Package: taxize 0.10.0
Zachary Foster
taxize: Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
Authors:
taxize_0.10.0.tar.gz
taxize_0.10.0.zip(r-4.5)taxize_0.10.0.zip(r-4.4)taxize_0.10.0.zip(r-4.3)
taxize_0.10.0.tgz(r-4.5-any)taxize_0.10.0.tgz(r-4.4-any)taxize_0.10.0.tgz(r-4.3-any)
taxize_0.10.0.tar.gz(r-4.5-noble)taxize_0.10.0.tar.gz(r-4.4-noble)
taxize_0.10.0.tgz(r-4.4-emscripten)taxize_0.10.0.tgz(r-4.3-emscripten)
taxize.pdf |taxize.html✨
taxize/json (API)
NEWS
| # Install 'taxize' in R: |
| install.packages('taxize', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/taxize/issues50 issues
Pkgdown site:https://docs.ropensci.org
- apg_families - MOBOT family names
- apg_orders - MOBOT order names
- plantGenusNames - Vector of plant genus names from ThePlantList
- plantNames - Vector of plant species (genus - specific epithet) names from ThePlantList
- rank_ref - Lookup-table for IDs of taxonomic ranks
- rank_ref_zoo - Lookup-table for IDs of taxonomic ranks
- species_plantarum_binomials - Species names from Species Plantarum
- theplantlist - Lookup-table for family, genus, and species names for ThePlantList
- worrms_ranks - WORMS ranks
On CRAN:taxize-0.10.0(2025-02-07)
Conda:r-taxize-0.10.0(2025-03-25)
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
Last updated 11 days agofrom:ce5371d6b3 (on master). Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 04 2025 |
| R-4.5-win | OK | Mar 04 2025 |
| R-4.5-mac | OK | Mar 04 2025 |
| R-4.5-linux | OK | Mar 04 2025 |
| R-4.4-win | OK | Mar 04 2025 |
| R-4.4-mac | OK | Mar 04 2025 |
| R-4.4-linux | OK | Mar 04 2025 |
| R-4.3-win | OK | Mar 04 2025 |
| R-4.3-mac | OK | Mar 04 2025 |
Exports:apg_lookupapgFamiliesapgOrdersas.boldidas.colidas.eolidas.gbifidas.iucnas.natservidas.nbnidas.powas.tolidas.tpsidas.tsnas.ubioidas.uidas.wikias.wormsidbold_childrenbold_downstreambold_pingbold_searchchildrenclass2treeclassificationcol_childrencol_classificationcol_downstreamcol_pingcol_searchcomm2scidownstreameol_dataobjectseol_hierarchyeol_invasiveeol_pageseol_pingeol_searcheuboneubon_capabilitieseubon_childreneubon_hierarchyeubon_searchfg_all_updated_namesfg_author_searchfg_deprecated_namesfg_epithet_searchfg_name_by_keyfg_name_full_by_lsidfg_name_searchfg_pinggbif_downstreamgbif_name_usagegbif_parsegbif_pinggenbank2uidget_boldidget_boldid_get_colidget_colid_get_eolidget_eolid_get_gbifidget_gbifid_get_genesget_genes_availget_idsget_ids_get_iucnget_natservidget_natservid_get_nbnidget_nbnid_get_powget_pow_get_seqsget_tolidget_tolid_get_tpsidget_tpsid_get_tsnget_tsn_get_ubioidget_ubioid_get_uidget_uid_get_wikiget_wiki_get_wormsidget_wormsid_getkeygisd_isinvasivegna_data_sourcesgna_parsegna_searchgna_verifiergni_detailsgni_parsegni_seachgnr_datasourcesgnr_resolveid2nameioniplant_resolveipni_pingipni_searchitis_acceptnameitis_downstreamitis_getrecorditis_hierarchyitis_kingdomnamesitis_lsiditis_nameitis_nativeitis_pingitis_refsitis_taxrankitis_termsiucn_getnameiucn_idiucn_statusiucn_summarylowest_commonnames_listnbn_classificationnbn_pingnbn_searchnbn_synonymsncbi_childrenncbi_downstreamncbi_get_taxon_summaryncbi_getbyidncbi_getbynamencbi_pingncbi_searchphylomatic_formatphylomatic_treeplantminerpow_lookuppow_searchpow_synonymsrankaggresolvesci2commscrapenamesstatus_codessynonymssynonyms_dftax_aggtax_nametax_ranktaxize_capwordstaxize_citetaxize_ldfasttaxize_optionstaxon_cleartaxon_lasttnrstnrs_sourcestol_resolvetp_acceptednamestp_accnamestp_classificationtp_disttp_namedistributionstp_namereferencestp_refstp_searchtp_summarytp_synonymstpl_familiestpl_gettpl_searchtropicos_pingubio_classificationubio_classification_searchubio_idubio_pingubio_searchubio_synonymsupstreamuse_entrezuse_eoluse_iucnuse_tropicosvascan_pingvascan_searchworms_downstream
Dependencies:apeaskpassassertthatbackportsbase64encbitbit64bslibcachemcheckmateclicliprclustercolorspacecpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobandjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo
