Function reference • taxize

taxize

taxize-package taxize: Taxonomic Information from Around the Web

taxize-defunct defunct: Defunct functions in taxize

taxize_cite(): Get citations and licenses for data sources used in taxize

taxize-params: taxize parameters

taxize_options(): taxize options

Authentication

taxize-authentication authentication: taxize authentication

getkey(): Function to get API key.

use_tropicos() use_entrez() use_iucn(): Helpers to set up authentication for the different providers.

High level functions

Functions that work across sources

children(): Retrieve immediate children taxa for a given taxon name or ID.

classification() cbind(<classification>) rbind(<classification>) cbind(<classification_ids>) rbind(<classification_ids>): Retrieve the taxonomic hierarchy for a given taxon ID.

downstream(): Retrieve the downstream taxa for a given taxon name or ID.

upstream(): Retrieve the upstream taxa for a given taxon name or ID.

comm2sci(): Get scientific names from common names.

sci2comm(): Get common names from scientific names.

id2name(): Taxonomic IDs to taxonomic names

lowest_common(): Retrieve the lowest common taxon and rank for a given taxon name or ID

resolve(): Resolve names from different data sources

synonyms() synonyms_df(): Retrieve synonyms from various sources given input taxonomic names or identifiers

tax_name(): Get taxonomic names for a given rank

tax_rank(): Get rank for a given taxonomic name.

Ping

col_ping() eol_ping() itis_ping() ncbi_ping() tropicos_ping() nbn_ping() gbif_ping() bold_ping() ipni_ping() vascan_ping() fg_ping(): Ping an API used in taxize to see if it's working.

status_codes(): Get HTTP status codes

Get taxon identifiers

get_id_details: Details on get_*() functions

taxon_last() taxon_clear(): Last taxon state object from a get_* function call

get_boldid() as.boldid() as.data.frame(<boldid>) get_boldid_(): Get the BOLD (Barcode of Life) code for a search term.

get_eolid() as.eolid() as.data.frame(<eolid>) get_eolid_(): Get the EOL ID from Encyclopedia of Life from taxonomic names.

get_gbifid() as.gbifid() as.data.frame(<gbifid>) get_gbifid_(): Get the GBIF backbone taxon ID from taxonomic names.

get_ids() get_ids_(): Retrieve taxonomic identifiers for a given taxon name.

get_iucn() as.iucn() as.data.frame(<iucn>): Get a IUCN Redlist taxon

get_natservid() as.natservid() as.data.frame(<natservid>) get_natservid_(): Get NatureServe taxonomic ID for a taxon name

get_nbnid() as.nbnid() as.data.frame(<nbnid>) get_nbnid_(): Get the UK National Biodiversity Network ID from taxonomic names.

get_pow() as.pow() as.data.frame(<pow>) get_pow_(): Get Kew's Plants of the World code for a taxon

get_tolid() as.tolid() as.data.frame(<tolid>) get_tolid_(): Get the OTT id for a search term

get_tpsid() as.tpsid() as.data.frame(<tpsid>) get_tpsid_(): Get the NameID codes from Tropicos for taxonomic names.

get_tsn() as.tsn() as.data.frame(<tsn>) get_tsn_(): Get the TSN code for a search term.

get_uid() as.uid() as.data.frame(<uid>) get_uid_(): Get the UID codes from NCBI for taxonomic names.

get_wiki() as.wiki() as.data.frame(<wiki>) get_wiki_(): Get the page name for a Wiki taxon

get_wormsid() as.wormsid() as.data.frame(<wormsid>) get_wormsid_(): Get Worms ID for a taxon name

Datasets

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 (WoRMS)

worrms_ranks: WORMS ranks

species_plantarum_binomials: Species names from Species Plantarum

theplantlist: Lookup-table for family, genus, and species names for ThePlantList

Random names

names_list(): Get a random vector of species names.

Name Resolution Services

gni_details(): Search for taxonomic name details using the Global Names Index

gni_search(): Search for taxonomic names using the Global Names Index

gnr_datasources(): Global Names Resolver Data Sources

gnr_resolve(): Resolve names using Global Names Resolver

iplant_resolve(): iPlant name resolution

tol_resolve(): Resolve names using Open Tree of Life (OTL) resolver

Name Parsers

gn_parse(): Parse scientific names using Global Names Parser

gni_parse(): Parse scientific names using EOL's name parser.

gbif_parse(): Parse taxon names using the GBIF name parser.

