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.

Author
Francois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Date of publication
2016-09-20 00:45:03
Maintainer
Francois Michonneau <francois.michonneau@gmail.com>
License
BSD_2_clause + file LICENSE
Version
3.0.1
URLs

View on CRAN

Man pages

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
list_trees
List trees ids in objects returned by 'studies_find_studies'...
match_names
Inspect and Update alternative matches for a name returned by...
match_names-methods
'ott_id' and 'flags' for taxonomic names matched by...
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...
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...
taxonomy_about
Information about the Open Tree Taxonomy
taxonomy-methods
Methods for Taxonomy
taxonomy_mrca
Taxonomic MRCA
taxonomy_subtree
Taxonomy subtree
taxonomy_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
Information about the Tree of Life
tol_induced_subtree
Subtree from the Open Tree of Life
tol_mrca
MRCA of taxa from the synthetic tree
tol_node_info
Node info
tol_subtree
Extract a subtree from the synthetic tree

Files in this package

rotl
rotl/inst
rotl/inst/CITATION
rotl/inst/extdata
rotl/inst/extdata/egg.csv
rotl/inst/extdata/protist_mutation_rates.csv
rotl/inst/doc
rotl/inst/doc/how-to-use-rotl.R
rotl/inst/doc/meta-analysis.R
rotl/inst/doc/data_mashups.R
rotl/inst/doc/data_mashups.Rmd
rotl/inst/doc/meta-analysis.html
rotl/inst/doc/meta-analysis.Rmd
rotl/inst/doc/how-to-use-rotl.html
rotl/inst/doc/how-to-use-rotl.Rmd
rotl/inst/doc/data_mashups.html
rotl/tests
rotl/tests/testthat
rotl/tests/testthat/test-api-taxonomy.R
rotl/tests/testthat/test-taxonomy.R
rotl/tests/testthat/test-tnrs.R
rotl/tests/testthat/test-deduplicate_labels.R
rotl/tests/testthat/test-tol.R
rotl/tests/testthat/test-api-studies.R
rotl/tests/testthat/test-external.R
rotl/tests/testthat/test-api-tnrs.R
rotl/tests/testthat/test-match_names.R
rotl/tests/testthat/test-api-tol.R
rotl/tests/testthat/test-API.R
rotl/tests/testthat/test-base.R
rotl/tests/testthat/test-tree_to_labels.R
rotl/tests/testthat/test-studies.R
rotl/tests/tree_of_life.json
rotl/tests/test-all.R
rotl/NAMESPACE
rotl/NEWS.md
rotl/R
rotl/R/studies-utils.R
rotl/R/tnrs.R
rotl/R/api-taxonomy.R
rotl/R/api-collections.R
rotl/R/tax_utils.R
rotl/R/methods.R
rotl/R/api-studies.R
rotl/R/taxonomy.R
rotl/R/api-tnrs.R
rotl/R/api-tol.R
rotl/R/match_names.R
rotl/R/studies.R
rotl/R/tree_to_labels.R
rotl/R/base.R
rotl/R/deduplicate_labels.R
rotl/R/external_data.R
rotl/R/tol.R
rotl/R/studies-methods.R
rotl/R/rotl-package.R
rotl/vignettes
rotl/vignettes/data_mashups.Rmd
rotl/vignettes/meta-analysis.Rmd
rotl/vignettes/how-to-use-rotl.Rmd
rotl/vignettes/vignette.css
rotl/README.md
rotl/MD5
rotl/build
rotl/build/vignette.rds
rotl/DESCRIPTION
rotl/man
rotl/man/rotl.Rd
rotl/man/tnrs_match_names.Rd
rotl/man/taxonomy_taxon_info.Rd
rotl/man/tnrs_contexts.Rd
rotl/man/tol_about.Rd
rotl/man/get_study_subtree.Rd
rotl/man/tol_induced_subtree.Rd
rotl/man/get_study_meta.Rd
rotl/man/match_names-methods.Rd
rotl/man/taxonomy-methods.Rd
rotl/man/tax_lineage.Rd
rotl/man/list_trees.Rd
rotl/man/study_external_IDs.Rd
rotl/man/taxonomy_subtree.Rd
rotl/man/tol_node_info.Rd
rotl/man/tnrs_infer_context.Rd
rotl/man/source_list.Rd
rotl/man/taxonomy_about.Rd
rotl/man/studies_find_trees.Rd
rotl/man/match_names.Rd
rotl/man/studies_properties.Rd
rotl/man/get_study.Rd
rotl/man/tol_mrca.Rd
rotl/man/synonyms.match_names.Rd
rotl/man/tol_subtree.Rd
rotl/man/taxon_external_IDs.Rd
rotl/man/studies_find_studies.Rd
rotl/man/strip_ott_ids.Rd
rotl/man/taxonomy_mrca.Rd
rotl/man/get_study_tree.Rd
rotl/LICENSE