Tuesday, May 25, 2010

The successful launch of MEE

Usually, I view the release of a new journal with some skepticism. There are so many journals and it feels like academics are over-parsing fields, isolating researchers that should be communicating. However, sometimes a journal comes along and it is obvious that there is a need and the community responds to its arrival. Such is the case with the British Ecological Society's newest journal, Methods in Ecology and Evolution, started by Rob Freckleton. The idea that a journal would be dedicated to methods papers is a great idea. This era of ecology and evolution is one that is defined by rapid advances in experimental, technological and computational tools and keeping track of these advances is difficult. Having a single journal should make finding such papers easier, but more importantly provides a home for methodological and computational ecologists and evolutionary biologists, which will hopefully spur greater communication and interaction, fostering more rapid development of tools.

Two issues have been published and they have been populated by good, entertaining articles. I especially enjoyed the one by Bob O'Hara and Johan Kotze on why you shouldn't log transform count data. As a researcher, I've done this (instead of using a GLM with proper distribution) and as an editor, I've allowed this, but it has always felt wrong somehow, and this shows that it is.

The early success of the journal is not just the product of the good papers it has already published, but also because of the savvy use of electronic communication. They Tweet on Twitter, link fans through Facebook, blog about recent advances in methods from other journals and post podcast and videocast interviews with authors. These casts give readers access to authors' own explanations of how their methods can be used.

I am excited about this new journal and hope it has a great impact on the publication of methodological papers.

Tuesday, May 11, 2010

Picante's coming out party

This past decade has seen a rapid expansion of the use of evolutionary phylogenies in ecological studies. This expansion is largely due to the increased availability of phylogenies, but has resulted in new types of hypotheses and statistics aimed to test the phylogenetic patterns underpinning ecological communities. The main computational tool used has been phylocom, created by Cam Webb, David Ackerly and Steve Kembel, which has its own binaries to be installed on one’s computer. However, a new R package, picante has been created by Steve Kembel and colleagues which runs many of the same routines as in phylocom, but in the R framework, allowing one to tie these analyses in better with other, non-phylogenetic tests. Picante also has a number of features and tests not found in phylocom, including tests of phylobetadiversity and phylogenetic signal using Blomberg’s K.

Thanks Steve for all your hard work and for making these tests available to everyone.

Kembel, S., Cowan, P., Helmus, M., Cornwell, W., Morlon, H., Ackerly, D., Blomberg, S., & Webb, C. (2010). Picante: R tools for integrating phylogenies and ecology Bioinformatics DOI: 10.1093/bioinformatics/btq166