NCBI Taxonomy

ncbi_children(): Search NCBI for children of a taxon

ncbi_downstream(): Retrieve all taxa names downstream in hierarchy for NCBI

ncbi_get_taxon_summary(): NCBI taxon information from uids

genbank2uid(): Get NCBI taxonomy UID from GenBankID

Catalogue of Life

Global Biodiversity Information Facility

gbif_downstream(): Retrieve all taxonomic names downstream in hierarchy for GBIF

gbif_name_usage(): Lookup details for specific names in all taxonomies in GBIF.

gbif_parse(): Parse taxon names using the GBIF name parser.

scrapenames(): Resolve names using Global Names Recognition and Discovery.

Encyclopedia of Life

eol_dataobjects(): Given the identifier for a data object, return all metadata about the object

eol_pages(): Search for pages in EOL database using a taxonconceptID.

eol_search(): Search for terms in EOL database.

EUBON

eubon_capabilities(): EUBON capabilities

eubon_children(): EUBON children

eubon_hierarchy(): EUBON hierarchy

eubon_search(): EUBON taxonomy search

Index Fungorum

fg_name_search() fg_author_search() fg_epithet_search() fg_name_by_key() fg_name_full_by_lsid() fg_all_updated_names() fg_deprecated_names(): Index Fungorum

Integrated Taxonomic Information Service

itis_acceptname(): Retrieve accepted TSN and name

itis_downstream(): Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.

itis_getrecord(): Get full ITIS record for one or more ITIS TSN's or lsid's.

itis_hierarchy(): ITIS hierarchy

itis_kingdomnames(): Get kingdom names

itis_lsid(): Get TSN from LSID

itis_name(): Get taxonomic names for a given taxonomic name query.

itis_native(): Get jurisdiction data, i.e., native or not native in a region.

itis_refs(): Get references related to a ITIS TSN.

itis_taxrank(): Retrieve taxonomic rank name from given TSN.

itis_terms(): Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.

UK National Biodiversity Network

nbn_classification(): Search UK National Biodiversity Network database for taxonomic classification

nbn_search(): Search UK National Biodiversity Network

nbn_synonyms(): Return all synonyms for a taxon name with a given id from NBN

Tropicos

tp_accnames(): Return all accepted names for a taxon name with a given id.

tp_dist(): Return all distribution records for for a taxon name with a given id.

tp_refs(): Return all reference records for for a taxon name with a given id.

tp_search(): Search Tropicos by scientific name, common name, or Tropicos ID.

tp_summary(): Return summary data a taxon name with a given id.

tp_synonyms(): Return all synonyms for a taxon name with a given id.

The Plant List

tpl_families(): Get The Plant List families.

tpl_get(): Get The Plant List csv files.

tpl_search(): A light wrapper around the taxonstand fxn to call Theplantlist.org database.

Kew’s Plants of the World

pow_lookup(): Lookup taxa in Kew's Plants of the World

pow_search(): Search Kew's Plants of the World

pow_synonyms(): Lookup synonyms in Kew's Plants of the World

IUCN

iucn_getname(): Get any matching IUCN species names

iucn_id(): Get an ID for a IUCN listed taxon

iucn_status(): Extractor functions for iucn-class.

iucn_summary(): Get a summary from the IUCN Red List

Angiosperm Phylogeny Group

apgOrders() apgFamilies(): Get APG names

apg_families: MOBOT family names

apg_lookup(): Lookup in the APGIII taxonomy and replace family names

apg_orders: MOBOT order names

Other data sources

bold_search(): Search Barcode of Life for taxonomic IDs

bold_downstream(): Retrieve all taxa names downstream in hierarchy for BOLD

ion(): ION - Index to Organism Names

ipni_search(): Search for names in the International Plant Names Index (IPNI).

plantminer(): Search for taxonomy data from Plantminer.com

vascan_search(): Search the CANADENSYS Vascan API.

worms_downstream(): Retrieve all taxa names downstream in hierarchy for WORMS

Utilities

class2tree() plot(<classtree>) print(<classtree>): Convert a list of classifications to a tree.

rankagg(): Aggregate data by given taxonomic rank

tax_agg() print(<tax_agg>): Aggregate species data to given taxonomic rank

taxize_capwords(): Capitalize the first letter of a character string.

Defunct methods

taxize-defunct defunct: Defunct functions in taxize

ubio_ping(): uBio ping

tnrs(): Phylotastic Taxonomic Name Resolution Service.

tnrs_sources(): TNRS sources