taxize: Taxonomic Information from Around the Web

Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

AuthorScott Chamberlain [aut, cre], Eduard Szoecs [aut], Zachary Foster [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb]
Date of publication2017-01-19 11:17:48
MaintainerScott Chamberlain <myrmecocystus@gmail.com>
LicenseMIT + file LICENSE
Version0.8.4
https://github.com/ropensci/taxize

View on CRAN

Man pages

apg: Get APG names

apg_families: MOBOT family names

apg_lookup: Lookup in the APGIII taxonomy and replace family names

apg_orders: MOBOT order names

bold_search: Search Barcode of Life for taxonomic IDs

children: Retrieve immediate children taxa for a given taxon name or...

class2tree: Convert list of classifications to a tree.

classification: Retrieve the taxonomic hierarchy for a given taxon ID.

col_children: Search Catalogue of Life for for direct children of a...

col_classification-defunct: Search Catalogue of Life for taxonomic classifications.

col_downstream: Use Catalogue of Life to get downstream taxa to a given...

col_search: Search Catalogue of Life for taxonomic IDs

comm2sci: Get scientific names from common names.

downstream: Retrieve the downstream taxa for a given taxon name or ID.

eol_dataobjects: Given the identifier for a data object, return all metadata...

eol_hierarchy-defunct: Retrieve the taxonomic hierarchy from given EOL taxonID.

eol_invasive-defunct: Search for presence of taxonomic names in EOL invasive...

eol_pages: Search for pages in EOL database using a taxonconceptID.

eol_search: Search for terms in EOL database.

eubon: EUBON taxonomy search

eubon_capabilities: EUBON capabilites

eubon_children: EUBON children

eubon_hierarchy: EUBON hierarchy

fungorum: Index Fungorum

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.

genbank2uid: Get NCBI taxonomy UID from GenBankID

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_eolid: Get the EOL ID from Encyclopedia of Life from taxonomic...

get_gbifid: Get the GBIF backbone taxon ID from taxonomic names.

get_genes_avail-defunct: Retrieve gene sequences from NCBI by accession number.

get_genes-defunct: Retrieve gene sequences from NCBI by accession number.

get_ids: Retrieve taxonomic identifiers for a given taxon name.

getkey: Function to get API key.

get_natservid: Get NatureServe taxonomic ID for a taxon name

get_nbnid: Get the UK National Biodiversity Network ID from taxonomic...

get_seqs-defunct: Retrieve gene sequences from NCBI by accession number.

get_tolid: Get the OTT id for a search term

get_tpsid: Get the NameID codes from Tropicos for taxonomic names.

get_tsn: Get the TSN code for a search term.

get_ubioid-defunct: Get the uBio id for a search term

get_uid: Get the UID codes from NCBI for taxonomic names.

get_wormsid: Get Worms ID for a taxon name

gisd_invasive-defunct: Check invasive species status for a set of species from GISD...

gni_details: Search for taxonomic name details using the Global Names...

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.

ion: ION - Index to Organism Names

iplant_resolve: iPlant name resolution

ipni_search: Search for names in the International Plant Names Index...

itis_acceptname: Retrieve accepted TSN and name

itis_downstream: Retrieve all taxa names or TSNs downstream in hierarchy from...

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-deprecated: Get taxonomic names for a given taxonomic name query.

itis_native: Get jurisdiction data, i.e., native or not native in a...

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...

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

lowest_common: Retrieve the lowest common taxon and rank for a given taxon...

names_list: Get a random vector of species names.

nbn_classification: Search UK National Biodiversity Network database for...

nbn_search: Search UK National Biodiversity Network database

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_getbyid-defunct: Retrieve gene sequences from NCBI by accession number.

ncbi_getbyname-defunct: Retrieve gene sequences from NCBI by taxon name and gene...

ncbi_get_taxon_summary: NCBI taxon information from uids

ncbi_search-defunct: Search for gene sequences available for taxa from NCBI.

phylomatic_format-defunct: Get family names to make Phylomatic input object, and output...

phylomatic_tree-defunct: 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...

rankagg: Aggregate data by given taxonomic rank

rank_ref: Lookup-table for IDs of taxonomic ranks

resolve: Resolve names from different data sources

sci2comm: 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...

tax_agg: Aggregate species data to given taxonomic rank

taxize_capwords: Capitalize the first letter of a character string.

