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taxize (version 0.7.6)

Taxonomic Information from Around the Web

Description

Interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, and getting taxonomic 'hierarchies'.

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Install

install.packages('taxize')

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4,169

Version

0.7.6

License

MIT + file LICENSE

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Repository

https://github.com/ropensci/taxize

Maintainer

Scott Chamberlain

Last Published

May 11th, 2016

Functions in taxize (0.7.6)

children

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

eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.

getitistermsfromscientificname

Get itis terms from scientific names

gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.

apg_lookup

Lookup in the APGIII taxonomy and replace family names

get_nbnid

Get the UK National Biodiversity Network ID from taxonomic names.

apg

Get APG names

getvernacularlanguages

Provides a list of the unique languages used in the vernacular table.

get_colid

Get the Catalogue of Life ID from taxonomic names.

get_ids

Retrieve taxonomic identifiers for a given taxon name.

get_ubioid

Get the uBio id for a search term

fungorum

Index Fungorum

getjurisdictionvalues

Get possible jurisdiction values

searchforanymatchpaged

Search for any matched page

classification

Retrieve the taxonomic hierarchy for a given taxon ID.

comm2sci

Get scientific names from common names.

gbif_downstream

Retrieve all taxa names downstream in hierarchy for GBIF

eol_dataobjects

Given the identifier for a data object, return all metadata about the object

getcredibilityratingfromtsn

Get credibility rating from tsn

genbank2uid

Get NCBI taxonomy UID from GenBankID

get_genes

Retrieve gene sequences from NCBI by accession number.

getrecordfromlsid

Gets the partial ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.

col_search

Search Catalogue of Life for taxonomic IDs

getcoveragefromtsn

Get coverge from tsn

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

col_children

Search Catalogue of Life for for direct children of a particular taxon.

eol_invasive

Search for presence of taxonomic names in EOL invasive species databases.

searchbycommonnamebeginswith

Search for tsn by common name beginning with

gnr_resolve

Resolve names using Global Names Resolver.

getkingdomnamefromtsn

Get kingdom names from tsn

getexpertsfromtsn

Get expert information for the TSN.

gettaxonomicusagefromtsn

Returns the usage information for the TSN.

downstream

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

getanymatchcount

Get any match count.

get_boldid

Get the BOLD (Barcode of Life) code for a search term.

get_tpsid

Get the NameID codes from Tropicos for taxonomic names.

col_downstream

Use Catalogue of Life to get downstream taxa to a given taxonomic level.

eol_search

Search for terms in EOL database.

getreviewyearfromtsn

Returns the review year for the TSN.

nbn_synonyms

Return all synonyms for a taxon name with a given id from NBN

tp_refs

Return all reference records for for a taxon name with a given id.

getfullrecordfromlsid

Returns the full ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.

bold_search

Search Barcode of Life for taxonomic IDs

itis_searchcommon

Searches common name and acts as thin wrapper around searchbycommonnamebeginswith and searchbycommonnameendswith

getjurisdictionoriginvalues

Get jurisdiction origin values

get_genes_avail

Retrieve gene sequences from NCBI by accession number.

get_eolid

Get the EOL ID from Encyclopedia of Life from taxonomic names.

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

get_seqs

Retrieve gene sequences from NCBI by accession number.

tp_synonyms

Return all synonyms for a taxon name with a given id.

getlsidfromtsn

Gets the unique LSID for the TSN, or an empty result if there is no match.

itis_hierarchy

ITIS hierarchy

sci2comm

Get common names from scientific names.

class2tree

Convert list of classifications to a tree.

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.

getitistermsfromcommonname

Get itis terms from common names

gethierarchydownfromtsn

Get hierarchy down from tsn

getcredibilityratings

Get possible credibility ratings

getkey

Function to get API key.

getlastchangedate

Provides the date the ITIS database was last updated.

itis_terms

Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.

searchbycommonnameendswith

Search for tsn by common name ending with

names_list

Get a random vector of species names.

ipni_search

Search for names in the International Plant Names Index (IPNI).

getothersourcesfromtsn

Returns a list of the other sources used for the TSN.

itis_getrecord

Get full ITIS record for one or more ITIS TSN's or lsid's.

iucn_summary

Get a summary from the IUCN Red List

ncbi_search

Search for gene sequences available for taxa from NCBI.

itis-api

Low level functions for working with the ITIS API.

status_codes

Get HTTP status codes

ncbi_children

Search NCBI for children of a taxon

getranknames

Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.

apg_families

MOBOT family names

tpl_families

Get The Plant List families.

ion

ION - Index to Organism Names

getunacceptabilityreasonfromtsn

Returns the unacceptability reason, if any, for the TSN.

nbn_search

Search UK National Biodiversity Network database

col_classification

Search Catalogue of Life for taxonomic classifications.

