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taxize (version 0.4.0)

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

8,786

Version

0.4.0

License

MIT + file LICENSE

Issues

50

Pull Requests

0

Stars

296

Forks

63

Maintainer

Scott Chamberlain

Last Published

September 9th, 2014

Functions in taxize (0.4.0)

col_downstream

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

Get global species completeness from tsn
getlastchangedate

Provides the date the ITIS database was last updated.
getfullhierarchyfromtsn

Get full hierarchy from tsn
col_classification

Search Catalogue of Life for taxonomic classifications.
eol_ping

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

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

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

Lookup-table for APGIII order names
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
getscientificnamefromtsn

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

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

Deprecated functions in taxize
itis_hierarchy

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

Table of APGIII generic names
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
eol_dataobjects

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

Get accepted names from tsn
downstream

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

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

Get common names from tsn
gbif_name_usage

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

Get the uBio id for a search term.
resolve

Resolve names from many different sources
getkingdomnamefromtsn

Get kingdom names from tsn
searchbyscientificname

Search by scientific name
children

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

Search for taxonomic names using the Global Names Index.
getdescription

Get description of the ITIS service
searchforanymatch

Search for any match
eol_invasive

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

Retrieve gene sequences from NCBI by accession number.
get_ids

Retrieve taxonomic identifiers for a given taxon name.
get_seqs

Retrieve gene sequences from NCBI by accession number.
getitistermsfromscientificname

Get itis terms from scientific names
iucn_getname

Get any matching IUCN species names
plantGenusNames

Vector of 793 genus names of plants
ncbi_getbyname

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

Get jurisdiction origin values
rank_ref

Lookup-table for IDs of taxonomic ranks
apg_families

Lookup-table for APGIII family names
itis_acceptname

Retrieve accepted TSN (with accepted name).
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
comm2sci

Get scientific names from common names.
eol_pages

Search for pages in EOL database using a taxonconceptID.
getpublicationsfromtsn

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

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

Vector of 1,182 species names of plants
tax_name

Get taxonomic names for a given rank.
gnr_resolve

Resolve names using Global Names Resolver.
itis_name

Get taxonomic names for a given taxonomic name query.
scrapenames

Resolve names using Global Names Recognition and Discovery.
getcredibilityratingfromtsn

Get credibility rating from tsn
ipni_search

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

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

Search for terms in EOL database.
bold_search

Search Barcode of Life for taxonomic IDs
searchbycommonnameendswith

Search for tsn by common name ending with
searchbycommonnamebeginswith

Search for tsn by common name beginning with
getsynonymnamesfromtsn

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

Get full record from TSN.
iucn_summary

Get a summary from the IUCN Red List.
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
theplantlist

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

Get coverge from tsn
gethierarchyupfromtsn

Get hierarchy up from tsn
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
itis_terms

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

Returns the kingdom and rank information for the TSN.
itis_taxrank

Retrieve taxonomic rank name from given TSN.
getitistermsfromcommonname

Get itis terms from common names
class2tree

Convert list of classifications to a tree.
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
tp_namereferences

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

Get all possible kingdom names
getvernacularlanguages

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

Get hierarchy down from tsn
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.
tpl_families

Get The Plant List families.
tp_classification

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

Get sources for the Phylotastic Taxonomic Name Resolution Service.
getlsidfromtsn

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

Parse taxon names using the GBIF name parser.
tp_accnames

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

Get kingdom names.
rankagg

Aggregate data by given taxonomic rank
ubio_synonyms

Search uBio for taxonomic synonyms by hierarchiesID.
getcurrencyfromtsn

Get currency from tsn
col_search

Search Catalogue of Life for taxonomic IDs
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
tp_dist

Return all distribution 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
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
tpl_search

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

Search for taxonomy data from Plantminer.com
tp_namedistributions

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

This function will return NameBankIDs that match given search terms
tp_summary

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

Get references related to a ITIS TSN.
ncbi_search

Search for gene sequences available for a species from NCBI.
sci2comm

Get common names from scientific names.
taxize_ldfast

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

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

Search the Phylotastic Taxonomic Name Resolution Service.
ifelsedata

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

Get rank for a given taxonomic name.
getjurisdictionvalues

Get possible jurisdiction values
ubio_classification

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

Capitalize the first letter of a character string.
getgeographicvalues

Get all possible geographic values
tp_refs

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

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

Parse scientific names using EOL's name parser.
taxize-package

Taxonomic information from around the web.
tp_acceptednames

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

Retrieve the taxonomic hierarchy for a given taxon ID.
gisd_isinvasive

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

Extractor functions for iucn-class.
gni_details

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

Get any match count.
getreviewyearfromtsn

Returns the review year for the TSN.
getcommentdetailfromtsn

Get comment detail from TSN
itis_getrecord

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

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

iPlant name resolution
getcoremetadatafromtsn

Get core metadata from tsn
tp_search

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

Get citations and licenses for data sources used in taxize
vascan_search

Search the CANADENSYS Vascan API.
tpl_get

Get The Plant List csv files.
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.
gnr_datasources

Get data sources for the Global Names Resolver.
phylomatic_format

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

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

Search for any matched page
ubio_id

Search uBio by namebank ID.
getkey

Function to get API key.
get_eolid

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

Get the GBIF backbone taxon ID from taxonomic names.
getexpertsfromtsn

Get expert information for the TSN.
get_uid

Get the UID codes from NCBI for taxonomic names.
getcredibilityratings

Get possible credibility ratings
gettsnfromlsid

Gets the TSN corresponding to the LSID, 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.
apg_lookup

Lookup in the APGII taxonomy and replace family names.
get_tsn

Get the TSN code for a search term.
getitisterms

Get itis terms from common names
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
getdatedatafromtsn

Get date data from tsn
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
itis_kingdomnames

Get kingdom names.
names_list

Get a random vector of species names.
tax_agg

Aggregate species data to given taxonomic rank