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taxize (version 0.7.4)

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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Version

0.7.4

License

MIT + file LICENSE

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Repository

https://github.com/ropensci/taxize

Maintainer

Scott Chamberlain

Last Published

March 9th, 2016

Functions in taxize (0.7.4)

iucn_getname

Get any matching IUCN species names

downstream

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

get_boldid

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

gni_details

Search for taxonomic name details using the Global Names Index.

genbank2uid

Get NCBI taxonomy UID from GenBankID

tp_summary

Return summary data a taxon name with a given id.

apg_families

MOBOT family names

class2tree

Convert list of classifications to a tree.

get_tpsid

Get the NameID codes from Tropicos for taxonomic names.

getcoremetadatafromtsn

Get core metadata from tsn

apg_orders

MOBOT order names

col_classification

Search Catalogue of Life for taxonomic classifications.

gethierarchydownfromtsn

Get hierarchy down from tsn

getunacceptabilityreasonfromtsn

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

ncbi_search

Search for gene sequences available for taxa from NCBI.

comm2sci

Get scientific names from common names.

eol_invasive

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

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

col_children

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

getlsidfromtsn

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

eol_dataobjects

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

getacceptednamesfromtsn

Get accepted names from tsn

getitistermsfromcommonname

Get itis terms from common names

gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.

getreviewyearfromtsn

Returns the review year for the TSN.

getjurisdictionoriginvalues

Get jurisdiction origin values

gettsnfromlsid

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

sci2comm

Get common names from scientific names.

ipni_search

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

getfullhierarchyfromtsn

Get full hierarchy from tsn

itis_name

Get taxonomic names for a given taxonomic name query.

itis_refs

Get references related to a ITIS TSN.

tnrs

Phylotastic Taxonomic Name Resolution Service.

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

children

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

getgeographicvalues

Get all possible geographic values

getfullrecordfromtsn

Get full record from TSN.

gni_parse

Parse scientific names using EOL's name parser.

col_downstream

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

classification

Retrieve the taxonomic hierarchy for a given taxon ID.

getjurisdictionvalues

Get possible jurisdiction values

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

tp_accnames

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

gnr_resolve

Resolve names using Global Names Resolver.

gnr_datasources

Get data sources for the Global Names Resolver.

getothersourcesfromtsn

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

eol_pages

Search for pages in EOL database using a taxonconceptID.

rankagg

Aggregate data by given taxonomic rank

getcoveragefromtsn

Get coverge from tsn

getsynonymnamesfromtsn

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

getcommonnamesfromtsn

Get common names from tsn

ncbi_getbyname

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

gethierarchyupfromtsn

Get hierarchy up from tsn

getvernacularlanguages

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

itis_terms

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

ion

ION - Index to Organism Names

iplant_resolve

iPlant name resolution

tp_dist

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

itis_acceptname

Retrieve accepted TSN (with accepted name).

get_uid

Get the UID codes from NCBI for taxonomic names.

eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.

plantNames

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

taxize_capwords

Capitalize the first letter of a character string.

theplantlist

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

itis_lsid

Get kingdom names

getkey

Function to get API key.

taxize_ldfast

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

ubio_classification_search

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

phylomatic_format

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

getranknames

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

iucn_id

Get an ID for a IUCN listed taxon

tp_namereferences

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

gbif_parse

Parse taxon names using the GBIF name parser.

eol_search

Search for terms in EOL database.

status_codes

Get HTTP status codes

get_nbnid

Get the UK National Biodiversity Network ID from taxonomic names.

apg

Get APG names

itis_downstream

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

gettsnbyvernacularlanguage

Get tsn by vernacular language

getdescription

Get description of the ITIS service

itis_kingdomnames

Get kingdom names

itis_native

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

searchforanymatchpaged

Search for any matched page

ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.

nbn_classification

Search UK National Biodiversity Network database for taxonomic classification

bold_search

Search Barcode of Life for taxonomic IDs

tnrs_sources

TNRS sources

taxize-package

Taxonomic Information from Around the Web

searchbyscientificname

Search by scientific name

get_genes_avail

Retrieve gene sequences from NCBI by accession number.

get_genes

Retrieve gene sequences from NCBI by accession number.

iucn_summary

Get a summary from the IUCN Red List

gbif_downstream

Retrieve all taxa names downstream in hierarchy for GBIF

Get The Plant List csv files.

get_eolid

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

lowest_common

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

getitisterms

Get itis terms from common names

get_colid

Get the Catalogue of Life ID from taxonomic names.

nbn_search

Search UK National Biodiversity Network database

scrapenames

Resolve names using Global Names Recognition and Discovery.

tax_agg

Aggregate species data to given taxonomic rank

getkingdomnamefromtsn

Get kingdom names from tsn

ubio_id

Search uBio by namebank ID.

ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.

resolve

Resolve names from different data sources

rank_ref

Lookup-table for IDs of taxonomic ranks

eubon

EU BON taxonomy

tp_namedistributions

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

getcurrencyfromtsn

Get currency from tsn

tp_acceptednames

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

tp_synonyms

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

getcommentdetailfromtsn

Get comment detail from TSN

getdatedatafromtsn

Get date data from tsn

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

get_ids

Retrieve taxonomic identifiers for a given taxon name.

getitistermsfromscientificname

Get itis terms from scientific names

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.

getexpertsfromtsn

Get expert information for the TSN.

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

ncbi_get_taxon_summary

NCBI taxon information from uids

itis_hierarchy

ITIS hierarchy

get_seqs

Retrieve gene sequences from NCBI by accession number.

getkingdomnames

Get all possible kingdom names

getscientificnamefromtsn

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

getcredibilityratingfromtsn

Get credibility rating from tsn

names_list

Get a random vector of species names.

gettaxonomicusagefromtsn

Returns the usage information for the TSN.

iucn_status

Extractor functions for iucn-class.

tax_rank

Get rank for a given taxonomic name.

tp_refs

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

vascan_search

Search the CANADENSYS Vascan API.

taxize-defunct

Defunct functions in taxize

plantminer

Search for taxonomy data from Plantminer.com

gni_search

Search for taxonomic names using the Global Names Index.

phylomatic_tree

Query Phylomatic for a phylogenetic tree.

searchbycommonname

Search for tsn by common name

tpl_families

Get The Plant List families.

ncbi_children

Search NCBI for children of a taxon

tp_classification

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

nbn_synonyms

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

tpl_search

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

ubio_search

This function will return NameBankIDs that match given search terms

ping

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

tp_search

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

upstream

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

col_search

Search Catalogue of Life for taxonomic IDs

get_ubioid

Get the uBio id for a search term

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

ubio_ping

uBio ping

get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.

get_tsn

Get the TSN code for a search term.

getcredibilityratings

Get possible credibility ratings

getlastchangedate

Provides the date the ITIS database was last updated.

itis_searchcommon

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

gisd_isinvasive

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

fungorum

Index Fungorum

searchbycommonnameendswith

Search for tsn by common name ending with

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.

itis_getrecord

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

taxize_cite

Get citations and licenses for data sources used in taxize

itis-api

Low level functions for working with the ITIS API.

ubio_classification

uBio classification

plantGenusNames

Vector of plant genus names from ThePlantList

searchbycommonnamebeginswith

Search for tsn by common name beginning with

synonyms

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

tax_name

Get taxonomic names for a given rank.

itis_taxrank

Retrieve taxonomic rank name from given TSN.

apg_lookup

Lookup in the APGIII taxonomy and replace family names