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

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

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