rotl, an R package to interact with the Open Tree of Life data

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1 Whitney Laboratory of Marine Bioscience, University of Florida, Saint Augustine, Florida, United States
2 Division of Invertebrate Zoology, Florida Museum of Natural History, Gainesville, Florida, United States
3 Department of Ecology & Evolutionary Biology, University of Michigan - Ann Arbor, Ann Arbor, Michigan, United States
4 Arizona State University, Tempe, Arizona, United States
DOI
10.7287/peerj.preprints.1471v3
Published
Accepted
Subject Areas
Computational Biology, Ecology, Evolutionary Studies, Computational Science
Keywords
phylogenetics, API, R, comparative methods
Copyright
© 2016 Michonneau et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Michonneau F, Brown JW, Winter D. 2016. rotl, an R package to interact with the Open Tree of Life data. PeerJ Preprints 4:e1471v3

Abstract

1. While phylogenies have been getting easier to build, it has been difficult to re-use, combine, and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. 2. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package to search and download data from the Open Tree of Life directly in R. 3. rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyze, and visualize phylogenies. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyze biodiversity data. 4. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data, and allows their integration with statistical methods and data sources available in R.

Author Comment

This is the revised version of the manuscript following the release of v3.0 of the OTL APIs and the accompanying release of v3.0.0 of the rotl package. It is also the (hopefully) final revision of the manuscript before publication in "Methods in Ecology and Evolution".