Package: taxize 0.9.102

Zachary Foster

taxize: Taxonomic Information from Around the Web

Interacts with a suite of web 'APIs' 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.

Authors:Scott Chamberlain [aut], Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd]

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taxize/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize

13.41 score 265 stars 28 packages 1.5k scripts 9.9k downloads 31 mentions 186 exports 120 dependencies

Last updated 3 months agofrom:904866d8e2. Checks:OK: 6 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKAug 21 2024
R-4.5-linuxNOTESep 12 2024
R-4.4-winOKAug 21 2024
R-4.4-macOKAug 21 2024
R-4.3-winOKAug 21 2024
R-4.3-macOKAug 21 2024

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_isinvasivegn_parsegni_detailsgni_parsegni_searchgnr_datasourcesgnr_resolveid2nameioniplant_resolveipni_pingipni_searchitis_acceptnameitis_downstreamitis_getrecorditis_hierarchyitis_kingdomnamesitis_lsiditis_nameitis_nativeitis_pingitis_refsitis_taxrankitis_termsiucn_getnameiucn_idiucn_statusiucn_summaryiucn_summary_idlowest_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:apeaskpassassertthatbackportsbase64encbitbit64boldbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrulcurldata.tabledigestdplyrevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplyphangornpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppreadrrentrezrexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapisassscalessolriumstringistringrsystibbletidyselecttinytextriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

