Package index • rotl

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