Package: rotl 3.1.0
Francois Michonneau
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.
Authors:
rotl_3.1.0.tar.gz
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rotl_3.1.0.tgz(r-4.4-any)rotl_3.1.0.tgz(r-4.3-any)
rotl_3.1.0.tar.gz(r-4.5-noble)rotl_3.1.0.tar.gz(r-4.4-noble)
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rotl.pdf |rotl.html✨
rotl/json (API)
NEWS
| # Install 'rotl' in R: |
| install.packages('rotl', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/rotl/issues
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
Last updated 1 years agofrom:57e800c2b1 (on master). Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 28 2024 |
| R-4.5-win | NOTE | Oct 28 2024 |
| R-4.5-linux | NOTE | Oct 28 2024 |
| R-4.4-win | NOTE | Oct 28 2024 |
| R-4.4-mac | NOTE | Oct 28 2024 |
| R-4.3-win | OK | Oct 28 2024 |
| R-4.3-mac | OK | Oct 28 2024 |
Exports:candidate_for_synthflagsget_publicationget_studyget_study_metaget_study_subtreeget_study_treeget_study_yearget_tree_idsinspectis_in_treeis_suppressedlist_treesott_idsource_liststrip_ott_idsstudies_find_studiesstudies_find_treesstudies_propertiesstudy_external_IDssynonymstax_lineagetax_nametax_ranktax_sourcestaxon_external_IDstaxonomy_abouttaxonomy_mrcataxonomy_subtreetaxonomy_taxon_infotnrs_contextstnrs_infer_contexttnrs_match_namestol_abouttol_induced_subtreetol_lineagetol_mrcatol_node_infotol_subtreeunique_name
Dependencies:apeaskpassclicrayoncurldigestgluehmshttrjsonlitelatticelifecyclemimenlmeopensslpkgconfigprettyunitsprogressR6RcpprentrezrlangrnclsysvctrsXML
Connecting data to Open Tree trees
Rendered fromdata_mashups.Rmdusingknitr::rmarkdownon Oct 28 2024.Last update: 2023-06-13
Started: 2015-07-09
How to use rotl?
Rendered fromrotl.Rmdusingknitr::rmarkdownon Oct 28 2024.Last update: 2023-06-13
Started: 2019-03-21
Using the Open Tree synthesis in a comparative analysis
Rendered frommeta-analysis.Rmdusingknitr::rmarkdownon Oct 28 2024.Last update: 2023-06-13
Started: 2015-10-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get all the trees associated with a particular study | get_study |
| Study Subtree | get_study_subtree |
| Study Tree | get_study_tree |
| Study Metadata | candidate_for_synth candidate_for_synth.study_meta get_publication get_publication.study_meta get_study_meta get_study_year get_study_year.study_meta get_tree_ids get_tree_ids.study_meta |
| Inspect and Update alternative matches for a name returned by tnrs_match_names | inspect inspect.match_names update.match_names |
| Check that OTT ids occur in the Synthetic Tree | is_in_tree |
| List trees ids in objects returned by 'studies_find_studies' and 'studies_find_trees'. | list_trees list_trees.matched_studies |
| 'ott_id' and 'flags' for taxonomic names matched by 'tnrs_match_names' | flags flags.match_names ott_id.match_names |
| An Interface to the Open Tree of Life API | rotl |
| List of studies used in the Tree of Life | source_list source_list.tol_summary |
| Strip OTT ids from tip labels | strip_ott_ids |
| Find a Study | studies_find_studies |
| Find Trees | studies_find_trees |
| Properties of the Studies | studies_properties |
| Get external identifiers for data associated with an Open Tree study | study_external_IDs |
| List the synonyms for a given name | synonyms.match_names |
| Lineage of a taxon | tax_lineage tax_lineage.taxon_info |
| Methods for Taxonomy | is_suppressed ott_id synonyms tax_name tax_rank tax_sources unique_name |
| Get external identifiers for data associated with an Open Tree taxon | taxon_external_IDs |
| Information about the Open Tree Taxonomy | taxonomy_about |
| Taxonomic MRCA | flags.taxon_mrca is_suppressed.taxon_mrca ott_id.taxon_mrca taxonomy_mrca tax_name.taxon_mrca tax_rank.taxon_mrca tax_sources.taxon_mrca unique_name.taxon_mrca |
| Taxonomy subtree | taxonomy_subtree |
| Taxon information | flags.taxon_info is_suppressed.taxon_info ott_id.taxon_info synonyms.taxon_info taxonomy_taxon_info tax_name.taxon_info tax_rank.taxon_info tax_sources.taxon_info unique_name.taxon_info |
| TNRS contexts | tnrs_contexts |
| Infer the taxonomic context from a list of names | tnrs_infer_context |
| Match names to the Open Tree Taxonomy | tnrs_match_names |
| Information about the Tree of Life | ott_id.tol_summary tax_name.tol_summary tax_rank.tol_summary tax_sources.tol_summary tol_about unique_name.tol_summary |
| Subtree from the Open Tree of Life | tol_induced_subtree |
| Node info | ott_id.tol_node source_list.tol_node tax_lineage.tol_node tax_name.tol_node tax_rank.tol_node tax_sources.tol_node tol_lineage tol_lineage.tol_node tol_node_info unique_name.tol_node |
| MRCA of taxa from the synthetic tree | ott_id.tol_mrca source_list.tol_mrca tax_name.tol_mrca tax_rank.tol_mrca tax_sources.tol_mrca tol_mrca unique_name.tol_mrca |
| Extract a subtree from the synthetic tree | tol_subtree |
