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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

Issues

52

Pull Requests

0

Stars

281

Forks

62

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
itis_hierarchy

ITIS hierarchy
itis_kingdomnames

Get kingdom names
tnrs

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.