Taxonomic search and phylogeny retrieval.


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Documentation for package ‘taxize’ version 0.0.2

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