Citation
To cite taxize in publications use at least the first, if not both:
Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research, 2:191. URL: https://f1000research.com/articles/2-191/v2
Scott Chamberlain, Eduard Szoecs, Zachary Foster, Zebulun Arendsee, Carl Boettiger, Karthik Ram, Ignasi Bartomeus, John Baumgartner, James O'Donnell, Jari Oksanen, Bastian Greshake Tzovaras, Philippe Marchand, Vinh Tran, Maëlle Salmon, Gaopeng Li, and Matthias Grenié. (2020) taxize: Taxonomic information from around the web. R package version 0.9.98. https://github.com/ropensci/taxize
Corresponding BibTeX entries:
@Article{,
title = {taxize - taxonomic search and retrieval in R},
journal = {F1000Research},
author = {{Scott Chamberlain} and {Eduard Szocs}},
year = {2013},
url = {https://f1000research.com/articles/2-191/v2},
}
@Manual{,
title = {taxize: Taxonomic information from around the web},
author = {Scott Chamberlain and Eduard Szoecs and Zachary Foster
and Zebulun Arendsee and Carl Boettiger and Karthik Ram and
Ignasi Bartomeus and John Baumgartner and James O'Donnell and
Jari Oksanen and Bastian Greshake Tzovaras and Philippe Marchand
and Vinh Tran and Maëlle Salmon and Gaopeng Li and Matthias
Grenié},
year = {2020},
note = {R package version 0.9.98},
url = {https://github.com/ropensci/taxize},
}
Readme and manuals
taxize
taxize allows users to search over many taxonomic data sources for
species names (scientific and common) and download up and downstream
taxonomic hierarchical information - among other things.
Package documentation: https://docs.ropensci.org/taxize/
Installation
Stable version from CRAN
install.packages("taxize")
Development version from GitHub
Windows users install Rtools first.
install.packages("remotes")
# remotes::install_github("ropensci/taxize")
install.packages("taxize", repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))
library('taxize')
Screencast
Contributing
See our CONTRIBUTING document.
Contributors
Collected via GitHub Issues: honors all contributors in alphabetical order. Code contributors are in bold.
afkoeppel - ahhurlbert - albnd - Alectoria - andzandz11 - anirvan - antagomir - arendsee - ArielGreiner - arw36 - ashenkin - ashiklom - benjaminschwetz - benmarwick - bienflorencia - binkySallly - bomeara - BridgettCollis - bw4sz - cboettig - cdeterman - ChrKoenig - chuckrp - clarson2191 - claudenozeres - cmzambranat - cparsania - daattali - DanielGMead - DarrenObbard - davharris - davidvilanova - diogoprov - dlebauer - dlenz1 - dougwyu - dschlaep - EDiLD - edwbaker - emhart - eregenyi - fdschneider - fgabriel1891 - fischhoff - fmichonneau - fozy81 - gedankenstuecke - gimoya - git-og - glaroc - gpli - gustavobio - hlapp - ibartomeus - Ironholds - jabard89 - jangorecki - jarioksa - jebyrnes - jeroen - jimmyodonnell - joelnitta - johnbaums - jonmcalder - jordancasey - josephwb - jsgosnell - JulietteLgls - jwilk - kamapu - karthik - katrinleinweber - KevCaz - kgturner - kmeverson - Koalha - ljvillanueva - maelle - Markus2015 - matutosi - mcsiple - MikkoVihtakari - millerjef - miriamgrace - mpnelsen - MUSEZOOLVERT - nate-d-olson - nmatzke - npch - ocstringham - p-neves - p-schaefer - padpadpadpad - paternogbc - patperu - pederengelstad - philippi - Phylloxera - pmarchand1 - pozsgaig - pssguy - raredd - rec3141 - Rekyt - RodgerG - rossmounce - sariya - sastoudt - scelmendorf - sckott - SimonGoring - snsheth - snubian - Squiercg - sunray1 - taddallas - tdjames1 - tmkurobe - toczydlowski - tpaulson1 - tpoisot - TrashBirdEcology - trvinh - vijaybarve - wcornwell - willpearse - wpetry - yhg926 - zachary-foster
Road map
Check out our milestones to see what we plan to get done for each version.
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
taxizein R doingcitation(package = 'taxize') - Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
