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taxize (version 0.6.0)

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

5,250

Version

0.6.0

License

MIT + file LICENSE

Issues

51

Pull Requests

0

Stars

280

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62

Maintainer

Scott Chamberlain

Last Published

June 13th, 2015

Functions in taxize (0.6.0)

apg_families

MOBOT family names
eol_dataobjects

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

Get global species completeness from tsn
itis_lsid

Get kingdom names.
col_search

Search Catalogue of Life for taxonomic IDs
get_nbnid

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

Parse scientific names using EOL's name parser.
gettsnbyvernacularlanguage

Get tsn by vernacular language
itis_native

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

Get full hierarchy from tsn
col_children

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

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

Search Barcode of Life for taxonomic IDs
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
getanymatchcount

Get any match count.
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
downstream

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

Get hierarchy up from 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.
itis_terms

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

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

Get geographic divisions from tsn
get_seqs

Retrieve gene sequences from NCBI by accession number.
getsynonymnamesfromtsn

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

Search Catalogue of Life for taxonomic classifications.
taxize_capwords

Capitalize the first letter of a character string.
col_downstream

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

Function to get API key.
plantminer

Search for taxonomy data from Plantminer.com
gbif_parse

Parse taxon names using the GBIF name parser.
gbif_name_usage

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

Get currency from tsn
apg_lookup

Lookup in the APGIII taxonomy and replace family names
getkingdomnamefromtsn

Get kingdom names from tsn
eol_invasive

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

Get the TSN code for a search term.
ncbi_search

Search for gene sequences available for taxa from NCBI.
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
itis_getrecord

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

Search NCBI for children of a taxon
children

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

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

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

Get jurisdiction origin values
searchforanymatch

Search for any match
getkingdomnames

Get all possible kingdom names
gisd_isinvasive

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

Retrieve gene sequences from NCBI by accession number.
getcredibilityratings

Get possible credibility ratings
taxize-defunct

Defunct functions in taxize
get_eolid

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

iPlant name resolution
getcommentdetailfromtsn

Get comment detail from TSN
eol_pages

Search for pages in EOL database using a taxonconceptID.
getcoremetadatafromtsn

Get core metadata from tsn
tp_dist

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

Search uBio for taxonomic synonyms by hierarchiesID.
getitisterms

Get itis terms from common names
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
getitistermsfromcommonname

Get itis terms from common names
ipni_search

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

Search for terms in EOL database.
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
ncbi_getbyname

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

This function will return NameBankIDs that match given search terms
itis_kingdomnames

Get kingdom names.
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
searchbycommonnameendswith

Search for tsn by common name ending with
getgeographicvalues

Get all possible geographic values
ncbi_get_taxon_summary

NCBI taxon information from uids
tpl_get

Get The Plant List csv files.
ifelsedata

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

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

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

Get expert information for the TSN.
genbank2uid

Get NCBI taxonomy UID from GenBankID
itis_searchcommon

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

Returns the review year for the TSN.
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
get_ubioid

Get the uBio id for a search term.
apg

Get APG names
get_colid

Get the Catalogue of Life ID from taxonomic names.
getdescription

Get description of the ITIS service
getunacceptabilityreasonfromtsn

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

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

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

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

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

Lookup-table for IDs of taxonomic ranks
searchbycommonnamebeginswith

Search for tsn by common name beginning with
gnr_resolve

Resolve names using Global Names Resolver.
iucn_status

Extractor functions for iucn-class.
tpl_search

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

Resolve names using Global Names Recognition and Discovery.
getcommonnamesfromtsn

Get common names from tsn
getacceptednamesfromtsn

Get accepted names from tsn
tax_agg

Aggregate species data to given taxonomic rank
get_boldid

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

Get possible jurisdiction values
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
vascan_search

Search the CANADENSYS Vascan API.
itis_acceptname

Retrieve accepted TSN (with accepted name).
ubio_classification

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

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

Get citations and licenses for data sources used in taxize
tax_name

Get taxonomic names for a given rank.
itis_refs

Get references related to a ITIS TSN.
itis_taxrank

Retrieve taxonomic rank name from given TSN.
itis_downstream

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

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

Search UK National Biodiversity Network database
itis_name

Get taxonomic names for a given taxonomic name query.
tp_acceptednames

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

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

Get a random vector of species names.
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
getothersourcesfromtsn

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

Search by scientific name
sci2comm

Get common names from scientific names.
tp_namedistributions

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

Search the Phylotastic Taxonomic Name Resolution Service.
gnr_datasources

Get data sources for the Global Names Resolver.
getfullrecordfromtsn

Get full record from TSN.
tp_summary

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

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

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

Search UK National Biodiversity Network database for taxonomic classification
iucn_getname

Get any matching IUCN species names
gni_search

Search for taxonomic names using the Global Names Index.
ubio_classification_search

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

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

Taxonomic information from around the web.
plantGenusNames

Vector of plant genus names from ThePlantList
searchforanymatchpaged

Search for any matched page
upstream

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

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

Return all synonyms for a taxon name with a given id.
class2tree

Convert list of classifications to a tree.
getcoveragefromtsn

Get coverge from tsn
get_uid

Get the UID codes from NCBI for taxonomic names.
getdatedatafromtsn

Get date data from tsn
gethierarchydownfromtsn

Get hierarchy down from tsn
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
itis-api

Low level functions for working with the ITIS API.
getlastchangedate

Provides the date the ITIS database was last updated.
status_codes

Get HTTP status codes
tax_rank

Get rank for a given taxonomic name.
tpl_families

Get The Plant List families.
tp_accnames

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

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

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

Resolve names from many different sources
searchbycommonname

Search for tsn by common name
taxize-deprecated

Deprecated functions in taxize
apg_orders

MOBOT order names
comm2sci

Get scientific names from common names.
get_ids

Retrieve taxonomic identifiers for a given taxon name.
getitistermsfromscientificname

Get itis terms from scientific names
getcredibilityratingfromtsn

Get credibility rating from tsn
rankagg

Aggregate data by given taxonomic rank
iucn_summary

Get a summary from the IUCN Red List.
ubio_id

Search uBio by namebank ID.