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-4.5-any)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://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

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

Pkgdown site:https://docs.ropensci.org

On CRAN:

Conda:

itistaxizetaxonomic-databasestaxonomy

5.86 score 31 stars 1 packages 86 scripts 123 downloads 31 exports 124 dependencies

Last updated 2 months agofrom:83488da50a (on master). Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 06 2025
R-4.5-winNOTEMar 06 2025
R-4.5-macNOTEMar 06 2025
R-4.5-linuxNOTEMar 06 2025
R-4.4-winNOTEMar 06 2025
R-4.4-macNOTEMar 06 2025
R-4.4-linuxNOTEMar 06 2025
R-4.3-winNOTEMar 06 2025
R-4.3-macNOTEMar 06 2025

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:apeaskpassassertthatbackportsbase64encbitbit64blobbslibcachemcheckmateclicliprclustercolorspacecpp11crayoncrulcurldata.tableDBIdbplyrdigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshoardrhtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobandjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplogrplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistRSQLiterstudioapisassscalessolriumstringistringrsystaxizetibbletidyrtidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

Citation

To cite taxizedb in publications use:

Chamberlain S, Arendsee Z, Stirling T (2025). taxizedb: Tools for Working with 'Taxonomic' Databases. doi:10.5281/zenodo.1158055, R package version 0.3.1.

Corresponding BibTeX entry: 

  @Manual{,
    title = {taxizedb: Tools for Working with 'Taxonomic' Databases},
    author = {Scott Chamberlain and Zebulun Arendsee and Tamas
      Stirling},
    year = {2025},
    note = {R package version 0.3.1},
    doi = {10.5281/zenodo.1158055},
  }

Readme and manuals

taxizedb

taxizedb - Tools for Working with Taxonomic Databases

Docs: https://docs.ropensci.org/taxizedb/

taxizedb is an R package for interacting with taxonomic databases. Its functionality can be divided in two parts: 1. You can download the databases to your platform 2. You can query the downloaded databases to retrieve taxonomic information.

This two step approach is different from tools which interact with web services for each query, and has a number of advantages:

  • Once you download a database you can work with it offline
  • Once you download a database querying it is super fast
  • As long as you store your database files all the queries in your analysis will be fully reproducible

Data sources

When you download a database with taxizedb it will automatically convert it to SQLite and then all query functions will interact with this SQLite database. However, not all taxonomic databases are publicly available, or can be converted to SQLite. The following databases are supported:

Get in touch in the issues with any ideas on new data sources.

Data sources - legacy support

The Plant List (TPL) has been replaced by World Flora Online. The website seems to be down so taxizedb can no longer facilitate new downloads. However, already downloaded database files can still be queried using taxizedb functions, for reproducibility.

Package API

This package for each data sources performs the following tasks:

  • Downloaded taxonomic databases db_download_*
  • Create dplyr SQL backend via dbplyr::src_dbi - src_*
  • Query and get data back into a data.frame - sql_collect
  • Manage cached database files - tdb_cache
  • Retrieve immediate descendents of a taxon - children
  • Retrieve the taxonomic hierarchies from local database - classification
  • Retrieve all taxa descending from a vector of taxa - downstream
  • Convert species names to taxon IDs - name2taxid
  • Convert taxon IDs to species names - taxid2name
  • Convert taxon IDs to ranks - taxid2rank

You can use the src connections with dplyr, etc. to do operations downstream. Or use the database connection to do raw SQL queries.

Installation

CRAN version

install.packages("taxizedb")

dev version

# remotes::install_github("ropensci/taxizedb")
install.packages("taxizedb", repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Citation

To cite taxizedb in publications use:

Meta

ropensci

Help Manual

Help pageTopics
taxizedb-package taxizedb-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 databasesdb_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