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.

Install the latest version of this package by entering the following in R:
install.packages("rotl")
AuthorFrancois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Date of publication2017-03-04 07:27:19
MaintainerFrancois Michonneau <francois.michonneau@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version3.0.3
https://github.com/ropensci/rotl

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

is_in_tree: Check that OTT ids occur in the Synthetic 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

Functions

candidate_for_synth Man page
candidate_for_synth.study_meta Man page
flags Man page
flags.match_names Man page
flags.taxon_info Man page
flags.taxon_mrca Man page
get_publication Man page
get_publication.study_meta Man page
get_study Man page
get_study_meta Man page
get_study_subtree Man page
get_study_tree Man page
get_study_year Man page
get_study_year.study_meta Man page
get_tree_ids Man page
get_tree_ids.study_meta Man page
inspect Man page
inspect.match_names Man page
is_in_tree Man page
is_suppressed Man page
is_suppressed.taxon_info Man page
is_suppressed.taxon_mrca Man page
list_trees Man page
list_trees.matched_studies Man page
ott_id Man page
ott_id.match_names Man page
ott_id.taxon_info Man page
ott_id.taxon_mrca Man page
ott_id.tol_mrca Man page
ott_id.tol_node Man page
ott_id.tol_summary Man page
rotl Man page
rotl-package Man page
source_list Man page
source_list.tol_mrca Man page
source_list.tol_node Man page
source_list.tol_summary Man page
strip_ott_ids Man page
studies_find_studies Man page
studies_find_trees Man page
studies_properties Man page
study_external_IDs Man page
synonyms Man page
synonyms.match_names Man page
synonyms.taxon_info Man page
tax_lineage Man page
tax_lineage.taxon_info Man page
tax_lineage.tol_node Man page
tax_name Man page
tax_name.taxon_info Man page
tax_name.taxon_mrca Man page
tax_name.tol_mrca Man page
tax_name.tol_node Man page
tax_name.tol_summary Man page
taxon_external_IDs Man page
taxonomy_about Man page
taxonomy_mrca Man page
taxonomy_subtree Man page
taxonomy_taxon_info Man page
tax_rank Man page
tax_rank.taxon_info Man page
tax_rank.taxon_mrca Man page
tax_rank.tol_mrca Man page
tax_rank.tol_node Man page
tax_rank.tol_summary Man page
tax_sources Man page
tax_sources.taxon_info Man page
tax_sources.taxon_mrca Man page
tax_sources.tol_mrca Man page
tax_sources.tol_node Man page
tax_sources.tol_summary Man page
tnrs_contexts Man page
tnrs_infer_context Man page
tnrs_match_names Man page
tol_about Man page
tol_induced_subtree Man page
tol_lineage Man page
tol_lineage.tol_node Man page
tol_mrca Man page
tol_node_info Man page
tol_subtree Man page
unique_name Man page
unique_name.taxon_info Man page
unique_name.taxon_mrca Man page
unique_name.tol_mrca Man page
unique_name.tol_node Man page
unique_name.tol_summary Man page
update.match_names Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.