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taxize (version 0.2.0)

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

0.2.0

License

CC0

Maintainer

Scott Chamberlain

Last Published

February 17th, 2014

Functions in taxize (0.2.0)

getacceptednamesfromtsn

Get accepted names from tsn
gbif_parse

Parse taxon names using the GBIF name parser.
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
getanymatchcount

Get any match count.
get_ids

Retrieve taxonomic identifiers for a given taxon name.
col_children

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

Retrieve accepted TSN (with accepted name).
col_search

Search Catalogue of Life for taxonomic IDs
getcurrencyfromtsn

Get currency from tsn
itis_refs

Get references related to a ITIS TSN.
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
getcommentdetailfromtsn

Get comment detail from TSN
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
getdatedatafromtsn

Get date data from tsn
getitisterms

Get itis terms from common names
get_genes

Retrieve gene sequences from NCBI by accession number.
get_tsn

Get the TSN code for a search term.
getjurisdictionoriginvalues

Get jurisdiction origin values
getgeographicdivisionsfromtsn

Get geographic divisions from tsn
class2tree

Convert list of classifications to a tree.
apg_families

Lookup-table for APGIII family names
col_classification

Search Catalogue of Life for taxonomic classifications.
getfullhierarchyfromtsn

Get full hierarchy from tsn
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
gni_parse

Parse scientific names using EOL's name parser.
get_colid

Get the Catalogue of Life ID from taxonomic names.
getgeographicvalues

Get all possible geographic values
getunacceptabilityreasonfromtsn

Returns the unacceptability reason, if any, for the TSN.
comm2sci

Get scientific names from common names.
getexpertsfromtsn

Get expert information for the TSN.
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
get_eolid

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

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

Get itis terms from scientific names
getjurisdictionvalues

Get possible jurisdiction values
eol_pages

Search for pages in EOL database using a taxonconceptID.
gethierarchyupfromtsn

Get hierarchy up from tsn
tax_rank

Get rank for a given taxonomic name.
eol_ping

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

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

Search for taxonomic names using the Global Names Index.
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.
searchbycommonnamebeginswith

Search for tsn by common name beginning with
getranknames

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

Get hierarchy down from tsn
getcredibilityratingfromtsn

Get credibility rating from tsn
getsynonymnamesfromtsn

Returns a list of the synonyms (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.
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
getfullrecordfromtsn

Get full record from TSN.
eol_invasive

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

Get core metadata from tsn
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
apg_orders

Lookup-table for APGIII order names
gbif_suggestfields

Fields available in gbif_suggest function
getcredibilityratings

Get possible credibility ratings
get_uid

Get the UID codes from NCBI for taxonomic names.
getcoveragefromtsn

Get coverge from tsn
getitistermsfromcommonname

Get itis terms from common names
getdescription

Get description of the ITIS service
getkingdomnamefromtsn

Get kingdom names from tsn
getxmldata

Function to parse xml data and decode strings
col_downstream

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

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

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

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

Retrieve accepted TSN (with accepted name)
getpublicationsfromtsn

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

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

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

Get common names from tsn
getkingdomnames

Get all possible kingdom names
gnr_resolve

Resolve names using Global Names Resolver.
ubio_classification_search

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

Get The Plant List csv files.
gisd_isinvasive

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

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

Returns the parent TSN for the entered TSN.
apg_genera

Table of APGIII generic names
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
tpl_families

Get The Plant List families.
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.
rankagg

Aggregate data by given taxonomic rank
getreviewyearfromtsn

Returns the review year for the TSN.
getothersourcesfromtsn

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

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

Provides the date the ITIS database was last updated.
taxize_ldfast

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

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

Search by scientific name
getkey

Function to get API key.
itis_taxrank

Retrieve taxonomic rank name from given TSN.
plantNames

Vector of 1,182 species names of plants
tp_namedistributions

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

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

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

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

Get kingdom names.
searchbycommonnameendswith

Search for tsn by common name ending with
itis_getrecord

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

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

Get taxonomic names for a given taxonomic name query.
sci2comm

Get common names from scientific names.
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.
gnr_datasources

Get data sources for the Global Names Resolver.
itis_lsid

Get kingdom names.
taxize_capwords

Capitalize the first letter of a character string.
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
taxize-deprecated

Deprecated functions in taxize
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
iucn_getname

Get any matching IUCN species names
plantminer

Search for taxonomy data from Plantminer.com
scrapenames

Resolve names using Global Names Recognition and Discovery.
tax_name

Get taxonomic names for a given rank.
rank_ref

Lookup-table for IDs of taxonomic ranks
gni_details

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

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

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

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

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

Taxnomic search and phylogeny retrieval.
tp_namereferences

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

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

Extractor functions for iucn-class.
ubio_id

Search uBio by namebank ID.
itis_native

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

Aggregate species data to given taxonomic rank
theplantlist

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

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

Search for any match
tp_classification

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

Search uBio by namebank ID.
names_list

Get a random vector of species names.
vascan_search

Search the CANADENSYS Vascan API.
searchbycommonname

Search for tsn by common name
ubio_search

This function will return NameBankIDs that match given search terms
searchforanymatchpaged

Search for any matched page
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
tp_accnames

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

Search for terms in EOL database.
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
get_seqs

Retrieve gene sequences from NCBI by accession number.
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
plantGenusNames

Vector of 793 genus names of plants
eol_dataobjects

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