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taxize (version 0.6.6)

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

5,250

Version

0.6.6

License

MIT + file LICENSE

Issues

51

Pull Requests

0

Stars

281

Forks

62

Maintainer

Scott Chamberlain

Last Published

October 1st, 2015

Functions in taxize (0.6.6)

col_search

Search Catalogue of Life for taxonomic IDs
bold_search

Search Barcode of Life for taxonomic IDs
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.
getvernacularlanguages

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

Parse taxon names using the GBIF name parser.
getfullrecordfromtsn

Get full record from TSN.
get_seqs

Retrieve gene sequences from NCBI by accession number.
apg_orders

MOBOT order names
gbif_name_usage

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

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

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

Get the EOL ID from Encyclopedia of Life from taxonomic names.
comm2sci

Get scientific names from common names.
getacceptednamesfromtsn

Get accepted names from tsn
col_classification

Search Catalogue of Life for taxonomic classifications.
getitisterms

Get itis terms from common names
iucn_id

Get an ID for a IUCN listed taxon
eol_pages

Search for pages in EOL database using a taxonconceptID.
apg_families

MOBOT family names
genbank2uid

Get NCBI taxonomy UID from GenBankID
get_genes

Retrieve gene sequences from NCBI by accession number.
ncbi_getbyname

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

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

Get comment detail from TSN
eol_search

Search for terms in EOL database.
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
iucn_summary

Get a summary from the IUCN Red List
getfullhierarchyfromtsn

Get full hierarchy from tsn
getunacceptabilityreasonfromtsn

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

Get itis terms from common names
upstream

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

Get the Catalogue of Life ID from taxonomic names.
col_children

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

Retrieve taxonomic rank name from given TSN.
itis_kingdomnames

Get kingdom 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.
get_boldid

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

Low level functions for working with the ITIS API.
nbn_search

Search UK National Biodiversity Network database
getcredibilityratingfromtsn

Get credibility rating from tsn
nbn_synonyms

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

Get kingdom names
getanymatchcount

Get any match count.
getdatedatafromtsn

Get date data from tsn
getscientificnamefromtsn

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

Get possible jurisdiction values
getothersourcesfromtsn

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

Get description of the ITIS service
tp_accnames

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

Search for tsn by common name ending with
children

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

Get the UK National Biodiversity Network ID from taxonomic names.
getranknames

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

Use Catalogue of Life to get downstream taxa to a given taxonomic level.
class2tree

Convert list of classifications to a tree.
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
theplantlist

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

Parse scientific names using EOL's name parser.
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
getcoremetadatafromtsn

Get core metadata from tsn
scrapenames

Resolve names using Global Names Recognition and Discovery.
itis_acceptname

Retrieve accepted TSN (with accepted name).
taxize_cite

Get citations and licenses for data sources used in taxize
tp_summary

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

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

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

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

Get APG names
tpl_get

Get The Plant List csv files.
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
tp_namereferences

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

Get hierarchy down from tsn
getcommonnamesfromtsn

Get common names from tsn
tp_search

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

Retrieve the taxonomic hierarchy from given EOL taxonID.
apg_lookup

Lookup in the APGIII taxonomy and replace family names
getkingdomnamefromtsn

Get kingdom names from tsn
itis_searchcommon

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

Search UK National Biodiversity Network database for taxonomic classification
taxize-deprecated

Deprecated functions in taxize
get_uid

Get the UID codes from NCBI for taxonomic names.
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
getkey

Function to get API key.
itis_downstream

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

Get possible credibility ratings
rank_ref

Lookup-table for IDs of taxonomic ranks
itis_terms

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

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

Get the TSN code for a search term.
tp_acceptednames

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

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

TNRS sources
ncbi_children

Search NCBI for children of a taxon
ipni_search

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

Get currency from tsn
gettsnfromlsid

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

Get expert information for the TSN.
get_ubioid

Get the uBio id for a search term
getreviewyearfromtsn

Returns the review year for the TSN.
plantminer

Search for taxonomy data from Plantminer.com
ubio_classification

uBio classification
itis_refs

Get references related to a ITIS TSN.
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
ubio_search

This function will return NameBankIDs that match given search terms
itis_native

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

ITIS hierarchy
get_ids

Retrieve taxonomic identifiers for a given taxon name.
gisd_isinvasive

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

Get all possible kingdom names
sci2comm

Get common names from scientific names.
searchbycommonname

Search for tsn by common name
tp_refs

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

Capitalize the first letter of a character string.
searchbycommonnamebeginswith

Search for tsn by common name beginning with
gni_details

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

Get a random vector of species names.
ncbi_search

Search for gene sequences available for taxa from NCBI.
gettsnbyvernacularlanguage

Get tsn by vernacular language
tpl_families

Get The Plant List families.
vascan_search

Search the CANADENSYS Vascan API.
tp_synonyms

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

Returns the parent TSN for the entered TSN.
searchforanymatch

Search for any match
iucn_getname

Get any matching IUCN species names
phylomatic_format

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

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

Get rank for a given taxonomic name.
plantNames

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

Search by scientific name
plantGenusNames

Vector of plant genus names from ThePlantList
getitistermsfromscientificname

Get itis terms from scientific names
tax_agg

Aggregate species data to given taxonomic rank
ubio_ping

uBio ping
taxize-defunct

Defunct functions in taxize
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
tp_namedistributions

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

Get HTTP status codes
rankagg

Aggregate data by given taxonomic rank
ncbi_get_taxon_summary

NCBI taxon information from uids
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
ubio_id

Search uBio by namebank ID.
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
gnr_resolve

Resolve names using Global Names Resolver.
tp_dist

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

Search for any matched page
tnrs

Phylotastic Taxonomic Name Resolution Service.
ubio_classification_search

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

Get coverge from tsn
tax_name

Get taxonomic names for a given rank.
getjurisdictionoriginvalues

Get jurisdiction origin values
eol_invasive

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

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

Get hierarchy up from tsn
iplant_resolve

iPlant name resolution
gni_search

Search for taxonomic names using the Global Names Index.
getgeographicvalues

Get all possible geographic values
getlastchangedate

Provides the date the ITIS database was last updated.
gnr_datasources

Get data sources for the Global Names Resolver.
itis_name

Get taxonomic names for a given taxonomic name query.
iucn_status

Extractor functions for iucn-class.
resolve

Resolve names from different data sources
taxize_ldfast

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

Taxnomic search and phylogeny retrieval.