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taxize (version 0.5.2)

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

0.5.2

License

MIT + file LICENSE

Issues

51

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0

Stars

280

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62

Maintainer

Scott Chamberlain

Last Published

December 19th, 2014

Functions in taxize (0.5.2)

downstream

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

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

Get global species completeness from tsn
comm2sci

Get scientific names from common names.
apg_genera

Table of APGIII generic names
getfullhierarchyfromtsn

Get full hierarchy from tsn
col_search

Search Catalogue of Life for taxonomic IDs
getscientificnamefromtsn

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

Search for terms in EOL database.
getitisterms

Get itis terms from common names
itis_terms

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

Lookup-table for APGIII order names
itis_downstream

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

Get the uBio id for a search term.
eol_pages

Search for pages in EOL database using a taxonconceptID.
get_seqs

Retrieve gene sequences from NCBI by accession number.
getcredibilityratingfromtsn

Get credibility rating from tsn
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
getjurisdictionoriginvalues

Get jurisdiction origin values
get_colid

Get the Catalogue of Life ID from taxonomic names.
getreviewyearfromtsn

Returns the review year for the TSN.
getkingdomnames

Get all possible kingdom names
getgeographicvalues

Get all possible geographic values
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
gnr_resolve

Resolve names using Global Names Resolver.
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
col_downstream

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

Get date data from tsn
itis_taxrank

Retrieve taxonomic rank name from given TSN.
getjurisdictionvalues

Get possible jurisdiction values
getdescription

Get description of the ITIS service
itis_refs

Get references related to a ITIS TSN.
iucn_status

Extractor functions for iucn-class.
plantGenusNames

Vector of 793 genus names of plants
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.
getitistermsfromcommonname

Get itis terms from common names
searchforanymatch

Search for any match
rank_ref

Lookup-table for IDs of taxonomic ranks
getpublicationsfromtsn

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

Get the GBIF backbone taxon ID from taxonomic names.
eol_dataobjects

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

Get taxonomic names for a given taxonomic name query.
status_codes

Get HTTP status codes
get_eolid

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

Returns the usage information for the TSN.
getcredibilityratings

Get possible credibility ratings
gethierarchydownfromtsn

Get hierarchy down from tsn
tpl_families

Get The Plant List families.
taxize_capwords

Capitalize the first letter of a character string.
searchbycommonname

Search for tsn by common name
get_nbnid

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

Vector of 1,182 species names of plants
getcoveragefromtsn

Get coverge from tsn
getitistermsfromscientificname

Get itis terms from scientific names
children

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

Retrieve the taxonomic hierarchy from given EOL taxonID.
genbank2uid

Get NCBI taxonomy UID from GenBankID
getcommonnamesfromtsn

Get common names from tsn
gbif_parse

Parse taxon names using the GBIF name parser.
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
get_genes

Retrieve gene sequences from NCBI by accession number.
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
get_tsn

Get the TSN code for a search term.
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
phylomatic_format

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

Get a summary from the IUCN Red List.
ipni_search

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

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

Get full record from TSN.
getanymatchcount

Get any match count.
gbif_name_usage

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

Get core metadata from tsn
gnr_datasources

Get data sources for the Global Names Resolver.
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
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.
getacceptednamesfromtsn

Get accepted names from tsn
gettsnfromlsid

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

Parse scientific names using EOL's name parser.
tpl_search

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

Resolve names using Global Names Recognition and Discovery.
getunacceptabilityreasonfromtsn

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

iPlant name resolution
ncbi_children

Search NCBI for children of a taxon
get_uid

Get the UID codes from NCBI for taxonomic names.
getothersourcesfromtsn

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

Resolve names from many different sources
upstream

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

Get a random vector of species names.
tp_namereferences

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

Get hierarchy up from tsn
nbn_synonyms

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

Search UK National Biodiversity Network database
theplantlist

Lookup-table for family, genus, and species names for ThePlantList
itis-api

Low level functions for working with the ITIS API.
ncbi_search

Search for gene sequences available for taxa from NCBI.
bold_search

Search Barcode of Life for taxonomic IDs
iucn_getname

Get any matching IUCN species names
vascan_search

Search the CANADENSYS Vascan API.
sci2comm

Get common names from scientific names.
tp_summary

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

Get sources for the Phylotastic Taxonomic Name Resolution Service.
gni_search

Search for taxonomic names using the Global Names Index.
rankagg

Aggregate data by given taxonomic rank
itis_lsid

Get kingdom names.
tp_accnames

Return all accepted names for a taxon name with a given id.
taxize-package

Taxonomic information from around the web.
taxize-deprecated

Deprecated functions in taxize
taxize-defunct

Defunct functions in taxize
ncbi_getbyname

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

Get comment detail from TSN
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
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
get_ids

Retrieve taxonomic identifiers for a given taxon name.
gisd_isinvasive

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

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

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

Aggregate species data to given taxonomic rank
taxize_cite

Get citations and licenses for data sources used in taxize
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
nbn_classifcation

Search UK National Biodiversity Network database for taxonomic classification
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
ncbi_get_taxon_summary

NCBI taxon information from uids
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
searchforanymatchpaged

Search for any matched page
synonyms

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

Search for tsn by common name beginning with
tp_classification

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

Get rank for a given taxonomic name.
getkey

Function to get API key.
taxize_ldfast

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

Search uBio for taxonomic synonyms by hierarchiesID.
tp_acceptednames

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

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

Search uBio by namebank ID.
tp_dist

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

Search for taxonomy data from Plantminer.com
getranknames

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

Get taxonomic names for a given rank.
getkingdomnamefromtsn

Get kingdom names from tsn
eol_invasive

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

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

Search for tsn by common name ending with
tp_search

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

Get currency from tsn
ubio_classification_search

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

Get expert information for the TSN.
apg_families

Lookup-table for APGIII family names
col_children

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

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

This function will return all ClassificationBank data pertaining to a particular ClassificationBankID
class2tree

Convert list of classifications to a tree.
col_classification

Search Catalogue of Life for taxonomic classifications.
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.
gettsnbyvernacularlanguage

Get tsn by vernacular language
getlastchangedate

Provides the date the ITIS database was last updated.
getvernacularlanguages

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

Retrieve accepted TSN (with accepted name).
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
tp_refs

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

Get The Plant List csv files.
itis_hierarchy

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

Search by scientific name