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taxize (version 0.3.0)

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

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Version

0.3.0

License

MIT + file LICENSE

Issues

50

Pull Requests

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296

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63

Maintainer

Scott Chamberlain

Last Published

May 20th, 2014

Functions in taxize (0.3.0)

get_seqs

Retrieve gene sequences from NCBI by accession number.
gni_search

Search for taxonomic names using the Global Names Index.
getothersourcesfromtsn

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

Returns the author information for the TSN.
get_uid

Get the UID codes from NCBI for taxonomic names.
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
getanymatchcount

Get any match count.
apg_orders

Lookup-table for APGIII order names
tax_rank

Get rank for a given taxonomic name.
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.
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
getpublicationsfromtsn

Returns a list of the pulications used for the TSN.
eol_ping

Ping EOL API to see if it's working.
getitistermsfromscientificname

Get itis terms from scientific names
getcommonnamesfromtsn

Get common names from tsn
col_search

Search Catalogue of Life for taxonomic IDs
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
get_eolid

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

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

Search Catalogue of Life for taxonomic classifications.
searchbycommonname

Search for tsn by common name
taxize_capwords

Capitalize the first letter of a character string.
getcredibilityratingfromtsn

Get credibility rating from tsn
getdatedatafromtsn

Get date data from tsn
get_tsn

Get the TSN code for a search term.
gethierarchydownfromtsn

Get hierarchy down from tsn
gbif_name_usage

Lookup details for specific names in all taxonomies in GBIF.
apg_genera

Table of APGIII generic names
getjurisdictionvalues

Get possible jurisdiction values
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
gni_parse

Parse scientific names using EOL's name parser.
getunacceptabilityreasonfromtsn

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

Get kingdom names from tsn
eol_dataobjects

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

Retrieve the taxonomic hierarchy from given EOL taxonID.
ifelsedata

Function to parse xml data, decode strings, and return NULL if logical is zero.
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.
comm2sci

Get scientific names from common names.
eol_search

Search for terms in EOL database.
names_list

Get a random vector of species names.
eol_pages

Search for pages in EOL database using a taxonconceptID.
itis_getrecord

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

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

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

Get possible credibility ratings
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
gnr_resolve

Resolve names using Global Names Resolver.
getkingdomnames

Get all possible kingdom names
getexpertsfromtsn

Get expert information for the TSN.
getreviewyearfromtsn

Returns the review year for the TSN.
searchbyscientificname

Search by scientific name
getgeographicvalues

Get all possible geographic values
getcoremetadatafromtsn

Get core metadata from tsn
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
iucn_summary

Get a summary from the IUCN Red List.
ncbi_getbyname

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

Get accepted names from tsn
ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.
get_genes

Retrieve gene sequences from NCBI by accession number.
class2tree

Convert list of classifications to a tree.
gethierarchyupfromtsn

Get hierarchy up from tsn
getfullrecordfromtsn

Get full record from TSN.
apg_families

Lookup-table for APGIII family names
ubio_classification

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

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

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

Lookup-table for IDs of taxonomic ranks
getjurisdictionoriginvalues

Get jurisdiction origin values
ncbi_search

Search for gene sequences available for a species from NCBI.
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
phylomatic_format

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

Function to get API key.
tp_namereferences

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

Return summary data a taxon name with a given id.
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
getitistermsfromcommonname

Get itis terms from common names
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
itis_terms

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

Get comment detail from TSN
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
tp_dist

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

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

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

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

Get taxonomic names for a given taxonomic name query.
gnr_datasources

Get data sources for the Global Names Resolver.
getitisterms

Get itis terms from common names
iucn_status

Extractor functions for iucn-class.
getcoveragefromtsn

Get coverge from tsn
plantNames

Vector of 1,182 species names of plants
taxize-package

Taxnomic search and phylogeny retrieval.
itis_kingdomnames

Get kingdom names.
itis_lsid

Get kingdom names.
searchbycommonnamebeginswith

Search for tsn by common name beginning with
getcurrencyfromtsn

Get currency from tsn
get_ids

Retrieve taxonomic identifiers for a given taxon name.
vascan_search

Search the CANADENSYS Vascan API.
getscientificnamefromtsn

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

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

Resolve names using Global Names Recognition and Discovery.
getvernacularlanguages

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

Ping the ITIS API to see if it's working.
gni_details

Search for taxonomic name details using the Global Names Index.
getlastchangedate

Provides the date the ITIS database was last updated.
searchforanymatch

Search for any match
itis_hierarchy

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

Retrieve taxonomic rank name from given TSN.
iplant_resolve

iplant resolution
itis_acceptname

Retrieve accepted TSN (with accepted name).
apg_lookup

Lookup in the APGII taxonomy and replace family names.
itis_searchcommon

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

Resolve names from many different sources
tax_agg

Aggregate species data to given taxonomic rank
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
getdescription

Get description of the ITIS service
tp_classification

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

Get taxonomic names for a given rank.
ipni_search

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

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

Get references related to a ITIS TSN.
taxize-deprecated

Deprecated functions in taxize
searchforanymatchpaged

Search for any matched page
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
rankagg

Aggregate data by given taxonomic rank
tp_search

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

Get The Plant List csv files.
theplantlist

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

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

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

Vector of 793 genus names of plants
plantminer

Search for taxonomy data from Plantminer.com
tp_refs

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

Get The Plant List families.
taxize_ldfast

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

Search uBio by namebank ID.
tpl_search

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

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

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

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

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

Get full hierarchy from tsn
iucn_getname

Get any matching IUCN species names
getlsidfromtsn

Gets the unique LSID for the TSN, or an empty result if there is no match.
sci2comm

Get common names from scientific names.
searchbycommonnameendswith

Search for tsn by common name ending with
ubio_search

This function will return NameBankIDs that match given search terms
gbif_parse

Parse taxon names using the GBIF name parser.
get_colid

Get the Catalogue of Life ID from taxonomic names.