Sunday Book Review: Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis (Springer 2006)

We've talked a bit about the use of R for phylogenetic comparative analyses. We love it. One of the biggest complaints with this software has always been its the steep learning curve. Paradis' book takes us big step toward the elimination of this obstacle.

By introducing the R package known as ape, Paradis has done already done more than anyone to bring R to phylogeneticists. His books now makes it possible for even a novice R user to get their feet wet with a broad range of R applications related to phylogenetics and evolution. Although many of the R applications to evolutionary biology introduced by Paradis remain relatively primitive (e.g., direct analysis of sequence data, reconstruction of phylogenetic trees), the phylogenetic applications he discusses are at the bleeding edge. The flexibility R offers for graphical output of phylogenetic trees are also unrivaled.

There are really only two problems worth noting with this book, one ironic, the other tragic. The irony is that book espousing the benefits of free software (and even written using the free typesetting software LaTeX) is anything but free itself. The bloodsuckers at Springer are actually trying to extract >$50 for this slim 211 page paperback. If you're short on cheddar you might try contacting Paradis, word on the street is that he's a good dude. The tragic problem is that the book is already out of date and incorrect in places, due in part to some untimely, and seemingly unnecessary, revisions of ape's code by Paradis himself. I was tearing my hair out for a good long while before I figured out that he had changed the format of the $edge portion of ape's default tree format. Internal nodes were previously labeled with negative integers, but are not coded with positive integers.

R will change the way you do science. Paradis will help. The good will of the community will get you the rest of the way.