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taxize (version 0.1.5)

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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Version

Install

install.packages('taxize')

Monthly Downloads

5,250

Version

0.1.5

License

CC0

Maintainer

Scott Chamberlain

Last Published

November 19th, 2013

Functions in taxize (0.1.5)

gbif_parse

Parse taxon names using the GBIF name parser.
eol_hierarchy

Retrieve the taxonomic hierarchy from given EOL taxonID.
getcredibilityratings

Get possible credibility ratings
getcoveragefromtsn

Get coverge from tsn
getpublicationsfromtsn

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

Get the TSN code for a search term.
getglobalspeciescompletenessfromtsn

Get global species completeness from tsn
get_genes_avail

Retrieve gene sequences available for a species from NCBI.
searchbycommonnamebeginswith

Search for tsn by common name beginning with
classification

Retrieve the taxonomic hierarchy for a given taxon ID.
getdatedatafromtsn

Get date data from tsn
getothersourcesfromtsn

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

Function to collapse a double phylogenetic tree root
gettaxonauthorshipfromtsn

Returns the author information for the TSN.
eol_search

Search for terms in EOL database.
apg_families

Lookup-table for APGIII family names
col_search

Search Catalogue of Life for taxonomic IDs
get_seqs

Retrieve nucleotide sequences from NCBI.
getscientificnamefromtsn

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

Get all possible geographic values
getfullrecordfromtsn

Get full record from TSN.
gettaxonomicusagefromtsn

Returns the usage information for the TSN.
getcredibilityratingfromtsn

Get credibility rating from tsn
getcommentdetailfromtsn

Get comment detail from TSN
ifelsedata

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

Get geographic divisions from tsn
getvernacularlanguages

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

Print a message if verbose is TRUE, but don't if FALSE
itis_downstream

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

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

Aggregate data by given taxonomic rank
getkingdomnames

Get all possible kingdom names
getdescription

Get description of the ITIS service
getjurisdictionaloriginfromtsn

Get jurisdictional origin from tsn
getanymatchcount

Get any match count.
gisd_isinvasive

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

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

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

Get the NameID codes from Tropicos for taxonomic names.
getsynonymnamesfromtsn

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

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

Retrieve gene sequences from NCBI by accession number.
getitistermsfromcommonname

Get itis terms from common names
iucn_status

Extractor functions for iucn-class.
itis_lsid

Get kingdom names.
get_uid

Get the UID codes from NCBI for taxonomic names.
tpl_families

Get The Plant List families.
getjurisdictionvalues

Get possible jurisdiction values
getlsidfromtsn

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

Get accepted names from tsn
plantGenusNames

Vector of 793 genus names of plants
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_pages

Search for pages in EOL database using a taxonconceptID.
gnr_resolve

Resolve names using Global Names Resolver.
plantminer

Search for taxonomy data from Plantminer.com
itis_refs

Get references related to a ITIS TSN.
tpl_get

Get The Plant List csv files.
colldouble

Function to to do things
eol_invasive

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

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

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

Get hierarchy up from tsn
getkingdomnamefromtsn

Get kingdom names from tsn
getcoremetadatafromtsn

Get core metadata from tsn
gettsnbyvernacularlanguage

Retrieve accepted TSN (with accepted name)
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.
get_eolid

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

Lookup-table for IDs of taxonomic ranks
get_colid

Get the Catalogue of Life ID from taxonomic names.
searchbycommonname

Search for tsn by common name
itis_getrecord

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

Search for any match
searchbyscientificname

Search by scientific name
gni_parse

Parse scientific names using EOL's name parser.
itis_kingdomnames

Get kingdom names.
plantNames

Vector of 1,182 species names of plants
tnrs

Search the Phylotastic Taxonomic Name Resolution Service.
tax_rank

Get rank for a given taxonomic name.
taxize_capwords

Capitalize the first letter of a character string.
gni_search

Search for taxonomic names using the Global Names Index.
itis_taxrank

Retrieve taxonomic rank name from given TSN.
ubio_synonyms

Search uBio by namebank ID.
itis_native

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

Get data sources for the Global Names Resolver.
sci2comm

Get common names from scientific names.
getkey

Function to get API key.
getxml_syns

Function to parse xml data and decode strings
apg_lookup

Lookup in the APGII taxonomy and replace family names.
tp_namedistributions

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

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

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

Ping the ITIS API to see if it's working.
taxize-package

Taxnomic search and phylogeny retrieval.
ubio_id

Search uBio by namebank ID.
iucn_getname

Get any matching IUCN species names
ubio_classification_search

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

Get a summary from the IUCN Red List.
getitistermsfromscientificname

Get itis terms from scientific names
searchbycommonnameendswith

Search for tsn by common name ending with
tp_classification

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

Get jurisdiction origin values
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.
gettaxonomicranknamefromtsn

Returns the kingdom and rank information for the TSN.
itis_terms

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

Get sources for the Phylotastic Taxonomic Name Resolution Service.
getexpertsfromtsn

Get expert information for the TSN.
tax_agg

Aggregate species data to given taxonomic rank
tp_synonyms

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

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

Search Catalogue of Life for taxonomic classifications.
apg_orders

Lookup-table for APGIII order names
comm2sci

Get scientific names from common names.
get_ids

Retrieve taxonomic identifiers for a given taxon name.
eol_dataobjects

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

Get full hierarchy from tsn
names_list

Get a random vector of species names.
tp_summary

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

Get currency from tsn
ubio_classification

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

Returns the review year for the TSN.
gni_details

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

Search for any matched page
getcommonnamesfromtsn

Get common names from tsn
phylomatic_tree

Format tree string, submit to Phylomatic, get newick or nexml tree.
synonyms

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

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

This function will return NameBankIDs that match given search terms
gethierarchydownfromtsn

Get hierarchy down from tsn
getitisterms

Get itis terms from common names
getparenttsnfromtsn

Returns the parent TSN for the entered TSN.
ldfast

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

Get taxonomic names for a given taxonomic name query.
getlastchangedate

Provides the date the ITIS database was last updated.
getxmldata

Function to parse xml data and decode strings
itis_acceptname

Retrieve accepted TSN (with accepted name).
tpl_search

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