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

Reference

taxize

Authentication

High level functions

Ping

Get taxon identifiers

Datasets

Random names

Name Resolution Services

Name Parsers

NCBI Taxonomy

Catalogue of Life

Global Biodiversity Information Facility

Encyclopedia of Life

EUBON

Index Fungorum

Integrated Taxonomic Information Service

UK National Biodiversity Network

Tropicos

The Plant List

Kew’s Plants of the World

IUCN

Angiosperm Phylogeny Group

Other data sources

Utilities

Defunct methods