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rotl

Interface to the 'Open Tree of Life' API

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.

Functions (31)

get_study

Get all the trees associated with a particular study

get_study_meta

Study Metadata

get_study_subtree

Study Subtree

get_study_tree

Study Tree

is_in_tree

Check that OTT ids occur in the Synthetic Tree

list_trees

List trees ids in objects returned by studies_find_studies and studies_find_trees.

match_names

Inspect and Update alternative matches for a name returned by tnrs_match_names

match_names-methods

ott_id and flags for taxonomic names matched by tnrs_match_names

rotl

An Interface to the Open Tree of Life API

source_list

List of studies used in the Tree of Life

strip_ott_ids

Strip OTT ids from tip labels

studies_find_studies

Find a Study

studies_find_trees

Find Trees

studies_properties

Properties of the Studies

study_external_IDs

Get external identifiers for data associated with an Open Tree study

synonyms.match_names

List the synonyms for a given name

tax_lineage

Lineage of a taxon

taxon_external_IDs

Get external identifiers for data associated with an Open Tree taxon

taxonomy-methods

Methods for Taxonomy

taxonomy_about

Information about the Open Tree Taxonomy

taxonomy_mrca

Taxonomic MRCA

taxonomy_subtree

Taxonomy subtree

taxonomy_taxon_info

Taxon information

tnrs_contexts

TNRS contexts

tnrs_infer_context

Infer the taxonomic context from a list of names

tnrs_match_names

Match names to the Open Tree Taxonomy

tol_about

Information about the Tree of Life

tol_induced_subtree

Subtree from the Open Tree of Life

tol_mrca

MRCA of taxa from the synthetic tree

tol_node_info

Node info

tol_subtree

Extract a subtree from the synthetic tree

rotl

Interface to the 'Open Tree of Life' API

v3.0.11

BSD_2_clause + file LICENSE

Authors

Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)

Initial release

rotl

Functions (31)

rotl

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