taxize_cite: Get citations and licenses for data sources used in taxize

taxize-defunct: Defunct functions in taxize

taxize_ldfast: Replacement function for ldply that should be faster in all...

taxize-package: Taxonomic Information from Around the Web

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...

tnrs: Phylotastic Taxonomic Name Resolution Service.

tnrs_sources: TNRS sources

tol_resolve: Resolve names using Open Tree of Life (OTL) resolver

tp_acceptednames-deprecated: Return all accepted names for a taxon name with a given id.

tp_accnames: Return all accepted names for a taxon name with a given id.

tp_classification-defunct: Return all synonyms for a taxon name with a given id.

tp_dist: Return all distribution records for for a taxon name with a...

tpl_families: Get The Plant List families.

tpl_get: Get The Plant List csv files.

tpl_search-defunct: A light wrapper around the taxonstand fxn to call...

tp_namedistributions-deprecated: Return all distribution records for for a taxon name with a...

tp_namereferences-deprecated: Return all reference records for for a taxon name with a...

tp_refs: Return all reference records for for a taxon name with a...

tp_search: Search Tropicos by scientific name, common name, or Tropicos...

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.

ubio_classification-defunct: uBio classification

ubio_classification_search-defunct: This function will return ClassificationBankIDs...

ubio_id-defunct: Search uBio by namebank ID.

ubio_ping-defunct: uBio ping

ubio_search-defunct: This function will return NameBankIDs that match given search...

ubio_synonyms-defunct: Search uBio for taxonomic synonyms by hierarchiesID.

upstream: Retrieve the upstream taxa for a given taxon name or ID.

vascan_search: Search the CANADENSYS Vascan API.