searchbycommonname

Search for tsn by common name

getcommonnamesfromtsn

Get common names from tsn

getcurrencyfromtsn

Get currency from tsn

phylomatic_format

Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

apg_orders

MOBOT order names

gisd_isinvasive

Check invasive species status for a set of species from GISD database

iucn_id

Get an ID for a IUCN listed taxon

getfullrecordfromtsn

Get full record from TSN.

gethierarchyupfromtsn

Get hierarchy up from tsn

getkingdomnames

Get all possible kingdom names

itis_refs

Get references related to a ITIS TSN.

searchforanymatch

Search for any match

taxize-package

Taxonomic Information from Around the Web

gnr_datasources

Get data sources for the Global Names Resolver.

gni_details

Search for taxonomic name details using the Global Names Index.

ping

Ping an API used in taxize to see if it's working.

plantNames

Vector of plant species (genus - specific epithet) names from ThePlantList

iucn_getname

Get any matching IUCN species names

ubio_classification_search

This function will return ClassificationBankIDs (hierarchiesIDs) that refer to the given NamebankID

phylomatic_tree

Query Phylomatic for a phylogenetic tree.

taxize-defunct

Defunct functions in taxize

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

itis_acceptname

Retrieve accepted TSN (with accepted name).

gettsnfromlsid

Gets the TSN corresponding to the LSID, or an empty result if there is no match.

tnrs_sources

TNRS sources

tax_agg

Aggregate species data to given taxonomic rank

resolve

Resolve names from different data sources

getgeographicvalues

Get all possible geographic values

ncbi_getbyname

Retrieve gene sequences from NCBI by taxon name and gene names.

getcoremetadatafromtsn

Get core metadata from tsn

vascan_search

Search the CANADENSYS Vascan API.

tp_acceptednames

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

theplantlist

Lookup-table for family, genus, and species names for ThePlantList

ubio_search

This function will return NameBankIDs that match given search terms

synonyms

Retrieve synonyms from various sources given input taxonomic names or identifiers.

ubio_classification

uBio classification

ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.

searchbyscientificname

Search by scientific name

tnrs

Phylotastic Taxonomic Name Resolution Service.

ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.

nbn_classification

Search UK National Biodiversity Network database for taxonomic classification

tax_name

Get taxonomic names for a given rank.

plantGenusNames

Vector of plant genus names from ThePlantList

itis_lsid

Get kingdom names

plantminer

Search for taxonomy data from Plantminer.com

getdescription

Get description of the ITIS service

tp_classification

Return all synonyms for a taxon name with a given id.

tpl_search

A light wrapper around the taxonstand fxn to call Theplantlist.org database.

ubio_id

Search uBio by namebank ID.

itis_downstream

Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.

lowest_common

Retrieve the lowest common taxon and rank for a given taxon name or ID

rankagg

Aggregate data by given taxonomic rank

getscientificnamefromtsn

Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.

tp_namereferences

Return all reference records for for a taxon name with a given id.

getsynonymnamesfromtsn

Returns a list of the synonyms (if any) for the TSN.

tp_summary

Return summary data a taxon name with a given id.

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.

gni_search

Search for taxonomic names using the Global Names Index.

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

taxize_capwords

Capitalize the first letter of a character string.

tol_resolve

Resolve names using Open Tree of Life resolver

iucn_status

Extractor functions for iucn-class.

tp_dist

Return all distribution records for for a taxon name with a given id.

tp_search

Search Tropicos by scientific name, common name, or Tropicos ID.

tp_namedistributions

Return all distribution records for for a taxon name with a given id.

eubon

EU BON taxonomy

tp_accnames

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

scrapenames

Resolve names using Global Names Recognition and Discovery.

tpl_get

Get The Plant List csv files.

tax_rank

Get rank for a given taxonomic name.

iplant_resolve

iPlant name resolution

taxize_cite

Get citations and licenses for data sources used in taxize

upstream

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

ncbi_get_taxon_summary

NCBI taxon information from uids

gbif_parse

Parse taxon names using the GBIF name parser.

get_tsn

Get the TSN code for a search term.

get_uid

Get the UID codes from NCBI for taxonomic names.

getdatedatafromtsn

Get date data from tsn

getfullhierarchyfromtsn

Get full hierarchy from tsn

getitisterms

Get itis terms from common names

gettsnbyvernacularlanguage

Get tsn by vernacular language

gni_parse

Parse scientific names using EOL's name parser.

itis_taxrank

Retrieve taxonomic rank name from given TSN.

eol_pages

Search for pages in EOL database using a taxonconceptID.

taxize_ldfast

Replacement function for ldply that should be faster in all cases.

Lookup-table for IDs of taxonomic ranks

getacceptednamesfromtsn

Get accepted names from tsn

getcommentdetailfromtsn

Get comment detail from TSN