⚠️There's a newer version (0.10.0) of this package.Take me there.

taxize (version 0.0.6)

Taxonomic information from around the web.

Description

Taxonomic information from around the web.

Copy Link

Version

Install

install.packages('taxize')

Monthly Downloads

5,426

Version

0.0.6

License

CC0

Maintainer

Scott Chamberlain

Last Published

August 1st, 2013

Functions in taxize (0.0.6)

eol_dataobjects

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

getdatedatafromtsn

Get date data from tsn

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.

eol_ping

Ping EOL API to see if it's working.

getlastchangedate

Provides the date the ITIS database was last updated.

getsynonymnamesfromtsn

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

getcurrencyfromtsn

Get currency from tsn

gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)

gni_details

Search for taxonomic name details using the Global Names Index.

getcoveragefromtsn

Get coverge from tsn

apg_orders

Lookup-table for APGIII order names

tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.

getacceptednamesfromtsn

Get accepted names from tsn

getcommonnamesfromtsn

Get common names from tsn

getjurisdictionoriginvalues

Get jurisdiction origin values

gettaxonomicusagefromtsn

Returns the usage information for the TSN.

getkingdomnamefromtsn

Get kingdom names from tsn

apg_families

Lookup-table for APGIII family names

iucn_summary

Get a summary from the IUCN Red List.

getkey

Function to get API key.

col_children

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

rank_ref

Lookup-table for IDs of taxonomic ranks

getcredibilityratings

Get possible credibility ratings

ubio_namebank

Search uBio namebank.

get_tsn

Get the TSN code for a search term.

tp_summary

Return summary data a taxon name with a given id.

gnr_datasources

Get data sources for the Global Names Resolver.

searchforanymatch

Search for any match

itis_acceptname

Retrieve accepted TSN (with accepted name).

gethierarchydownfromtsn

Get hierarchy down from tsn

apg_lookup

Lookup in the APGII taxonomy and replace family names.

taxize-package

Taxnomic search and phylogeny retrieval.

gethierarchyupfromtsn

Get hierarchy up from tsn

eol_pages

Search for pages in EOL database using a taxonconceptID.

getscientificnamefromtsn

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

eol_search

Search for terms in EOL database.

gettsnfromlsid

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

gisd_isinvasive

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

searchforanymatchpaged

Search for any matched page

get_genes

Retrieve gene sequences from NCBI by accession number.

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

getgeographicvalues

Get all possible geographic values

getitistermsfromcommonname

Get itis terms from common names

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

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.

get_seqs

Retrieve nucleotide sequences from NCBI.

tp_namedistributions

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

getcredibilityratingfromtsn

Get credibility rating from tsn

getjurisdictionvalues

Get possible jurisdiction values

tax_agg

Aggregate species data to given taxonomic rank

capwords

Capitalize the first letter of a character string.

classification

Retrieve the taxonomic hierarchy for a given taxon ID.

getothersourcesfromtsn

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

getexpertsfromtsn

Get expert information for the TSN.

col_downstream

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

itis_downstream

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

col_classification

Search Catalogue of Life for taxonomic classifications.

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

getfullrecordfromtsn

Get full record from TSN.

iucn_getname

Get any matching IUCN species names

getranknames

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

get_uid

Get the UID codes from NCBI for species names.

plantminer

Search for taxonomy data from Plantminer.com

getanymatchcount

Get any match count.

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

getunacceptabilityreasonfromtsn

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

tp_synonyms

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.

iucn_status

Extractor functions for iucn-class.

itis_phymat_format

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

searchbycommonnameendswith

Search for tsn by common name ending with

getfullhierarchyfromtsn

Get full hierarchy from tsn

phylomatic_tree

Format tree string, submit to Phylomatic, get newick tree.

rankagg

Aggregate data by given taxonomic rank

getlsidfromtsn

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

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

getvernacularlanguages

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

tpl_get

Get The Plant List csv files.

tnrs

Search the Phylotastic Taxonomic Name Resolution Service.

getkingdomnames

Get all possible kingdom names

tp_namereferences

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

searchbycommonname

Search for tsn by common name

eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.

getcoremetadatafromtsn

Get core metadata from tsn

itis_name

Get taxonomic names for a given taxonomic name query.

tax_rank

Get rank for a given taxonomic name.

gni_parse

Parse scientific names using EOL's name parser.

gnr_resolve

Resolve names using Global Names Resolver.

getdescription

Get description of the ITIS service

getreviewyearfromtsn

Returns the review year for the TSN.

itis_taxrank

Retrieve taxonomic rank name from given TSN.

getcommentdetailfromtsn

Get comment detail from TSN

getitistermsfromscientificname

Get itis terms from scientific names

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

gni_search

Search for taxonomic names using the Global Names Index.

searchbyscientificname

Search by scientific name

tp_acceptednames

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

get_genes_avail

Retrieve gene sequences available for a species from NCBI.

tax_name

Get taxonomic names for a given rank.

searchbycommonnamebeginswith

Search for tsn by common name beginning with