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taxize (version 0.2.2)

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')

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Version

0.2.2

License

CC0

Issues

51

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280

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Maintainer

Scott Chamberlain

Last Published

March 2nd, 2014

Functions in taxize (0.2.2)

apg_families

Lookup-table for APGIII family names
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
col_classification

Search Catalogue of Life for taxonomic classifications.
getjurisdictionvalues

Get possible jurisdiction values
get_tpsid

Get the NameID codes from Tropicos for taxonomic names.
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.
get_tsn

Get the TSN code for a search term.
col_children

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

Get geographic divisions from tsn
gbif_suggestfields

Fields available in gbif_suggest function
col_search

Search Catalogue of Life for taxonomic IDs
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
class2tree

Convert list of classifications to a tree.
eol_search

Search for terms in EOL database.
getdatedatafromtsn

Get date data from tsn
phylomatic_format

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

Get currency from tsn
getunacceptabilityreasonfromtsn

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

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

Function to get API key.
eol_invasive

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

Get credibility rating from tsn
gethierarchyupfromtsn

Get hierarchy up from tsn
get_uid

Get the UID codes from NCBI for taxonomic names.
get_gbifid

Get the GBIF backbone taxon ID from taxonomic names.
getranknames

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

Get any matching IUCN species names
getscientificnamefromtsn

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

Retrieve the downstream taxa for a given taxon name or ID.
comm2sci

Get scientific names from common names.
getcoveragefromtsn

Get coverge from tsn
itis_ping

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

Aggregate data by given taxonomic rank
itis_acceptname

Retrieve accepted TSN (with accepted name).
apg_orders

Lookup-table for APGIII order names
getxmldata

Function to parse xml data and decode strings
gnr_resolve

Resolve names using Global Names Resolver.
getkingdomnamefromtsn

Get kingdom names from tsn
getjurisdictionoriginvalues

Get jurisdiction origin values
gbif_parse

Parse taxon names using the GBIF name parser.
getreviewyearfromtsn

Returns the review year for the TSN.
ncbi_getbyname

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

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

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

Resolve names using Global Names Recognition and Discovery.
getcoremetadatafromtsn

Get core metadata from tsn
gni_parse

Parse scientific names using EOL's name parser.
apg_genera

Table of APGIII generic names
searchbycommonnamebeginswith

Search for tsn by common name beginning with
apg_lookup

Lookup in the APGII taxonomy and replace family names.
ncbi_search

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

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

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

Provides the date the ITIS database was last updated.
sci2comm

Get common names from scientific names.
itis_refs

Get references related to a ITIS 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.
getcommentdetailfromtsn

Get comment detail from TSN
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
getexpertsfromtsn

Get expert information for the TSN.
iucn_summary

Get a summary from the IUCN Red List.
getfullrecordfromtsn

Get full record from TSN.
get_colid

Get the Catalogue of Life ID from taxonomic names.
tax_name

Get taxonomic names for a given rank.
getcommonnamesfromtsn

Get common names from tsn
getvernacularlanguages

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

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

Returns the kingdom and rank information for the TSN.
getfullhierarchyfromtsn

Get full hierarchy from tsn
tp_acceptednames

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

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

Get taxonomic names for a given taxonomic name query.
eol_pages

Search for pages in EOL database using a taxonconceptID.
tp_synonyms

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

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

Get itis terms from common names
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
ubio_search

This function will return NameBankIDs that match given search terms
gnr_datasources

Get data sources for the Global Names Resolver.
taxize_ldfast

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

Retrieve gene sequences from NCBI by accession number.
gni_search

Search for taxonomic names using the Global Names Index.
ubio_classification

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

Extractor functions for iucn-class.
tpl_search

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

Get jurisdictional origin from tsn
get_ids

Retrieve taxonomic identifiers for a given taxon name.
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
getpublicationsfromtsn

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

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

Get itis terms from scientific names
getsynonymnamesfromtsn

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

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

Get any match count.
itis_kingdomnames

Get kingdom names.
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
getgeographicvalues

Get all possible geographic values
tax_rank

Get rank for a given taxonomic name.
gisd_isinvasive

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

Search for any matched page
getlsidfromtsn

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

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

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

Search uBio by namebank ID.
get_genes_avail

Retrieve gene sequences from NCBI by accession number.
ubio_classification_search

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

Vector of 793 genus names of plants
names_list

Get a random vector of species names.
tp_dist

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

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

Search by scientific name
ubio_synonyms

Search uBio by namebank ID.
tnrs_sources

Get sources for the Phylotastic Taxonomic Name Resolution Service.
itis_terms

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

Get hierarchy down from tsn
ncbi_getbyid

Retrieve gene sequences from NCBI by accession number.
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
rank_ref

Lookup-table for IDs of taxonomic ranks
itis_searchcommon

Searches common name and acts as thin wrapper around searchbycommonnamebeginswith and searchbycommonnameendswith
taxize-package

Taxnomic search and phylogeny retrieval.
searchbycommonname

Search for tsn by common name
itis_native

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

Get kingdom names.
plantNames

Vector of 1,182 species names of plants
synonyms

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

Get The Plant List families.
tp_search

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

Aggregate species data to given taxonomic rank
searchforanymatch

Search for any match
tpl_get

Get The Plant List csv files.
vascan_search

Search the CANADENSYS Vascan API.
col_downstream

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

Get description of the ITIS service
getkingdomnames

Get all possible kingdom names
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
tp_namedistributions

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

Retrieve taxonomic rank name from given TSN.
eol_ping

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

Retrieve gene sequences from NCBI by accession number.
getacceptednamesfromtsn

Get accepted names from tsn
getitistermsfromcommonname

Get itis terms from common names
getcredibilityratings

Get possible credibility ratings
phylomatic_tree

Query Phylomatic for a phylogenetic tree.
plantminer

Search for taxonomy data from Plantminer.com
searchbycommonnameendswith

Search for tsn by common name ending with
taxize_capwords

Capitalize the first letter of a character string.
taxize-deprecated

Deprecated functions in taxize