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.

AuthorFrancois Michonneau [aut, cre], Joseph Brown [aut], David Winter [aut]
Date of publication2016-09-20 00:45:03
MaintainerFrancois Michonneau <francois.michonneau@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version3.0.1
https://github.com/ropensci/rotl

View on CRAN

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_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

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

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