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Treebase: an R package for discovery, access and manipulation of online phylogenies
Article first published online: 11 OCT 2012
DOI: 10.1111/j.2041-210X.2012.00247.x
© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society
Additional Information
How to Cite
Boettiger, C., Temple Lang, D. (2012), Treebase: an R package for discovery, access and manipulation of online phylogenies. Methods in Ecology and Evolution, 3: 1060–1066. doi: 10.1111/j.2041-210X.2012.00247.x
Publication History
- Issue published online: 11 DEC 2012
- Article first published online: 11 OCT 2012
- Manuscript Accepted: 13 AUG 2012
- Manuscript Received: 26 JUN 2012
Keywords:
- application programming interface;
- database;
- programmatic;
- R ;
- software;
- TreeBASE;
- workflow
Summary
- 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.