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
taxizedb_0.3.1.zip(r-4.5)taxizedb_0.3.1.zip(r-4.4)taxizedb_0.3.1.zip(r-4.3)
taxizedb_0.3.1.tgz(r-4.4-any)taxizedb_0.3.1.tgz(r-4.3-any)
taxizedb_0.3.1.tar.gz(r-4.5-noble)taxizedb_0.3.1.tar.gz(r-4.4-noble)
taxizedb_0.3.1.tgz(r-4.4-emscripten)taxizedb_0.3.1.tgz(r-4.3-emscripten)
taxizedb.pdf |taxizedb.html
taxizedb/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://docs.ropensci.org

On CRAN:

itistaxizetaxonomic-databasestaxonomy

5.36 score 30 stars 1 packages 84 scripts 81 downloads 31 exports 43 dependencies

Last updated 2 years agofrom:5732f97771 (on 5732f9777142cd0034b64d5ae8b9aea0605cfaab). Checks:OK: 2 ERROR: 5. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-winERRORNov 13 2024
R-4.5-linuxOKNov 13 2024
R-4.4-winERRORNov 13 2024
R-4.4-macERRORNov 13 2024
R-4.3-winERRORNov 13 2024
R-4.3-macERRORNov 13 2024

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:bitbit64blobcachemclicliprcpp11crayoncurlDBIdbplyrdigestdplyrfansifastmapgenericsgluehmshoardrlifecyclemagrittrmemoisepillarpkgconfigplogrprettyunitsprogresspurrrR6rappdirsreadrrlangRSQLitestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

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