Interface to the 'Open Tree of Life' API
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Documentation for package ‘rotl’ version 3.1.0
Help Pages
| 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 |