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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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Install
install.packages('taxize')
Monthly Downloads
26,874
Version
0.1.0
License
CC0
Maintainer
Scott Chamberlain
Last Published
October 27th, 2013
Functions in taxize (0.1.0)
Search functions
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.