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taxize (version 0.0.5)

Taxonomic information from around the web.

Description

Taxonomic information from around the web.

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Version

Install

install.packages('taxize')

Monthly Downloads

5,286

Version

0.0.5

License

CC0

Maintainer

Scott Chamberlain

Last Published

February 19th, 2013

Functions in taxize (0.0.5)

getitistermsfromcommonname

Get itis terms from common names

classification

Get taxonomic hierarchy for a given taxon ID.

searchbycommonnamebeginswith

Search for tsn by common name beginning with

getgeographicvalues

Get all possible geographic values

getitistermsfromscientificname

Get itis terms from scientific names

gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)

gnr_resolve

Resolve names using Global Names Resolver.

tp_namereferences

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

itis_taxrank

Retrieve taxonomic rank name from given TSN.

taxize-package

Taxnomic search and phylogeny retrieval.

tp_synonyms

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

searchbycommonnameendswith

Search for tsn by common name ending with

tpl_search

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

ubio_namebank

Search uBio namebank.

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.

getjurisdictionoriginvalues

Get jurisdiction origin values

tpl_get

Get The Plant List csv files.

getothersourcesfromtsn

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

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

eol_pages

Search for pages in EOL database using a taxonconceptID.

eol_dataobjects

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

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_name

Get taxonomic names for a given taxonomic name query.

itis_downstream

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

getdescription

Get description of the ITIS service

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

getacceptednamesfromtsn

Get accepted names from tsn

getcoremetadatafromtsn

Get core metadata from tsn

gisd_isinvasive

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

get_genes_avail

Retrieve gene sequences available for a species from NCBI.

gethierarchyupfromtsn

Get hierarchy up from tsn

getfullhierarchyfromtsn

Get full hierarchy from tsn

getunacceptabilityreasonfromtsn

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

getcredibilityratings

Get possible credibility ratings

getcommonnamesfromtsn

Get common names from tsn

getcurrencyfromtsn

Get currency from tsn

searchbycommonname

Search for tsn by common name

phylomatic_tree

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

rank_ref

Lookup-table for IDs of taxonomic ranks

getlsidfromtsn

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

getdatedatafromtsn

Get date data from tsn

getvernacularlanguages

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

capwords

Capitalize the first letter of a character string.

getanymatchcount

Get any match count.

searchforanymatchpaged

Search for any matched page

getexpertsfromtsn

Get expert information for the TSN.

gni_details

Search for taxonomic name details using the Global Names Index.

eol_search

Search for terms in EOL database.

tp_summary

Return summary data a taxon name with a given id.

eol_hierarchy

Retrieve all taxonomic hierarchy from given EOL taxonID.

getcommentdetailfromtsn

Get comment detail from TSN

get_tsn

Get the TSN code for a search term.

get_genes

Retrieve gene sequences from NCBI by accession number.

getkingdomnamefromtsn

Get kingdom names from tsn

col_downstream

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

getkey

Function to get API key.

gni_search

Search for taxonomic names using the Global Names Index.

get_seqs

Retrieve nucleotide sequences from NCBI.

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

tax_name

Get taxonomic names for a given taxonomic name query.

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

searchforanymatch

Search for any match

eol_ping

Ping EOL API to see if it's working.

gettsnfromlsid

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

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

searchbyscientificname

Search by scientific name

itis_phymat_format

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

plantminer

Search for taxonomy data from Plantminer.com

gettaxonomicusagefromtsn

Returns the usage information for the TSN.

getscientificnamefromtsn

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

itis_acceptname

Retrieve accepted TSN (with accepted name).

tnrs

Search the Phylotastic Taxonomic Name Resolution Service.

gethierarchydownfromtsn

Get hierarchy down from tsn

getkingdomnames

Get all possible kingdom names

iucn_summary

Get a summary from the IUCN Red List.

get_uid

Get the UID codes from NCBI for species names.

gnr_datasources

Get data sources for the Global Names Resolver.

tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.

tp_acceptednames

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

col_children

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

getcredibilityratingfromtsn

Get credibility rating from tsn

getcoveragefromtsn

Get coverge from tsn

getsynonymnamesfromtsn

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

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

tp_namedistributions

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

col_classification

Search Catalogue of Life for taxonomic classifications.

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

getjurisdictionvalues

Get possible jurisdiction values

getlastchangedate

Provides the date the ITIS database was last updated.

getfullrecordfromtsn

Get full record from TSN.

getranknames

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

getreviewyearfromtsn

Returns the review year for the TSN.