Man pages for ropensci/taxize
Taxonomic Information from Around the Web

apgGet APG names
apg_familiesMOBOT family names
apg_lookupLookup in the APGIII taxonomy and replace family names
apg_ordersMOBOT order names
bold_searchSearch Barcode of Life for taxonomic IDs
childrenRetrieve immediate children taxa for a given taxon name or...
class2treeConvert a list of classifications to a tree.
classificationRetrieve the taxonomic hierarchy for a given taxon ID.
col_childrenSearch Catalogue of Life for for direct children of a...
col_classification-defunctSearch Catalogue of Life for taxonomic classifications.
col_downstreamUse Catalogue of Life to get downstream taxa to a given...
col_searchSearch Catalogue of Life for taxonomic IDs
comm2sciGet scientific names from common names.
downstreamRetrieve the downstream taxa for a given taxon name or ID.
eol_dataobjectsGiven the identifier for a data object, return all metadata...
eol_hierarchy-defunctRetrieve the taxonomic hierarchy from given EOL taxonID.
eol_invasive-defunctSearch for presence of taxonomic names in EOL invasive...
eol_pagesSearch for pages in EOL database using a taxonconceptID.
eol_searchSearch for terms in EOL database.
eubonEUBON taxonomy search
eubon_capabilitiesEUBON capabilities
eubon_childrenEUBON children
eubon_hierarchyEUBON hierarchy
fungorumIndex Fungorum
gbif_downstreamRetrieve all taxa names downstream in hierarchy for GBIF
gbif_name_usageLookup details for specific names in all taxonomies in GBIF.
gbif_parseParse taxon names using the GBIF name parser.
genbank2uidGet NCBI taxonomy UID from GenBankID
get_boldidGet the BOLD (Barcode of Life) code for a search term.
get_colidGet the Catalogue of Life ID from taxonomic names.
get_eolidGet the EOL ID from Encyclopedia of Life from taxonomic...
get_gbifidGet the GBIF backbone taxon ID from taxonomic names.
get_genes_avail-defunctRetrieve gene sequences from NCBI by accession number.
get_genes-defunctRetrieve gene sequences from NCBI by accession number.
get_id_detailsDetails on 'get_*()' functions
get_idsRetrieve taxonomic identifiers for a given taxon name.
get_iucnGet a IUCN Redlist taxon
getkeyFunction to get API key.
get_natservidGet NatureServe taxonomic ID for a taxon name
get_nbnidGet the UK National Biodiversity Network ID from taxonomic...
get_seqs-defunctRetrieve gene sequences from NCBI by accession number.
get_tolidGet the OTT id for a search term
get_tpsidGet the NameID codes from Tropicos for taxonomic names.
get_tsnGet the TSN code for a search term.
get_ubioid-defunctGet the uBio id for a search term
get_uidGet the UID codes from NCBI for taxonomic names.
get_wikiGet the page name for a Wiki taxon
get_wormsidGet Worms ID for a taxon name
gisd_invasive-defunctCheck invasive species status for a set of species from GISD...
gni_detailsSearch for taxonomic name details using the Global Names...
gni_parseParse scientific names using EOL's name parser.
gni_searchSearch for taxonomic names using the Global Names Index.
gnr_datasourcesGet data sources for the Global Names Resolver.
gnr_resolveResolve names using Global Names Resolver.
ionION - Index to Organism Names
iplant_resolveiPlant name resolution
ipni_searchSearch for names in the International Plant Names Index...
itis_acceptnameRetrieve accepted TSN and name
itis_downstreamRetrieve all taxa names or TSNs downstream in hierarchy from...
itis_getrecordGet full ITIS record for one or more ITIS TSN's or lsid's.
itis_hierarchyITIS hierarchy
itis_kingdomnamesGet kingdom names
itis_lsidGet TSN from LSID
itis_name-deprecatedGet taxonomic names for a given taxonomic name query.
itis_nativeGet jurisdiction data, i.e., native or not native in a...
itis_refsGet references related to a ITIS TSN.
