Taxonomic Information from Around the Web

Documentation for package ‘taxize’ version 0.10.0

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Taxonomic Information from Around the Web

-- A --

apg	Get APG names
apgFamilies	Get APG names
apgOrders	Get APG names
apg_families	MOBOT family names
apg_lookup	Lookup in the APGIII taxonomy and replace family names
apg_orders	MOBOT order names
as.boldid	Get the BOLD (Barcode of Life) code for a search term.
as.boldid.boldid	Get the BOLD (Barcode of Life) code for a search term.
as.boldid.character	Get the BOLD (Barcode of Life) code for a search term.
as.boldid.data.frame	Get the BOLD (Barcode of Life) code for a search term.
as.boldid.list	Get the BOLD (Barcode of Life) code for a search term.
as.boldid.numeric	Get the BOLD (Barcode of Life) code for a search term.
as.data.frame.boldid	Get the BOLD (Barcode of Life) code for a search term.
as.data.frame.eolid	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.data.frame.gbifid	Get the GBIF backbone taxon ID from taxonomic names.
as.data.frame.iucn	Get a IUCN Redlist taxon
as.data.frame.natservid	Get NatureServe taxonomic ID for a taxon name
as.data.frame.nbnid	Get the UK National Biodiversity Network ID from taxonomic names.
as.data.frame.pow	Get Kew's Plants of the World code for a taxon
as.data.frame.tolid	Get the OTT id for a search term
as.data.frame.tpsid	Get the NameID codes from Tropicos for taxonomic names.
as.data.frame.tsn	Get the TSN code for a search term.
as.data.frame.uid	Get the UID codes from NCBI for taxonomic names.
as.data.frame.wiki	Get the page name for a Wiki taxon
as.data.frame.wormsid	Get Worms ID for a taxon name
as.eolid	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.eolid.character	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.eolid.data.frame	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.eolid.eolid	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.eolid.list	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.eolid.numeric	Get the EOL ID from Encyclopedia of Life from taxonomic names.
as.gbifid	Get the GBIF backbone taxon ID from taxonomic names.
as.gbifid.character	Get the GBIF backbone taxon ID from taxonomic names.
as.gbifid.data.frame	Get the GBIF backbone taxon ID from taxonomic names.
as.gbifid.gbifid	Get the GBIF backbone taxon ID from taxonomic names.
as.gbifid.list	Get the GBIF backbone taxon ID from taxonomic names.
as.gbifid.numeric	Get the GBIF backbone taxon ID from taxonomic names.
as.iucn	Get a IUCN Redlist taxon
as.iucn.character	Get a IUCN Redlist taxon
as.iucn.data.frame	Get a IUCN Redlist taxon
as.iucn.iucn	Get a IUCN Redlist taxon
as.iucn.list	Get a IUCN Redlist taxon
as.iucn.numeric	Get a IUCN Redlist taxon
as.natservid	Get NatureServe taxonomic ID for a taxon name
as.natservid.character	Get NatureServe taxonomic ID for a taxon name
as.natservid.data.frame	Get NatureServe taxonomic ID for a taxon name
as.natservid.list	Get NatureServe taxonomic ID for a taxon name
as.natservid.natservid	Get NatureServe taxonomic ID for a taxon name
as.natservid.numeric	Get NatureServe taxonomic ID for a taxon name
as.nbnid	Get the UK National Biodiversity Network ID from taxonomic names.
as.nbnid.character	Get the UK National Biodiversity Network ID from taxonomic names.
as.nbnid.data.frame	Get the UK National Biodiversity Network ID from taxonomic names.
as.nbnid.list	Get the UK National Biodiversity Network ID from taxonomic names.
as.nbnid.nbnid	Get the UK National Biodiversity Network ID from taxonomic names.
as.pow	Get Kew's Plants of the World code for a taxon
as.pow.character	Get Kew's Plants of the World code for a taxon
as.pow.data.frame	Get Kew's Plants of the World code for a taxon
as.pow.list	Get Kew's Plants of the World code for a taxon
as.pow.pow	Get Kew's Plants of the World code for a taxon
as.tolid	Get the OTT id for a search term
as.tolid.character	Get the OTT id for a search term
as.tolid.data.frame	Get the OTT id for a search term
as.tolid.list	Get the OTT id for a search term
as.tolid.numeric	Get the OTT id for a search term
as.tolid.tolid	Get the OTT id for a search term
as.tpsid	Get the NameID codes from Tropicos for taxonomic names.
as.tpsid.character	Get the NameID codes from Tropicos for taxonomic names.
as.tpsid.data.frame	Get the NameID codes from Tropicos for taxonomic names.
as.tpsid.list	Get the NameID codes from Tropicos for taxonomic names.
as.tpsid.numeric	Get the NameID codes from Tropicos for taxonomic names.
as.tpsid.tpsid	Get the NameID codes from Tropicos for taxonomic names.
as.tsn	Get the TSN code for a search term.
as.tsn.character	Get the TSN code for a search term.
as.tsn.data.frame	Get the TSN code for a search term.
as.tsn.list	Get the TSN code for a search term.
as.tsn.numeric	Get the TSN code for a search term.
as.tsn.tsn	Get the TSN code for a search term.
as.uid	Get the UID codes from NCBI for taxonomic names.
as.uid.character	Get the UID codes from NCBI for taxonomic names.
as.uid.data.frame	Get the UID codes from NCBI for taxonomic names.
as.uid.list	Get the UID codes from NCBI for taxonomic names.
as.uid.numeric	Get the UID codes from NCBI for taxonomic names.
as.uid.uid	Get the UID codes from NCBI for taxonomic names.
as.wiki	Get the page name for a Wiki taxon
as.wiki.character	Get the page name for a Wiki taxon
as.wiki.data.frame	Get the page name for a Wiki taxon
as.wiki.list	Get the page name for a Wiki taxon
as.wiki.numeric	Get the page name for a Wiki taxon
as.wiki.wiki	Get the page name for a Wiki taxon
as.wormsid	Get Worms ID for a taxon name
as.wormsid.character	Get Worms ID for a taxon name
as.wormsid.data.frame	Get Worms ID for a taxon name
as.wormsid.list	Get Worms ID for a taxon name
as.wormsid.numeric	Get Worms ID for a taxon name
as.wormsid.wormsid	Get Worms ID for a taxon name
authentication	taxize authentication

