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taxize (version 0.0.2)
Taxonomic search and phylogeny retrieval.
Description
Taxonomic search and phylogeny retrieval.
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Install
install.packages('taxize')
Monthly Downloads
9,377
Version
0.0.2
License
CC0
Maintainer
Scott Chamberlain
Last Published
December 7th, 2012
Functions in taxize (0.0.2)
Search all functions
itis_downstream
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
get_genes_avail
Retrieve gene sequences available for a species from NCBI.
eol_pages
Search for pages in EOL database using a taxonconceptID.
plantminer
Search for taxonomy data from Plantminer.com
gnr_resolve
Resolve names using Global Names Resolver.
eol_hierarchy
Retrieve all taxonomic hierarchy from given EOL taxonID.
itis_taxrank
Retrieve taxonomic rank name from given TSN.
get_tsn
Get the TSN code for a search term.
itis_phymat_format
Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.
tp_namereferences
Return all reference records for for a taxon name with a given id.
tp_acceptednames
Return all accepted names for a taxon name with a given id.
getkey
Function to get API key.
eol_search
Search for terms in EOL database.
tp_summary
Return summary data a taxon name with a given id.
ubio_namebank
Search uBio namebank.
classification
Get taxonomic hierarchy for a given taxon ID.
tpl_search
A light wrapper around the taxonstand fxn to call Theplantlist.org database.
itis_name
Get taxonomic names for a given taxonomic name query.
tpl_get
Get The Plant List csv files.
iucn_summary
Get a summary from the IUCN Red List.
itis_acceptname
Retrieve accepted TSN (with accepted name).
gni_search
Search for taxonomic names using the Global Names Index.
phylomatic_tree
Format tree string, submit to Phylomatic, get newick tree.
itis
Use any function in ritis, searching by TSN or taxonomic name.
gni_details
Search for taxonomic name details using the Global Names Index.
gnr_datasources
Get data sources for the Global Names Resolver.
get_uid
Get the UID codes from NCBI for species names.
get_seqs
Retrieve nucleotide sequences from NCBI.
rank_ref
Lookup-table for IDs of taxonomic ranks
taxize-package
Taxnomic search and phylogeny retrieval.
tp_synonyms
Return all synonyms for a taxon name with a given id.
capwords
Capitalize the first letter of a character string.
eol_ping
Ping EOL API to see if it's working.
tp_namedistributions
Return all distribution records for for a taxon name with a given id.