All functions

get_study()

Get all the trees associated with a particular study

get_tree_ids() get_publication() candidate_for_synth() get_study_year() 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.

ott_id(<match_names>) flags()

ott_id and flags for taxonomic names matched by tnrs_match_names

inspect() update(<match_names>)

Inspect and Update alternative matches for a name returned 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

tax_rank() ott_id() synonyms() tax_sources() is_suppressed() unique_name() tax_name()

Methods for Taxonomy

taxonomy_about()

Information about the Open Tree Taxonomy

taxonomy_mrca() tax_rank(<taxon_mrca>) tax_name(<taxon_mrca>) ott_id(<taxon_mrca>) unique_name(<taxon_mrca>) tax_sources(<taxon_mrca>) flags(<taxon_mrca>) is_suppressed(<taxon_mrca>)

Taxonomic MRCA

taxonomy_subtree()

Taxonomy subtree

taxonomy_taxon_info() tax_rank(<taxon_info>) tax_name(<taxon_info>) unique_name(<taxon_info>) synonyms(<taxon_info>) ott_id(<taxon_info>) tax_sources(<taxon_info>) is_suppressed(<taxon_info>) flags(<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() tax_rank(<tol_summary>) tax_sources(<tol_summary>) unique_name(<tol_summary>) tax_name(<tol_summary>) ott_id(<tol_summary>)

Information about the Tree of Life

tol_induced_subtree()

Subtree from the Open Tree of Life

tol_mrca() tax_sources(<tol_mrca>) unique_name(<tol_mrca>) tax_name(<tol_mrca>) tax_rank(<tol_mrca>) ott_id(<tol_mrca>) source_list(<tol_mrca>)

MRCA of taxa from the synthetic tree

tol_lineage() tol_node_info() tax_rank(<tol_node>) tax_sources(<tol_node>) unique_name(<tol_node>) tax_name(<tol_node>) ott_id(<tol_node>) source_list(<tol_node>) tax_lineage(<tol_node>)

Node info

tol_subtree()

Extract a subtree from the synthetic tree