-- B --

bold_downstream	Retrieve all taxa names downstream in hierarchy for BOLD
bold_ping	Ping an API used in taxize to see if it's working.
bold_search	Search Barcode of Life for taxonomic IDs

-- C --

cbind.classification	Retrieve the taxonomic hierarchy for a given taxon ID.
cbind.classification_ids	Retrieve the taxonomic hierarchy for a given taxon ID.
children	Retrieve immediate children taxa for a given taxon name or ID.
children.boldid	Retrieve immediate children taxa for a given taxon name or ID.
children.default	Retrieve immediate children taxa for a given taxon name or ID.
children.ids	Retrieve immediate children taxa for a given taxon name or ID.
children.tsn	Retrieve immediate children taxa for a given taxon name or ID.
children.uid	Retrieve immediate children taxa for a given taxon name or ID.
children.wormsid	Retrieve immediate children taxa for a given taxon name or ID.
class2tree	Convert a list of classifications to a tree.
classification	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.boldid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.default	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.eolid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.gbifid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.ids	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.natservid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.nbnid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.pow	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.tolid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.tpsid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.tsn	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.uid	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.wiki	Retrieve the taxonomic hierarchy for a given taxon ID.
classification.wormsid	Retrieve the taxonomic hierarchy for a given taxon ID.
col_ping	Ping an API used in taxize to see if it's working.
comm2sci	Get scientific names from common names.
comm2sci.default	Get scientific names from common names.
comm2sci.tsn	Get scientific names from common names.
comm2sci.uid	Get scientific names from common names.