itis_taxrankRetrieve taxonomic rank name from given TSN.
itis_termsGet ITIS terms, i.e., tsn's, authors, common names, and...
iucn_getnameGet any matching IUCN species names
iucn_idGet an ID for a IUCN listed taxon
iucn_statusExtractor functions for 'iucn'-class.
iucn_summaryGet a summary from the IUCN Red List
key_helpersHelpers to set up authentication for the different providers.
limited_printPrint a subset of a character vector
lowest_commonRetrieve the lowest common taxon and rank for a given taxon...
names_listGet a random vector of species names.
nbn_classificationSearch UK National Biodiversity Network database for...
nbn_searchSearch UK National Biodiversity Network
nbn_synonymsReturn all synonyms for a taxon name with a given id from NBN
ncbi_childrenSearch NCBI for children of a taxon
ncbi_downstreamRetrieve all taxa names downstream in hierarchy for NCBI
ncbi_getbyid-defunctRetrieve gene sequences from NCBI by accession number.
ncbi_getbyname-defunctRetrieve gene sequences from NCBI by taxon name and gene...
ncbi_get_taxon_summaryNCBI taxon information from uids
ncbi_search-defunctSearch for gene sequences available for taxa from NCBI.
phylomatic_format-defunctGet family names to make Phylomatic input object, and output...
phylomatic_tree-defunctQuery Phylomatic for a phylogenetic tree.
pingPing an API used in taxize to see if it's working.
plantGenusNamesVector of plant genus names from ThePlantList
plantminerSearch for taxonomy data from
plantNamesVector of plant species (genus - specific epithet) names from...
rankaggAggregate data by given taxonomic rank
rank_refLookup-table for IDs of taxonomic ranks
resolveResolve names from different data sources
sci2commGet common names from scientific names.
scrapenamesResolve names using Global Names Recognition and Discovery.
status_codesGet HTTP status codes
synonymsRetrieve synonyms from various sources given input taxonomic...
tax_aggAggregate species data to given taxonomic rank
taxize_capwordsCapitalize the first letter of a character string.
taxize_citeGet citations and licenses for data sources used in taxize
taxize-defunctDefunct functions in taxize
taxize_ldfastReplacement function for ldply that should be faster in all...
taxize-packageTaxonomic Information from Around the Web
tax_nameGet taxonomic names for a given rank
tax_rankGet rank for a given taxonomic name.
theplantlistLookup-table for family, genus, and species names for...
tnrsPhylotastic Taxonomic Name Resolution Service.
tnrs_sourcesTNRS sources
tol_resolveResolve names using Open Tree of Life (OTL) resolver
tp_acceptednames-deprecatedReturn all accepted names for a taxon name with a given id.
tp_accnamesReturn all accepted names for a taxon name with a given id.
tp_classification-defunctReturn all synonyms for a taxon name with a given id.
tp_distReturn all distribution records for for a taxon name with a...
tpl_familiesGet The Plant List families.
tpl_getGet The Plant List csv files.
tpl_search-defunctA light wrapper around the taxonstand fxn to call...
tp_namedistributions-deprecatedReturn all distribution records for for a taxon name with a...
tp_namereferences-deprecatedReturn all reference records for for a taxon name with a...
tp_refsReturn all reference records for for a taxon name with a...
tp_searchSearch Tropicos by scientific name, common name, or Tropicos...
tp_summaryReturn summary data a taxon name with a given id.
tp_synonymsReturn all synonyms for a taxon name with a given id.
ubio_classification-defunctuBio classification
ubio_classification_search-defunctThis function will return ClassificationBankIDs...
ubio_id-defunctSearch uBio by namebank ID.
ubio_ping-defunctuBio ping
ubio_search-defunctThis function will return NameBankIDs that match given search...
ubio_synonyms-defunctSearch uBio for taxonomic synonyms by hierarchiesID.
upstreamRetrieve the upstream taxa for a given taxon name or ID.
vascan_searchSearch the CANADENSYS Vascan API.
ropensci/taxize documentation built on Oct. 19, 2018, 9:24 p.m.