R: Taxonomic Information from Around the Web

# Taxonomic Information from Around the Web

## Documentation for package ‘taxize’ version 0.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I L N P R S T U V

taxize-package | 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.colid | Get the Catalogue of Life ID from taxonomic names.
as.colid.character | Get the Catalogue of Life ID from taxonomic names.
as.colid.colid | Get the Catalogue of Life ID from taxonomic names.
as.colid.data.frame | Get the Catalogue of Life ID from taxonomic names.
as.colid.list | Get the Catalogue of Life ID from taxonomic names.
as.data.frame.boldid | Get the BOLD (Barcode of Life) code for a search term.
as.data.frame.colid | Get the Catalogue of Life ID from taxonomic names.
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.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.ubioid | Get the uBio id 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.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.ubioid | Get the uBio id for a search term
as.ubioid.character | Get the uBio id for a search term
as.ubioid.data.frame | Get the uBio id for a search term
as.ubioid.list | Get the uBio id for a search term
as.ubioid.numeric | Get the uBio id for a search term
as.ubioid.ubioid | Get the uBio id 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

## -- B --

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.colid | 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 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.colid | 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.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_children | Search Catalogue of Life for for direct children of a particular taxon.
col_downstream | Use Catalogue of Life to get downstream taxa to a given taxonomic level.
col_ping | Ping an API used in taxize to see if it's working.
col_search | Search Catalogue of Life for taxonomic IDs
comm2sci | 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.colid | 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.

## -- 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 | EUBON taxonomy search
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 taxa 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
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_colid | Get the Catalogue of Life ID from taxonomic names.
get_colid_ | Get the Catalogue of Life ID from taxonomic names.
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_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_ubioid | Get the uBio id for a search term
get_ubioid_ | Get the uBio id 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
gni_details | Search for taxonomic name details using the Global Names Index.
gni_parse | Parse scientific names using EOL's name parser.
gni_search | Search for taxonomic names using the Global Names Index.
gnr_datasources | Get data sources for the Global Names Resolver.
gnr_resolve | Resolve names using Global Names Resolver.

## -- I --

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
iucn_summary_id | Get a summary from the IUCN Red List

## -- L --

lowest_common | Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common.colid | 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 --

phylomatic_format | Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
phylomatic_tree | Query Phylomatic for a phylogenetic tree.
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 list of classifications to a tree.
print.classtree | Convert 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
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 | Resolve names using Global Names Recognition and Discovery.
status_codes | Get HTTP status codes
synonyms | Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms.colid | 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.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-defunct | Defunct functions in taxize
taxize_capwords | Capitalize the first letter of a character string.
taxize_cite | Get citations and licenses for data sources used in taxize
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
tnrs | Phylotastic Taxonomic Name Resolution Service.
tnrs_sources | TNRS sources
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_classification | uBio classification
ubio_classification_search | This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID
ubio_id | Search uBio by namebank ID.
ubio_ping | uBio ping
ubio_search | This function will return NameBankIDs that match given search terms
ubio_synonyms | Search uBio for taxonomic synonyms by hierarchiesID.
upstream | Retrieve the upstream taxa for a given taxon name or ID.
upstream.colid | 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.

## -- V --

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