-- D --

defunct	Defunct functions in taxize
downstream	Retrieve the downstream taxa for a given taxon name or ID.
downstream.boldid	Retrieve the downstream taxa for a given taxon name or ID.
downstream.default	Retrieve the downstream taxa for a given taxon name or ID.
downstream.gbifid	Retrieve the downstream taxa for a given taxon name or ID.
downstream.ids	Retrieve the downstream taxa for a given taxon name or ID.
downstream.tsn	Retrieve the downstream taxa for a given taxon name or ID.
downstream.uid	Retrieve the downstream taxa for a given taxon name or ID.
downstream.wormsid	Retrieve the downstream taxa for a given taxon name or ID.

-- E --

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_ping	Ping an API used in taxize to see if it's working.
eol_search	Search for terms in EOL database.
eubon_capabilities	EUBON capabilities
eubon_children	EUBON children
eubon_hierarchy	EUBON hierarchy
eubon_search	EUBON taxonomy search

-- F --

fg_all_updated_names	Index Fungorum
fg_author_search	Index Fungorum
fg_deprecated_names	Index Fungorum
fg_epithet_search	Index Fungorum
fg_name_by_key	Index Fungorum
fg_name_full_by_lsid	Index Fungorum
fg_name_search	Index Fungorum
fg_ping	Ping an API used in taxize to see if it's working.
fungorum	Index Fungorum

-- G --

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.
gbif_ping	Ping an API used in taxize to see if it's working.
genbank2uid	Get NCBI taxonomy UID from GenBankID
getkey	Function to get API key.
get_boldid	Get the BOLD (Barcode of Life) code for a search term.
get_boldid_	Get the BOLD (Barcode of Life) code for a search term.
get_eolid	Get the EOL ID from Encyclopedia of Life from taxonomic names.
get_eolid_	Get the EOL ID from Encyclopedia of Life from taxonomic names.
get_gbifid	Get the GBIF backbone taxon ID from taxonomic names.
get_gbifid_	Get the GBIF backbone taxon ID from taxonomic names.
get_ids	Retrieve taxonomic identifiers for a given taxon name.
get_ids_	Retrieve taxonomic identifiers for a given taxon name.
get_id_details	Details on get_*() functions
get_iucn	Get a IUCN Redlist taxon
get_natservid	Get NatureServe taxonomic ID for a taxon name
get_natservid_	Get NatureServe taxonomic ID for a taxon name
get_nbnid	Get the UK National Biodiversity Network ID from taxonomic names.
get_nbnid_	Get the UK National Biodiversity Network ID from taxonomic names.
get_pow	Get Kew's Plants of the World code for a taxon
get_pow_	Get Kew's Plants of the World code for a taxon
get_tolid	Get the OTT id for a search term
get_tolid_	Get the OTT id for a search term
get_tpsid	Get the NameID codes from Tropicos for taxonomic names.
get_tpsid_	Get the NameID codes from Tropicos for taxonomic names.
get_tsn	Get the TSN code for a search term.
get_tsn_	Get the TSN code for a search term.
get_uid	Get the UID codes from NCBI for taxonomic names.
get_uid_	Get the UID codes from NCBI for taxonomic names.
get_wiki	Get the page name for a Wiki taxon
get_wiki_	Get the page name for a Wiki taxon
get_wormsid	Get Worms ID for a taxon name
get_wormsid_	Get Worms ID for a taxon name
gna_data_sources	Get metadata about GNA data sources
gna_parse	Parse scientific names using Global Names Parser
gna_search	Search for taxonomic names using the Global Names Architecture
gna_verifier	Verify a list of scientific names against biodiversity data-sources.
gni_details	Search for taxonomic name details using the Global Names Index
gnr_datasources	Global Names Resolver Data Sources
gnr_resolve	Resolve names using Global Names Resolver

-- I --

id2name	Taxonomic IDs to taxonomic names
id2name.boldid	Taxonomic IDs to taxonomic names
id2name.default	Taxonomic IDs to taxonomic names
id2name.gbifid	Taxonomic IDs to taxonomic names
id2name.tolid	Taxonomic IDs to taxonomic names
id2name.tsn	Taxonomic IDs to taxonomic names
id2name.uid	Taxonomic IDs to taxonomic names
id2name.wormsid	Taxonomic IDs to taxonomic names
ion	ION - Index to Organism Names
iplant_resolve	iPlant name resolution
ipni_ping	Ping an API used in taxize to see if it's working.
ipni_search	Search for names in the International Plant Names Index (IPNI).
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_ping	Ping an API used in taxize to see if it's working.
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.
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

-- K --

key_helpers

Helpers to set up authentication for the different providers.