Files in this package

taxize
taxize/inst
taxize/inst/examples
taxize/inst/examples/species.txt
taxize/inst/CITATION
taxize/inst/ignore
taxize/inst/ignore/rbladj.r
taxize/inst/ignore/taxonclass2.R
taxize/inst/ignore/tests
taxize/inst/ignore/tests/test-ubio_id.R
taxize/inst/ignore/tests/test-ubio_namebank.R
taxize/inst/ignore/tests/test-ubio_synonyms.R
taxize/inst/ignore/tests/test-ubio_classification.R
taxize/inst/ignore/tests/test-ubio_search.R
taxize/inst/ignore/phylomatic_tree2.R
taxize/inst/ignore/taxonclass.R
taxize/inst/ignore/nature_serve.R
taxize/inst/ignore/try_with_timeout.R
taxize/inst/ignore/aou_notes.R
taxize/inst/ignore/taxonid.R
taxize/inst/ignore/phytools_fxns_touse.r
taxize/inst/doc
taxize/inst/doc/taxize_vignette.html
taxize/inst/doc/taxize_vignette.Rmd
taxize/inst/doc/name_cleaning.Rmd
taxize/inst/doc/taxize_infotable.Rmd
taxize/inst/doc/name_cleaning.html
taxize/inst/doc/taxize_infotable.html
taxize/inst/vign
taxize/inst/vign/cache
taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.RData
taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdb
taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.RData
taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdx
taxize/inst/vign/cache/__packages
taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdx
taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdb
taxize/inst/vign/taxize_infotable.md
taxize/inst/vign/taxize_vignette.md
taxize/inst/vign/taxize_vignette.Rmd
taxize/inst/vign/name_cleaning.Rmd
taxize/inst/vign/name_cleaning.md
taxize/inst/vign/taxize_infotable.Rmd
taxize/tests
taxize/tests/testthat
taxize/tests/testthat/test-col_children.R
taxize/tests/testthat/test-iucn_summary.R
taxize/tests/testthat/Rplots.pdf
taxize/tests/testthat/test-gbif_downstream.R
taxize/tests/testthat/test-tp_synonyms.R
taxize/tests/testthat/test-get_natservid.R
taxize/tests/testthat/test-tp_summary.R
taxize/tests/testthat/test-gni_parse.R
taxize/tests/testthat/test-itis_ping.R
taxize/tests/testthat/test-ion.R
taxize/tests/testthat/test-downstream.R
taxize/tests/testthat/test-get_tpsid.R
taxize/tests/testthat/test-tax_agg.R
taxize/tests/testthat/test-tnrs.R
taxize/tests/testthat/test-rankagg.R
taxize/tests/testthat/test-tp_accnames.R
taxize/tests/testthat/test-itis_kingdomnames.R
taxize/tests/testthat/test-fungorum.R
taxize/tests/testthat/test-comm2sci.R
taxize/tests/testthat/test-vascan_search.r
taxize/tests/testthat/test-itis_downstream.R
taxize/tests/testthat/test-eol_search.R
taxize/tests/testthat/test-get_ids.R
taxize/tests/testthat/test-eol_pages.R
taxize/tests/testthat/test-col_downstream.R
taxize/tests/testthat/test-itis_getrecord.R
taxize/tests/testthat/test-tnrs_sources.R
taxize/tests/testthat/test-iucn_getname.R
taxize/tests/testthat/test-eol_ping.R
taxize/tests/testthat/test-plantminer.R
taxize/tests/testthat/test-gnr_resolve.R
taxize/tests/testthat/test-bold_search.R
taxize/tests/testthat/test-eubon.R
taxize/tests/testthat/test-class2tree.R
taxize/tests/testthat/test-tp_search.R
taxize/tests/testthat/test-itis_taxrank.R
taxize/tests/testthat/test-itis_native.R
taxize/tests/testthat/test-get_tsn.R
taxize/tests/testthat/test-eol_dataobjects.R
taxize/tests/testthat/test-itis_terms.R
taxize/tests/testthat/test-tol_resolve.R
taxize/tests/testthat/test-gni_details.R
taxize/tests/testthat/test-gnr_datasources.R
taxize/tests/testthat/test-tax_name.R
taxize/tests/testthat/test-itis_refs.R
taxize/tests/testthat/test-gbif_parse.R
taxize/tests/testthat/test-get_uid.R
taxize/tests/testthat/test-lowest_common.R
taxize/tests/testthat/test-ipni_search.R
taxize/tests/testthat/test-ncbi_get_taxon_summary.R
taxize/tests/testthat/test-itis_lsid.R
taxize/tests/testthat/test-get_eolid.R
taxize/tests/testthat/test-itis_hierarchy.R
