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rotl (version 0.5.0)

Interface to the 'Open Tree of Life' API

Description

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

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Install

install.packages('rotl')

Monthly Downloads

9,145

Version

0.5.0

License

BSD_2_clause + file LICENSE

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Repository

https://github.com/ropensci/rotl

Maintainer

Francois Michonneau

Last Published

February 3rd, 2016

Functions in rotl (0.5.0)

studies_find_studies

Strip OTT ids from tip labels

synonyms.match_names

List the synonyms for a given name

tnrs_infer_context

Infer the taxonomic context from a list of names

Information about the Graph of Life

inspect.match_names

Inspect and Update alternative matches for a name returned by tnrs_match_names

Extract a subtree from the synthetic tree

tol_induced_subtree

Subtree from the Open Tree of Life

get_study_subtree

taxonomy_subtree

Taxonomy subtree

About the Open Tree Taxonomy

tnrs_match_names

Match names to the Open Tree Taxonomy

MRCA of taxa from the synthetic tree

List trees ids in objects returned by studies_find_studies and studies_find_trees.

Get all the trees associated with a particular study

ott_id.match_names

ott_id and flags for taxonomic names matched by tnrs_match_names

An Interface to the Open Tree of Life API

studies_properties

Properties of the Studies

Methods for Taxonomy

List of studies used in the Tree of Life

studies_find_trees

Taxon information

Information about the Tree of Life