- 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.
- 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.
- 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.
- 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.