taxize/tests/testthat/test-tp_refs.R
taxize/tests/testthat/test-get_gbifid.R
taxize/tests/testthat/test-get_colid.R
taxize/tests/testthat/test-itis_acceptname.R
taxize/tests/testthat/test-children.R
taxize/tests/testthat/test-sci2comm.R
taxize/tests/testthat/test-classification.R
taxize/tests/testthat/test-gni_search.R
taxize/tests/testthat/test-tax_rank.R
taxize/tests/testthat/test-synonyms.R
taxize/tests/testthat/test-col_search.R
taxize/tests/testthat/test-get_wormsid.R
taxize/tests/testthat/test-names_list.R
taxize/tests/testthat/test-iucn_id.R
taxize/tests/testthat/test-apgscraping.R
taxize/tests/testthat/test-ncbi_children.R
taxize/tests/testthat/test-tp_dist.R
taxize/tests/testthat/test-get_boldid.R
taxize/tests/testthat/test-ping.R
taxize/tests/test-all.R
taxize/NAMESPACE
taxize/NEWS.md
taxize/data
taxize/data/rank_ref.RData
taxize/data/plantGenusNames.RData
taxize/data/theplantlist.RData
taxize/data/apg_families.RData
taxize/data/apg_orders.RData
taxize/data/plantNames.RData
taxize/R
taxize/R/eol_utiils.R taxize/R/taxize-package.R taxize/R/gisd_isinvasive.R taxize/R/upstream.R taxize/R/eubon_capabilities.R taxize/R/gbif_name_usage.R taxize/R/itis_refs.R taxize/R/col_search.R taxize/R/ubio_synonyms.R taxize/R/iucn_id.R taxize/R/gni_parse.R taxize/R/get_ubioid.R taxize/R/nbn_search.R taxize/R/itis_getrecord.R taxize/R/apg_lookup.R taxize/R/gni_helpers.R taxize/R/get_ids.R taxize/R/gnr_datasources.R taxize/R/class2tree.R taxize/R/nbn_classification.R taxize/R/children.R taxize/R/phylomatic_tree.R taxize/R/tnrs.R taxize/R/tp_dist.R taxize/R/ubio_search.R taxize/R/taxize_ldfast.R taxize/R/eubon.R taxize/R/synonyms.R taxize/R/itis_native.R taxize/R/phylomatic_format.R taxize/R/resolve.R taxize/R/eol_search.R taxize/R/eol_dataobjects.R taxize/R/tol_resolve.R taxize/R/ping.R
taxize/R/tpl_families.r
taxize/R/ncbi_getbyid.R taxize/R/plantminer.R taxize/R/get_nbnid.R taxize/R/get_gbifid.R taxize/R/tp_synonyms.R taxize/R/ubio_classification.R taxize/R/ubio_classification_search.R taxize/R/itis_lsid.R taxize/R/gbif_helpers.R taxize/R/rankagg.R taxize/R/apg.R taxize/R/eol_pages.R taxize/R/ipni_search.R taxize/R/sci2comm.R taxize/R/gbif_parse.R taxize/R/ncbi_getbyname.R taxize/R/globals.R taxize/R/get_eolid.R
taxize/R/taxize_capwords.r
taxize/R/get_colid.R taxize/R/col_children.R
taxize/R/tnrs_sources.r
taxize/R/itis_downstream.R taxize/R/ncbi_children.R
taxize/R/names_list.r
taxize/R/downstream.R taxize/R/bold_search.R taxize/R/eubon_children.R
taxize/R/tpl_search.r
taxize/R/lowest_common.R taxize/R/tp_accnames.R
taxize/R/scrapenames.r
taxize/R/itis_terms.R taxize/R/get_uid.R taxize/R/eol_invasive.R taxize/R/get_tpsid.R taxize/R/getkey.R taxize/R/eol_hierarchy.R taxize/R/classification.R taxize/R/ion.R taxize/R/col_classification.R taxize/R/tax_name.R taxize/R/itis_hierarchy.R taxize/R/itis_taxrank.R taxize/R/genbank2uid.R taxize/R/get_natservid.R taxize/R/comm2sci.R taxize/R/status_codes.R taxize/R/tp_refs.R taxize/R/tax_rank.R taxize/R/iucn_summary.R taxize/R/fungorum.R
taxize/R/tpl_get.r
taxize/R/gnr_resolve.R taxize/R/iucn_getname.R taxize/R/get_boldid.R taxize/R/rename.R taxize/R/gni_details.R taxize/R/ubio_id.R taxize/R/tp_classification.R taxize/R/itis_name.R taxize/R/gni_search.R taxize/R/tax_agg.R taxize/R/tp_summary.R taxize/R/col_downstream.R taxize/R/eubon_hierarchy.R taxize/R/tp_search.R
taxize/R/vascan_search.r
taxize/R/gbif_downstream.R taxize/R/get_tolid.R taxize/R/nbn_synonyms.R taxize/R/iplant_resolve.R taxize/R/itis_kingdomnames.R taxize/R/zzz.R taxize/R/ncbi_get_taxon_summary.R taxize/R/get_tsn.R taxize/R/ncbi_search.R taxize/R/taxize_cite.R taxize/R/itis_acceptname.R taxize/R/get_wormsid.R
taxize/vignettes
taxize/vignettes/taxize_vignette.Rmd