-- L --

lowest_common	Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.default	Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.gbifid	Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.tolid	Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.tsn	Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.uid	Retrieve the lowest common taxon and rank for a given taxon name or ID

-- N --

names_list	Get a random vector of species names.
nbn_classification	Search UK National Biodiversity Network database for taxonomic classification
nbn_ping	Ping an API used in taxize to see if it's working.
nbn_search	Search UK National Biodiversity Network
nbn_synonyms	Return all synonyms for a taxon name with a given id from NBN
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
ncbi_ping	Ping an API used in taxize to see if it's working.

-- P --

ping	Ping an API used in taxize to see if it's working.
plantGenusNames	Vector of plant genus names from ThePlantList
plantminer	Search for taxonomy data from Plantminer.com
plantNames	Vector of plant species (genus - specific epithet) names from ThePlantList
plot.classtree	Convert a list of classifications to a tree.
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
print.classtree	Convert a list of classifications to a tree.
print.tax_agg	Aggregate species data to given taxonomic rank

-- R --

rankagg	Aggregate data by given taxonomic rank
rank_ref	Lookup-table for IDs of taxonomic ranks
rank_ref_zoo	Lookup-table for IDs of taxonomic ranks (WoRMS)
rbind.classification	Retrieve the taxonomic hierarchy for a given taxon ID.
rbind.classification_ids	Retrieve the taxonomic hierarchy for a given taxon ID.
resolve	Resolve names from different data sources

-- S --

sci2comm	Get common names from scientific names.
sci2comm.default	Get common names from scientific names.
sci2comm.iucn	Get common names from scientific names.
sci2comm.tsn	Get common names from scientific names.
sci2comm.uid	Get common names from scientific names.
sci2comm.wormsid	Get common names from scientific names.
scrapenames	Find taxon names using Global Names Recognition and Discovery
species_plantarum_binomials	Species names from Species Plantarum
status_codes	Get HTTP status codes
synonyms	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.default	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.ids	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.iucn	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.nbnid	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.pow	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.tpsid	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.tsn	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.wormsid	Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms_df	Retrieve synonyms from various sources given input taxonomic names or identifiers

-- T --

taxize	Taxonomic Information from Around the Web
taxize-authentication	taxize authentication
taxize-defunct	Defunct functions in taxize
taxize-params	taxize parameters
taxize_capwords	Capitalize the first letter of a character string.
taxize_cite	Get citations and licenses for data sources used in taxize
taxize_options	taxize options
taxon-state	Last taxon state object from a get_* function call
taxon_clear	Last taxon state object from a get_* function call
taxon_last	Last taxon state object from a get_* function call
tax_agg	Aggregate species data to given taxonomic rank
tax_name	Get taxonomic names for a given rank
tax_rank	Get rank for a given taxonomic name.
theplantlist	Lookup-table for family, genus, and species names for ThePlantList
tol_resolve	Resolve names using Open Tree of Life (OTL) resolver
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.
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.
tropicos_ping	Ping an API used in taxize to see if it's working.

-- U --

ubio_ping	uBio ping
upstream	Retrieve the upstream taxa for a given taxon name or ID.
upstream.default	Retrieve the upstream taxa for a given taxon name or ID.
upstream.ids	Retrieve the upstream taxa for a given taxon name or ID.
upstream.tsn	Retrieve the upstream taxa for a given taxon name or ID.
use_entrez	Helpers to set up authentication for the different providers.
use_iucn	Helpers to set up authentication for the different providers.
use_tropicos	Helpers to set up authentication for the different providers.

-- V --

vascan_ping	Ping an API used in taxize to see if it's working.
vascan_search	Search the CANADENSYS Vascan API.

-- W --

worms_downstream	Retrieve all taxa names downstream in hierarchy for WORMS
worrms_ranks	WORMS ranks