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:
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://community.r-multiverse.org', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/taxizedb/issues
Pkgdown:https://docs.ropensci.org
itistaxizetaxonomic-databasestaxonomy
Last updated 2 years agofrom:5732f97771 (on v0.3.1). Checks:OK: 1 ERROR: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 13 2024 |
| R-4.5-win | ERROR | Dec 13 2024 |
| R-4.5-linux | ERROR | Dec 13 2024 |
| R-4.4-win | ERROR | Dec 13 2024 |
| R-4.4-mac | ERROR | Dec 13 2024 |
| R-4.3-win | ERROR | Dec 13 2024 |
| R-4.3-mac | ERROR | Dec 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 page | Topics |
|---|---|
| taxizedb | taxizedb-package taxizedb |
| Retrieve immediate descendents of a taxon | children |
| Retrieve the taxonomic hierarchies from local database | classification |
| Download taxonomic databases | db_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 NEEDED | db_load-defunct db_load_col db_load_gbif db_load_itis db_load_ncbi db_load_tpl db_load_wikidata |
| database path | db_path |
| Retrieve all taxa descending from a vector of taxa | downstream |
| Convert species names to taxon IDs | name2taxid |
| Query and get data back into a data.frame | sql_collect |
| src - dplyr src objects | src_col src_gbif src_itis src_ncbi src_taxizedb src_tpl src_wfo src_wikidata |
| Get taxa at specific scientific ranks | taxa_at |
| Convert taxon IDs to scientific names | taxid2name |
| Convert taxon IDs to scientific ranks | taxid2rank |
| Caching | tdb_cache |