taxize/vignettes/name_cleaning.Rmd
taxize/vignettes/taxize_infotable.Rmd
taxize/README.md
taxize/MD5
taxize/build
taxize/build/vignette.rds
taxize/DESCRIPTION
taxize/man
taxize/man/tp_refs.Rd taxize/man/iucn_summary.Rd taxize/man/fungorum.Rd taxize/man/tax_agg.Rd taxize/man/col_search.Rd taxize/man/phylomatic_format-defunct.Rd taxize/man/apg.Rd taxize/man/itis_getrecord.Rd taxize/man/ncbi_get_taxon_summary.Rd taxize/man/get_natservid.Rd taxize/man/tp_search.Rd taxize/man/iplant_resolve.Rd taxize/man/sci2comm.Rd taxize/man/children.Rd taxize/man/get_tpsid.Rd taxize/man/tnrs.Rd taxize/man/get_tsn.Rd taxize/man/iucn_getname.Rd taxize/man/iucn_id.Rd taxize/man/ubio_id-defunct.Rd taxize/man/ubio_ping-defunct.Rd taxize/man/taxize-package.Rd taxize/man/gbif_name_usage.Rd taxize/man/nbn_classification.Rd taxize/man/gni_parse.Rd taxize/man/get_ids.Rd taxize/man/nbn_synonyms.Rd taxize/man/tp_dist.Rd taxize/man/get_seqs-defunct.Rd taxize/man/get_ubioid-defunct.Rd taxize/man/eol_dataobjects.Rd taxize/man/ion.Rd taxize/man/itis_terms.Rd taxize/man/eubon_capabilities.Rd taxize/man/gbif_parse.Rd taxize/man/get_boldid.Rd taxize/man/get_nbnid.Rd taxize/man/get_eolid.Rd taxize/man/itis_taxrank.Rd taxize/man/taxize_capwords.Rd taxize/man/apg_orders.Rd taxize/man/vascan_search.Rd taxize/man/eubon_children.Rd taxize/man/col_classification-defunct.Rd taxize/man/tp_accnames.Rd taxize/man/col_children.Rd taxize/man/tp_acceptednames-deprecated.Rd taxize/man/theplantlist.Rd taxize/man/plantminer.Rd taxize/man/apg_families.Rd taxize/man/gnr_datasources.Rd taxize/man/ipni_search.Rd taxize/man/get_genes-defunct.Rd taxize/man/plantGenusNames.Rd taxize/man/gnr_resolve.Rd taxize/man/tp_namedistributions-deprecated.Rd taxize/man/ubio_search-defunct.Rd taxize/man/status_codes.Rd taxize/man/itis_lsid.Rd taxize/man/synonyms.Rd taxize/man/comm2sci.Rd taxize/man/phylomatic_tree-defunct.Rd taxize/man/itis_hierarchy.Rd taxize/man/iucn_status.Rd taxize/man/tol_resolve.Rd taxize/man/eubon.Rd taxize/man/rankagg.Rd taxize/man/genbank2uid.Rd taxize/man/tp_classification-defunct.Rd taxize/man/eol_search.Rd taxize/man/getkey.Rd taxize/man/tpl_families.Rd taxize/man/gni_search.Rd taxize/man/bold_search.Rd taxize/man/classification.Rd taxize/man/upstream.Rd taxize/man/itis_refs.Rd taxize/man/gisd_invasive-defunct.Rd taxize/man/ncbi_children.Rd taxize/man/tpl_search-defunct.Rd taxize/man/eubon_hierarchy.Rd taxize/man/nbn_search.Rd taxize/man/itis_downstream.Rd taxize/man/tax_name.Rd taxize/man/lowest_common.Rd taxize/man/tax_rank.Rd taxize/man/scrapenames.Rd taxize/man/eol_hierarchy-defunct.Rd taxize/man/tp_namereferences-deprecated.Rd taxize/man/resolve.Rd taxize/man/get_uid.Rd taxize/man/tp_synonyms.Rd taxize/man/get_wormsid.Rd taxize/man/get_gbifid.Rd taxize/man/get_colid.Rd taxize/man/rank_ref.Rd taxize/man/eol_pages.Rd taxize/man/tnrs_sources.Rd taxize/man/class2tree.Rd taxize/man/itis_name-deprecated.Rd taxize/man/taxize_cite.Rd taxize/man/ncbi_getbyid-defunct.Rd taxize/man/apg_lookup.Rd taxize/man/ubio_synonyms-defunct.Rd taxize/man/ncbi_getbyname-defunct.Rd taxize/man/gni_details.Rd taxize/man/itis_acceptname.Rd taxize/man/get_tolid.Rd taxize/man/ubio_classification_search-defunct.Rd taxize/man/itis_native.Rd taxize/man/ubio_classification-defunct.Rd taxize/man/downstream.Rd taxize/man/plantNames.Rd taxize/man/get_genes_avail-defunct.Rd taxize/man/eol_invasive-defunct.Rd taxize/man/ping.Rd taxize/man/taxize-defunct.Rd taxize/man/names_list.Rd taxize/man/gbif_downstream.Rd taxize/man/ncbi_search-defunct.Rd taxize/man/tpl_get.Rd taxize/man/itis_kingdomnames.Rd taxize/man/taxize_ldfast.Rd taxize/man/col_downstream.Rd taxize/man/tp_summary.Rd
taxize/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.