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taxize (version 0.6.2)

Taxonomic Information from Around the Web

Description

Taxonomic information from around the web. This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.

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Install

install.packages('taxize')

Monthly Downloads

8,786

Version

0.6.2

License

MIT + file LICENSE

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Repository

https://github.com/ropensci/taxize

Maintainer

Scott Chamberlain

Last Published

August 7th, 2015

Functions in taxize (0.6.2)

getanymatchcount

Get any match count.

getcoveragefromtsn

Get coverge from tsn

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

MOBOT family names

getacceptednamesfromtsn

Get accepted names from tsn

Get a random vector of species names.

getjurisdictionoriginvalues

Get jurisdiction origin values

Retrieve gene sequences from NCBI by accession number.

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

getcommentdetailfromtsn

Get comment detail from TSN

eol_dataobjects

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

phylomatic_format

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

Search for taxonomic name details using the Global Names Index.

getfullrecordfromtsn

Get full record from TSN.

gethierarchyupfromtsn

Get hierarchy up from tsn

Search Barcode of Life for taxonomic IDs

getgeographicvalues

Get all possible geographic values

Convert list of classifications to a tree.

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

searchbycommonnameendswith

Search for tsn by common name ending with

Get the Catalogue of Life ID from taxonomic names.

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

itis_downstream

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

This function will return NameBankIDs that match given search terms

Search Catalogue of Life for taxonomic IDs

getkingdomnamefromtsn

Get kingdom names from tsn

Parse taxon names using the GBIF name parser.

Get references related to a ITIS TSN.

Get the GBIF backbone taxon ID from taxonomic names.

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.

getcurrencyfromtsn

Get currency from tsn

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

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

MOBOT order names

gettaxonomicusagefromtsn

Returns the usage information for the TSN.

Retrieve gene sequences from NCBI by accession number.

nbn_classification

Search UK National Biodiversity Network database for taxonomic classification

Get the uBio id for a search term.

getitistermsfromscientificname

Get itis terms from scientific names

Search UK National Biodiversity Network database

get_genes_avail

Retrieve gene sequences from NCBI by accession number.

Get the UK National Biodiversity Network ID from taxonomic names.

Search for pages in EOL database using a taxonconceptID.

Get scientific names from common names.

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

gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.

Retrieve taxonomic identifiers for a given taxon name.

Get itis terms from common names

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

Search for terms in EOL database.

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

Get rank for a given taxonomic name.

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

getcredibilityratings

Get possible credibility ratings

Retrieve the taxonomic hierarchy from given EOL taxonID.

Retrieve taxonomic rank name from given TSN.

Get taxonomic names for a given taxonomic name query.

getgeographicdivisionsfromtsn

Get geographic divisions from tsn

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

Get the UID codes from NCBI for taxonomic names.

getcommonnamesfromtsn

Get common names from tsn

getparenttsnfromtsn

Returns the parent TSN for the entered TSN.

Get description of the ITIS service

getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn

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

Aggregate species data to given taxonomic rank

getpublicationsfromtsn

Returns a list of the pulications used for the TSN.

getvernacularlanguages

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

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

Resolve names using Global Names Resolver.

getsynonymnamesfromtsn

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

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

Function to get API key.

gethierarchydownfromtsn

Get hierarchy down from tsn

Get kingdom names.

Lookup in the APGIII taxonomy and replace family names

getunacceptabilityreasonfromtsn

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

ubio_classification_search

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

iPlant name resolution

plantGenusNames

Vector of plant genus names from ThePlantList

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

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

Get common names from scientific names.

ubio_classification

This function will return all ClassificationBank data pertaining to a particular ClassificationBankID

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

taxize_capwords

Capitalize the first letter of a character string.

Lookup-table for IDs of taxonomic ranks

Search the CANADENSYS Vascan API.

gisd_isinvasive

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

Defunct functions in taxize

itis_searchcommon

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

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

Resolve names using Global Names Recognition and Discovery.

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

gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.

Get The Plant List families.

Parse scientific names using EOL's name parser.

Retrieve gene sequences from NCBI by accession number.

Get the NameID codes from Tropicos for taxonomic names.

Get any matching IUCN species names

taxize-deprecated

Deprecated functions in taxize

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

itis_kingdomnames

Get kingdom names.

getitistermsfromcommonname

Get itis terms from common names

Extractor functions for iucn-class.

Retrieve the taxonomic hierarchy for a given taxon ID.

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

getlastchangedate

Provides the date the ITIS database was last updated.

searchbyscientificname

Search by scientific name

Search for taxonomic names using the Global Names Index.

getothersourcesfromtsn

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

Search NCBI for children of a taxon

gettaxonauthorshipfromtsn

Returns the author information for the TSN.

searchbycommonnamebeginswith

Search for tsn by common name beginning with

Get HTTP status codes

getglobalspeciescompletenessfromtsn

Get global species completeness from tsn

itis_acceptname

Retrieve accepted TSN (with accepted name).

Get hierarchies from TSN values, full, upstream only, or immediate downstream only

searchforanymatchpaged

Search for any matched page

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

Search for gene sequences available for taxa from NCBI.

Get a summary from the IUCN Red List

Get the TSN code for a search term.

getcoremetadatafromtsn

Get core metadata from tsn

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

getreviewyearfromtsn

Returns the review year for the TSN.

Get citations and licenses for data sources used in taxize

Search uBio for taxonomic synonyms by hierarchiesID.

getscientificnamefromtsn

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

tp_classification

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

Aggregate data by given taxonomic rank

getkingdomnames

Get all possible kingdom names

Taxnomic search and phylogeny retrieval.

Resolve names from different data sources

getexpertsfromtsn

Get expert information for the TSN.

Search uBio by namebank ID.

tp_namereferences

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

searchforanymatch

Search for any match

Return summary data a taxon name with a given id.

Phylotastic Taxonomic Name Resolution Service.

Search for taxonomy data from Plantminer.com

phylomatic_tree

Query Phylomatic for a phylogenetic tree.

Get The Plant List csv files.

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

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

gnr_datasources

Get data sources for the Global Names Resolver.

Get NCBI taxonomy UID from GenBankID

col_classification

Search Catalogue of Life for taxonomic classifications.

getcredibilityratingfromtsn

Get credibility rating from tsn

getjurisdictionvalues

Get possible jurisdiction values

Low level functions for working with the ITIS API.

ncbi_get_taxon_summary

NCBI taxon information from uids

searchbycommonname

Search for tsn by common name

tp_namedistributions

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

tp_acceptednames

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

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

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

getdatedatafromtsn

Get date data from tsn

getfullhierarchyfromtsn

Get full hierarchy from tsn

gettsnbyvernacularlanguage

Get tsn by vernacular language

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

Get taxonomic names for a given rank.