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taxize (version 0.1.8)

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

0.1.8

License

CC0

Maintainer

Scott Chamberlain

Last Published

December 27th, 2013

Functions in taxize (0.1.8)

rank_ref

Lookup-table for IDs of taxonomic ranks
eol_dataobjects

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

Get hierarchy down from tsn
apg_lookup

Lookup in the APGII taxonomy and replace family names.
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
col_children

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

Retrieve the taxonomic hierarchy for a given taxon ID.
get_eolid

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

Lookup-table for APGIII order names
getanymatchcount

Get any match count.
getparenttsnfromtsn

Returns the parent TSN for the entered 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.
getcoremetadatafromtsn

Get core metadata from tsn
col_search

Search Catalogue of Life for taxonomic IDs
getfullhierarchyfromtsn

Get full hierarchy from tsn
gnr_resolve

Resolve names using Global Names Resolver.
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
comm2sci

Get scientific names from common names.
searchbycommonname

Search for tsn by common name
getfullrecordfromtsn

Get full record from TSN.
get_ids

Retrieve taxonomic identifiers for a given taxon name.
col_classification

Search Catalogue of Life for taxonomic classifications.
getacceptednamesfromtsn

Get accepted names from tsn
tax_rank

Get rank for a given taxonomic name.
get_tsn

Get the TSN code for a search term.
ncbi_getbyname

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

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

Returns the review year for the TSN.
getjurisdictionoriginvalues

Get jurisdiction origin values
getscientificnamefromtsn

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

Search for taxonomy data from Plantminer.com
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
getcurrencyfromtsn

Get currency from tsn
getitistermsfromcommonname

Get itis terms from common names
searchbycommonnamebeginswith

Search for tsn by common name beginning with
getcommentdetailfromtsn

Get comment detail from TSN
ncbi_search

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

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

Function to parse xml data and decode strings
get_colid

Get the Catalogue of Life ID from taxonomic names.
getdatedatafromtsn

Get date data from tsn
get_genes

Retrieve gene sequences from NCBI by accession number.
getranknames

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

Get global species completeness from tsn
itis_native

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

Get common names from tsn
getlsidfromtsn

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

Get jurisdictional origin from tsn
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
eol_pages

Search for pages in EOL database using a taxonconceptID.
getjurisdictionvalues

Get possible jurisdiction values
getitisterms

Get itis terms from common names
getkingdomnamefromtsn

Get kingdom names from tsn
gbif_parse

Parse taxon names using the GBIF name parser.
get_seqs

Retrieve gene sequences from NCBI by accession number.
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
eol_search

Search for terms in EOL database.
getlastchangedate

Provides the date the ITIS database was last updated.
get_uid

Get the UID codes from NCBI for taxonomic names.
ubio_search

This function will return NameBankIDs that match given search terms
getcoveragefromtsn

Get coverge from tsn
tax_agg

Aggregate species data to given taxonomic rank
getcredibilityratingfromtsn

Get credibility rating from tsn
searchbycommonnameendswith

Search for tsn by common name ending with
tp_accnames

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

Get possible credibility ratings
iucn_summary

Get a summary from the IUCN Red List.
gnr_datasources

Get data sources for the Global Names Resolver.
gni_details

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

Function to get API key.
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
getkingdomnames

Get all possible kingdom names
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
itis_downstream

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

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

Search for taxonomic names using the Global Names Index.
col_downstream

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

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

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

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

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

Get hierarchy up from tsn
taxize_ldfast

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

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

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

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

Retrieve gene sequences from NCBI by accession number.
iucn_getname

Get any matching IUCN species names
itis_getrecord

Get full ITIS record for one or more ITIS TSN's or lsid's.
sci2comm

Get common names from scientific names.
taxize-deprecated

Deprecated functions in taxize
plantGenusNames

Vector of 793 genus names of plants
scrapenames

Resolve names using Global Names Recognition and Discovery.
tpl_search

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

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

Retrieve taxonomic rank name from given TSN.
tpl_get

Get The Plant List csv files.
rankagg

Aggregate data by given taxonomic rank
tp_dist

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

Get kingdom names.
ubio_synonyms

Search uBio by namebank ID.
taxize-package

Taxnomic search and phylogeny retrieval.
tp_search

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

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

Search uBio by namebank ID.
iucn_status

Extractor functions for iucn-class.
searchforanymatch

Search for any match
tax_name

Get taxonomic names for a given rank.
tp_classification

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

Get The Plant List families.
getitistermsfromscientificname

Get itis terms from scientific names
getgeographicvalues

Get all possible geographic values
tp_synonyms

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

Vector of 1,182 species names of plants
getunacceptabilityreasonfromtsn

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

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

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

Get kingdom names.
itis_acceptname

Retrieve accepted TSN (with accepted name).
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
itis_refs

Get references related to a ITIS TSN.
ubio_classification_search

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

Capitalize the first letter of a character string.
tp_acceptednames

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

Get description of the ITIS service
searchforanymatchpaged

Search for any matched page
synonyms

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

Search the CANADENSYS Vascan API.
eol_invasive

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

Get taxonomic names for a given taxonomic name query.
getsynonymnamesfromtsn

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

Search by scientific name
gni_parse

Parse scientific names using EOL's name parser.
apg_families

Lookup-table for APGIII family names
eol_ping

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

Get expert information for the TSN.
names_list

Get a random vector of species names.
itis_searchcommon

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

Search the Phylotastic Taxonomic Name Resolution Service.
tp_namereferences

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