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
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 Plantminer.com
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 April 14, 2018, 11:21 a.m.