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taxize (version 0.1.0)

Taxonomic information from around the web.

Description

Taxonomic information from around the web.

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Version

Install

install.packages('taxize')

Monthly Downloads

5,250

Version

0.1.0

License

CC0

Maintainer

Scott Chamberlain

Last Published

October 27th, 2013

Functions in taxize (0.1.0)

getdatedatafromtsn

Get date data from tsn
eol_search

Search for terms in EOL database.
getfullrecordfromtsn

Get full record from TSN.
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
getranknames

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

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

Search for pages in EOL database using a taxonconceptID.
getitistermsfromscientificname

Get itis terms from scientific names
gethierarchydownfromtsn

Get hierarchy down from tsn
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
getlastchangedate

Provides the date the ITIS database was last updated.
get_seqs

Retrieve nucleotide sequences from NCBI.
getjurisdictionoriginvalues

Get jurisdiction origin values
gethierarchyupfromtsn

Get hierarchy up from tsn
getcurrencyfromtsn

Get currency from tsn
apg_families

Lookup-table for APGIII family names
getcoremetadatafromtsn

Get core metadata from tsn
getvernacularlanguages

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

Get accepted names from tsn
itis_acceptname

Retrieve accepted TSN (with accepted 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.
gisd_isinvasive

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

Get description of the ITIS service
apg_lookup

Lookup in the APGII taxonomy and replace family names.
getpublicationsfromtsn

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

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

Get itis terms from common names
getcredibilityratings

Get possible credibility ratings
getcommonnamesfromtsn

Get common names from tsn
gni_search

Search for taxonomic names using the Global Names Index.
getanymatchcount

Get any match count.
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
eol_ping

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

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

Get coverge from tsn
gnr_datasources

Get data sources for the Global Names Resolver.
getgeographicvalues

Get all possible geographic values
itis_phymat_format

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

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

Get kingdom names from tsn
get_genes

Retrieve gene sequences from NCBI by accession number.
gnr_resolve

Resolve names using Global Names Resolver.
ldfast

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

Lookup-table for APGIII order names
getcredibilityratingfromtsn

Get credibility rating from tsn
getunacceptabilityreasonfromtsn

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

Retrieve the taxonomic hierarchy from given EOL taxonID.
iucn_getname

Get any matching IUCN species names
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
itis_name

Get taxonomic names for a given taxonomic name query.
get_tsn

Get the TSN code for a search term.
getfullhierarchyfromtsn

Get full hierarchy from tsn
getlsidfromtsn

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

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

Extractor functions for iucn-class.
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
tp_summary

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

Retrieve taxonomic rank name from given TSN.
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
gni_details

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

Format tree string, submit to Phylomatic, get newick tree.
iucn_summary

Get a summary from the IUCN Red List.
plantGenusNames

Vector of 793 genus names of plants
getscientificnamefromtsn

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

Get a random vector of species names.
tpl_search

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

Search Catalogue of Life for taxonomic classifications.
tp_namereferences

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

Get all possible kingdom names
getcommentdetailfromtsn

Get comment detail from TSN
tax_agg

Aggregate species data to given taxonomic rank
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.
searchbycommonnamebeginswith

Search for tsn by common name beginning with
tax_rank

Get rank for a given taxonomic name.
searchforanymatchpaged

Search for any matched page
rankagg

Aggregate data by given taxonomic rank
tax_name

Get taxonomic names for a given rank.
tp_acceptednames

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

Search for tsn by common name ending with
searchbycommonname

Search for tsn by common name
searchforanymatch

Search for any match
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
tpl_get

Get The Plant List csv files.
ubio_namebank

Search uBio namebank.
searchbyscientificname

Search by scientific name
taxize-package

Taxnomic search and phylogeny retrieval.
tp_synonyms

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

Get The Plant List families.
getexpertsfromtsn

Get expert information for the TSN.
getkey

Function to get API key.
gni_parse

Parse scientific names using EOL's name parser.
get_uid

Get the UID codes from NCBI for species names.
plantNames

Vector of 1,182 species names of plants
taxize_capwords

Capitalize the first letter of a character string.
plantminer

Search for taxonomy data from Plantminer.com
rank_ref

Lookup-table for IDs of taxonomic ranks
get_genes_avail

Retrieve gene sequences available for a species from NCBI.
getjurisdictionvalues

Get possible jurisdiction values
getreviewyearfromtsn

Returns the review year for the TSN.
getsynonymnamesfromtsn

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