclemagrittrmemoisepillarpkgconfigplogrprettyunitsprogresspurrrR6rappdirsreadrrlangRSQLitestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Readme and manuals

Help Manual

Help pageTopics
taxizedbtaxizedb-package taxizedb
Retrieve immediate descendents of a taxonchildren
Retrieve the taxonomic hierarchies from local databaseclassification
Download taxonomic databasesdb_download db_download_col db_download_gbif db_download_itis db_download_ncbi db_download_tpl db_download_wfo db_download_wikidata
Load taxonomic databases - NO LONGER NEEDEDdb_load-defunct db_load_col db_load_gbif db_load_itis db_load_ncbi db_load_tpl db_load_wikidata
database pathdb_path
Retrieve all taxa descending from a vector of taxadownstream
Convert species names to taxon IDsname2taxid
Query and get data back into a data.framesql_collect
src - dplyr src objectssrc_col src_gbif src_itis src_ncbi src_taxizedb src_tpl src_wfo src_wikidata
Get taxa at specific scientific rankstaxa_at
Convert taxon IDs to scientific namestaxid2name
Convert taxon IDs to scientific rankstaxid2rank
Cachingtdb_cache