Readme and manuals

Help Manual

Help pageTopics
Taxonomic Information from Around the Webtaxize-package taxize
Get APG namesapg apgFamilies apgOrders
MOBOT family namesapg_families
Lookup in the APGIII taxonomy and replace family namesapg_lookup
MOBOT order namesapg_orders
Retrieve all taxa names downstream in hierarchy for BOLDbold_downstream
Search Barcode of Life for taxonomic IDsbold_search
Retrieve immediate children taxa for a given taxon name or ID.children children.boldid children.default children.ids children.tsn children.uid children.wormsid
Convert a list of classifications to a tree.class2tree plot.classtree print.classtree
Retrieve the taxonomic hierarchy for a given taxon ID.cbind.classification cbind.classification_ids classification classification.boldid classification.default classification.eolid classification.gbifid classification.ids classification.natservid classification.nbnid classification.pow classification.tolid classification.tpsid classification.tsn classification.uid classification.wiki classification.wormsid rbind.classification rbind.classification_ids
Get scientific names from common names.comm2sci comm2sci.default comm2sci.tsn comm2sci.uid
Retrieve the downstream taxa for a given taxon name or ID.downstream downstream.boldid downstream.default downstream.gbifid downstream.ids downstream.tsn downstream.uid downstream.wormsid
Given the identifier for a data object, return all metadata about the objecteol_dataobjects
Search for pages in EOL database using a taxonconceptID.eol_pages
Search for terms in EOL database.eol_search
EUBON capabilitieseubon_capabilities
EUBON childreneubon_children
EUBON hierarchyeubon_hierarchy
EUBON taxonomy searcheubon_search
Index Fungorumfg_all_updated_names fg_author_search fg_deprecated_names fg_epithet_search fg_name_by_key fg_name_full_by_lsid fg_name_search fungorum
Retrieve all taxonomic names downstream in hierarchy for GBIFgbif_downstream
Lookup details for specific names in all taxonomies in GBIF.gbif_name_usage
Parse taxon names using the GBIF name parser.gbif_parse
Get NCBI taxonomy UID from GenBankIDgenbank2uid
Get the BOLD (Barcode of Life) code for a search term.as.boldid as.boldid.boldid as.boldid.character as.boldid.data.frame as.boldid.list as.boldid.numeric as.data.frame.boldid get_boldid get_boldid_
Get the EOL ID from Encyclopedia of Life from taxonomic names.as.data.frame.eolid as.eolid as.eolid.character as.eolid.data.frame as.eolid.eolid as.eolid.list as.eolid.numeric get_eolid get_eolid_
Get the GBIF backbone taxon ID from taxonomic names.as.data.frame.gbifid as.gbifid as.gbifid.character as.gbifid.data.frame as.gbifid.gbifid as.gbifid.list as.gbifid.numeric get_gbifid get_gbifid_
Details on get_*() functionsget_id_details
Retrieve taxonomic identifiers for a given taxon name.get_ids get_ids_
Get a IUCN Redlist taxonas.data.frame.iucn as.iucn as.iucn.character as.iucn.data.frame as.iucn.iucn as.iucn.list as.iucn.numeric get_iucn
Get NatureServe taxonomic ID for a taxon nameas.data.frame.natservid as.natservid as.natservid.character as.natservid.data.frame as.natservid.list as.natservid.natservid as.natservid.numeric get_natservid get_natservid_
Get the UK National Biodiversity Network ID from taxonomic names.as.data.frame.nbnid as.nbnid as.nbnid.character as.nbnid.data.frame as.nbnid.list as.nbnid.nbnid get_nbnid get_nbnid_
Get Kew's Plants of the World code for a taxonas.data.frame.pow as.pow as.pow.character as.pow.data.frame as.pow.list as.pow.pow get_pow get_pow_
Get the OTT id for a search termas.data.frame.tolid as.tolid as.tolid.character as.tolid.data.frame as.tolid.list as.tolid.numeric as.tolid.tolid get_tolid get_tolid_
Get the NameID codes from Tropicos for taxonomic names.as.data.frame.tpsid as.tpsid as.tpsid.character as.tpsid.data.frame as.tpsid.list as.tpsid.numeric as.tpsid.tpsid get_tpsid get_tpsid_
Get the TSN code for a search term.as.data.frame.tsn as.tsn as.tsn.character as.tsn.data.frame as.tsn.list as.tsn.numeric as.tsn.tsn get_tsn get_tsn_
Get the UID codes from NCBI for taxonomic names.as.data.frame.uid as.uid as.uid.character as.uid.data.frame as.uid.list as.uid.numeric as.uid.uid get_uid get_uid_
Get the page name for a Wiki taxonas.data.frame.wiki as.wiki as.wiki.character as.wiki.data.frame as.wiki.list as.wiki.numeric as.wiki.wiki get_wiki get_wiki_
Get Worms ID for a taxon nameas.data.frame.wormsid as.wormsid as.wormsid.character as.wormsid.data.frame as.wormsid.list as.wormsid.numeric as.wormsid.wormsid get_wormsid get_wormsid_
Function to get API key.getkey
Parse scientific names using Global Names Parsergn_parse
Search for taxonomic name details using the Global Names Indexgni_details
Parse scientific names using EOL's name parser.gni_parse
Search for taxonomic names using the Global Names Indexgni_search
Global Names Resolver Data Sourcesgnr_datasources
Resolve names using Global Names Resolvergnr_resolve
Taxonomic IDs to taxonomic namesid2name id2name.boldid id2name.default id2name.gbifid id2name.tolid id2name.tsn id2name.uid id2name.wormsid
ION - Index to Organism Namesion
iPlant name resolutioniplant_resolve
Search for names in the International Plant Names Index (IPNI).ipni_search
Retrieve accepted TSN and nameitis_acceptname
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.itis_downstream
Get full ITIS record for one or more ITIS TSN's or lsid's.itis_getrecord
ITIS hierarchyitis_hierarchy
Get kingdom namesitis_kingdomnames
Get TSN from LSIDitis_lsid
Get taxonomic names for a given taxonomic name query.itis_name
Get jurisdiction data, i.e., native or not native in a region.itis_native
Get references related to a ITIS TSN.itis_refs
Retrieve taxonomic rank name from given TSN.itis_taxrank
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.itis_terms
Get any matching IUCN species namesiucn_getname
Get an ID for a IUCN listed taxoniucn_id
Extractor functions for 'iucn'-class.iucn_status
Get a summary from the IUCN Red Listiucn_summary
Helpers to set up authentication for the different providers.key_helpers use_entrez use_iucn use_tropicos
Retrieve the lowest common taxon and rank for a given taxon name or IDlowest_common lowest_common.default lowest_common.gbifid lowest_common.tolid lowest_common.tsn lowest_common.uid
Get a random vector of species names.names_list
Search UK National Biodiversity Network database for taxonomic classificationnbn_classification
Search UK National Biodiversity Networknbn_search
Return all synonyms for a taxon name with a given id from NBNnbn_synonyms
Search NCBI for children of a taxonncbi_children
Retrieve all taxa names downstream in hierarchy for NCBIncbi_downstream
NCBI taxon information from uidsncbi_get_taxon_summary
Ping an API used in taxize to see if it's working.bold_ping col_ping eol_ping fg_ping gbif_ping ipni_ping itis_ping nbn_ping ncbi_ping ping tropicos_ping vascan_ping
Vector of plant genus names from ThePlantListplantGenusNames
Search for taxonomy data from Plantminer.complantminer
Vector of plant species (genus - specific epithet) names from ThePlantListplantNames
Lookup taxa in Kew's Plants of the Worldpow_lookup
Search Kew's Plants of the Worldpow_search
Lookup synonyms in Kew's Plants of the Worldpow_synonyms
Lookup-table for IDs of taxonomic ranksrank_ref
Lookup-table for IDs of taxonomic ranks (WoRMS)rank_ref_zoo
Aggregate data by given taxonomic rankrankagg
Resolve names from different data sourcesresolve
Get common names from scientific names.sci2comm sci2comm.default sci2comm.iucn sci2comm.tsn sci2comm.uid sci2comm.wormsid
Resolve names using Global Names Recognition and Discovery.scrapenames
Species names from Species Plantarumspecies_plantarum_binomials
Get HTTP status codesstatus_codes
Retrieve synonyms from various sources given input taxonomic names or identifierssynonyms synonyms.default synonyms.ids synonyms.iucn synonyms.nbnid synonyms.pow synonyms.tpsid synonyms.tsn synonyms.wormsid synonyms_df
Aggregate species data to given taxonomic rankprint.tax_agg tax_agg
Get taxonomic names for a given ranktax_name
Get rank for a given taxonomic name.tax_rank
Capitalize the first letter of a character string.taxize_capwords
Get citations and licenses for data sources used in taxizetaxize_cite
taxize optionstaxize_options
taxize authenticationauthentication taxize-authentication
Defunct functions in taxizedefunct taxize-defunct
taxize parameterstaxize-params
Last taxon state object from a get_* function calltaxon-state taxon_clear taxon_last
Lookup-table for family, genus, and species names for ThePlantListtheplantlist
Resolve names using Open Tree of Life (OTL) resolvertol_resolve
Return all accepted names for a taxon name with a given id.tp_accnames
Return all distribution records for for a taxon name with a given id.tp_dist
Return all reference records for for a taxon name with a given id.tp_refs
Search Tropicos by scientific name, common name, or Tropicos ID.tp_search
Return summary data a taxon name with a given id.tp_summary
Return all synonyms for a taxon name with a given id.tp_synonyms
Get The Plant List families.tpl_families
Get The Plant List csv files.tpl_get
A light wrapper around the taxonstand fxn to call Theplantlist.org database.tpl_search
uBio pingubio_ping
Retrieve the upstream taxa for a given taxon name or ID.upstream upstream.default upstream.ids upstream.tsn
Search the CANADENSYS Vascan API.vascan_search
Retrieve all taxa names downstream in hierarchy for WORMSworms_downstream
WORMS ranksworrms_ranks