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taxize (version 0.7.0)

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')

Monthly Downloads

5,250

Version

0.7.0

License

MIT + file LICENSE

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Repository

https://github.com/ropensci/taxize

Maintainer

Scott Chamberlain

Last Published

November 30th, 2015

Functions in taxize (0.7.0)

genbank2uid

Get NCBI taxonomy UID from GenBankID

get_uid

Get the UID codes from NCBI for taxonomic names.

apg

Get APG names

gbif_downstream

Retrieve all taxa names downstream in hierarchy for GBIF

getcommonnamesfromtsn

Get common names from tsn

col_classification

Search Catalogue of Life for taxonomic classifications.

getkingdomnames

Get all possible kingdom names

get_genes

Retrieve gene sequences from NCBI by accession number.

get_tpsid

Get the NameID codes from Tropicos for taxonomic names.

get_seqs

Retrieve gene sequences from NCBI by accession number.

getfullrecordfromtsn

Get full record from TSN.

apg_orders

MOBOT order names

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

itis_native

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

classification

Retrieve the taxonomic hierarchy for a given taxon ID.

get_ubioid

Get the uBio id for a search term

gni_details

Search for taxonomic name details using the Global Names Index.

class2tree

Convert list of classifications to a tree.

get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.

col_search

Search Catalogue of Life for taxonomic IDs

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

col_downstream

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

getexpertsfromtsn

Get expert information for the TSN.

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

get_genes_avail

Retrieve gene sequences from NCBI by accession number.

getcoveragefromtsn

Get coverge from tsn

eol_search

Search for terms in EOL database.

getlsidfromtsn

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

gethierarchyupfromtsn

Get hierarchy up from tsn

getothersourcesfromtsn

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

iucn_id

Get an ID for a IUCN listed taxon

getitistermsfromcommonname

Get itis terms from common names

eubon

EU BON taxonomy

getdescription

Get description of the ITIS service

eol_dataobjects

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

getcurrencyfromtsn

Get currency from tsn

eol_pages

Search for pages in EOL database using a taxonconceptID.

apg_lookup

Lookup in the APGIII taxonomy and replace family names

getranknames

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

eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

getitisterms

Get itis terms from common names

getkey

Function to get API key.

get_ids

Retrieve taxonomic identifiers for a given taxon name.

getfullhierarchyfromtsn

Get full hierarchy from tsn

gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.

sci2comm

Get common names from scientific names.

searchbycommonname

Search for tsn by common name

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.

col_children

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

gbif_parse

Parse taxon names using the GBIF name parser.

apg_families

MOBOT family names

getcoremetadatafromtsn

Get core metadata from tsn

nbn_search

Search UK National Biodiversity Network database

ncbi_getbyname

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

getkingdomnamefromtsn

Get kingdom names from tsn

children

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

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

theplantlist

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

nbn_synonyms

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

ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.

getunacceptabilityreasonfromtsn

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

synonyms

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

ncbi_search

Search for gene sequences available for taxa from NCBI.

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

getacceptednamesfromtsn

Get accepted names from tsn

taxize-defunct

Defunct functions in taxize

getcredibilityratings

Get possible credibility ratings

iucn_getname

Get any matching IUCN species names

tax_rank

Get rank for a given taxonomic name.

gnr_datasources

Get data sources for the Global Names Resolver.

searchforanymatchpaged

Search for any matched page

iplant_resolve

iPlant name resolution

tnrs_sources

TNRS sources

itis_acceptname

Retrieve accepted TSN (with accepted name).

getdatedatafromtsn

Get date data from tsn

get_nbnid

Get the UK National Biodiversity Network ID from taxonomic names.

tp_search

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

vascan_search

Search the CANADENSYS Vascan API.

taxize-package

Taxonomic Information from Around the Web

getjurisdictionoriginvalues

Get jurisdiction origin values

tpl_search

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

getlastchangedate

Provides the date the ITIS database was last updated.

gettsnfromlsid

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

tp_summary

Return summary data a taxon name with a given id.

taxize_ldfast

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

status_codes

Get HTTP status codes

itis-api

Low level functions for working with the ITIS API.

ubio_ping

uBio ping

gni_parse

Parse scientific names using EOL's name parser.

phylomatic_format

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

ubio_id

Search uBio by namebank ID.

searchforanymatch

Search for any match

itis_taxrank

Retrieve taxonomic rank name from given TSN.

ncbi_get_taxon_summary

NCBI taxon information from uids

iucn_status

Extractor functions for iucn-class.

tp_dist

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

itis_terms

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

gisd_isinvasive

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

gettaxonomicusagefromtsn

Returns the usage information for the 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.

gnr_resolve

Resolve names using Global Names Resolver.

getgeographicvalues

Get all possible geographic values

phylomatic_tree

Query Phylomatic for a phylogenetic tree.

itis_name

Get taxonomic names for a given taxonomic name query.

upstream

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

searchbycommonnameendswith

Search for tsn by common name ending with

getcommentdetailfromtsn

Get comment detail from TSN

itis_searchcommon

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

itis_getrecord

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

getanymatchcount

Get any match count.

searchbyscientificname

Search by scientific name

ncbi_children

Search NCBI for children of a taxon

itis_lsid

Get kingdom names

itis_refs

Get references related to a ITIS TSN.

ipni_search

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

iucn_summary

Get a summary from the IUCN Red List

tp_acceptednames

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

gni_search

Search for taxonomic names using the Global Names Index.

plantminer

Search for taxonomy data from Plantminer.com

nbn_classification

Search UK National Biodiversity Network database for taxonomic classification

Phylotastic Taxonomic Name Resolution Service.

rankagg

Aggregate data by given taxonomic rank

getjurisdictionvalues

Get possible jurisdiction values

tp_classification

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

tp_namereferences

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

ubio_classification_search

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

tpl_get

Get The Plant List csv files.

tp_refs

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.

rank_ref

Lookup-table for IDs of taxonomic ranks

tp_synonyms

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

scrapenames

Resolve names using Global Names Recognition and Discovery.

ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.

tax_name

Get taxonomic names for a given rank.

taxize_capwords

Capitalize the first letter of a character string.

ubio_search

This function will return NameBankIDs that match given search terms

tp_accnames

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

plantNames

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

taxize_cite

Get citations and licenses for data sources used in taxize

resolve

Resolve names from different data sources

ubio_classification

uBio classification

plantGenusNames

Vector of plant genus names from ThePlantList

tp_namedistributions

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

get_colid

Get the Catalogue of Life ID from taxonomic names.

comm2sci

Get scientific names from common names.

downstream

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

gethierarchydownfromtsn

Get hierarchy down from tsn

getscientificnamefromtsn

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

getreviewyearfromtsn

Returns the review year for the TSN.

ion

ION - Index to Organism Names

itis_downstream

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

names_list

Get a random vector of species names.

searchbycommonnamebeginswith

Search for tsn by common name beginning with

bold_search

Search Barcode of Life for taxonomic IDs

eol_invasive

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

fungorum

Index Fungorum

get_boldid

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

get_eolid

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

get_tsn

Get the TSN code for a search term.

getcredibilityratingfromtsn

Get credibility rating from tsn

getitistermsfromscientificname

Get itis terms from scientific names

getvernacularlanguages

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

tax_agg

Aggregate species data to given taxonomic rank

gettsnbyvernacularlanguage

Get tsn by vernacular language

tpl_families

Get The Plant List families.

ping

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