Treebase: An R package for discovery, access and manipulation of online phylogenies

Abstract

1. The TreeBASE portal is an important and rapidly growing repository of phylogenetic data. The R statistical environment has also become a primary tool for applied phylogenetic analyses across a range of questions, from comparative evolution to community ecology to conservation planning. 2. We have developed treebase, an open-source software package (freely available from http://cran.r-project.org/web/packages/treebase) for the R programming environment, providing simplified, programmatic and interactive access to phylogenetic data in the TreeBASE repository. 3. We illustrate how this package creates a bridge between the TreeBASE repository and the rapidly growing collection of R packages for phylogenetics that can reduce barriers to discovery and integration across phylogenetic research. 4. We show how the treebase package can be used to facilitate replication of previous studies and testing of methods and hypotheses across a large sample of phylogenies, which may help make such important reproducibility practices more common. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society.