R: Interface to the 'Open Tree of Life' API

# Interface to the 'Open Tree of Life' API

## Documentation for package ‘rotl’ version 3.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

rotl-package | An Interface to the Open Tree of Life API
candidate_for_synth | Study Metadata
candidate_for_synth.study_meta | Study Metadata
flags | 'ott_id' and 'flags' for taxonomic names matched by 'tnrs_match_names'
flags.match_names | 'ott_id' and 'flags' for taxonomic names matched by 'tnrs_match_names'
flags.taxon_info | Taxon information
flags.taxon_mrca | Taxonomic MRCA
get_publication | Study Metadata
get_publication.study_meta | Study Metadata
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
get_study_year | Study Metadata
get_study_year.study_meta | Study Metadata
get_tree_ids | Study Metadata
get_tree_ids.study_meta | Study Metadata
inspect | Inspect and Update alternative matches for a name returned by tnrs_match_names
inspect.match_names | Inspect and Update alternative matches for a name returned by tnrs_match_names
is_in_tree | Check that OTT ids occur in the Synthetic Tree
is_suppressed | Methods for Taxonomy
is_suppressed.taxon_info | Taxon information
is_suppressed.taxon_mrca | Taxonomic MRCA
list_trees | List trees ids in objects returned by 'studies_find_studies' and 'studies_find_trees'.
list_trees.matched_studies | List trees ids in objects returned by 'studies_find_studies' and 'studies_find_trees'.
ott_id | Methods for Taxonomy
ott_id.match_names | 'ott_id' and 'flags' for taxonomic names matched by 'tnrs_match_names'
ott_id.taxon_info | Taxon information
ott_id.taxon_mrca | Taxonomic MRCA
ott_id.tol_mrca | MRCA of taxa from the synthetic tree
ott_id.tol_node | Node info
ott_id.tol_summary | Information about the Tree of Life
rotl | An Interface to the Open Tree of Life API
source_list | List of studies used in the Tree of Life
source_list.tol_mrca | MRCA of taxa from the synthetic tree
source_list.tol_node | Node info
source_list.tol_summary | 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 | Methods for Taxonomy
synonyms.match_names | List the synonyms for a given name
synonyms.taxon_info | Taxon information
taxonomy_about | Information about the Open Tree Taxonomy
taxonomy_mrca | Taxonomic MRCA
taxonomy_subtree | Taxonomy subtree
taxonomy_taxon_info | Taxon information
taxon_external_IDs | Get external identifiers for data associated with an Open Tree taxon
tax_lineage | Lineage of a taxon
tax_lineage.taxon_info | Lineage of a taxon
tax_lineage.tol_node | Node info
tax_name | Methods for Taxonomy
tax_name.taxon_info | Taxon information
tax_name.taxon_mrca | Taxonomic MRCA
tax_name.tol_mrca | MRCA of taxa from the synthetic tree
tax_name.tol_node | Node info
tax_name.tol_summary | Information about the Tree of Life
tax_rank | Methods for Taxonomy
tax_rank.taxon_info | Taxon information
tax_rank.taxon_mrca | Taxonomic MRCA
tax_rank.tol_mrca | MRCA of taxa from the synthetic tree
tax_rank.tol_node | Node info
tax_rank.tol_summary | Information about the Tree of Life
tax_sources | Methods for Taxonomy
tax_sources.taxon_info | Taxon information
tax_sources.taxon_mrca | Taxonomic MRCA
tax_sources.tol_mrca | MRCA of taxa from the synthetic tree
tax_sources.tol_node | Node info
tax_sources.tol_summary | Information about the Tree of Life
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_lineage | Node info
tol_lineage.tol_node | Node info
tol_mrca | MRCA of taxa from the synthetic tree
tol_node_info | Node info
tol_subtree | Extract a subtree from the synthetic tree
unique_name | Methods for Taxonomy
unique_name.taxon_info | Taxon information
unique_name.taxon_mrca | Taxonomic MRCA
unique_name.tol_mrca | MRCA of taxa from the synthetic tree
unique_name.tol_node | Node info
unique_name.tol_summary | Information about the Tree of Life
update.match_names | Inspect and Update alternative matches for a name returned by tnrs_match_names