This blog has lasted a whole year already.  Thanks for reading and commenting. There are a couple of announcements:Less blogging:  I hope to put in many more years blogging here, but in full disclosure, I am blogging for Journal of Ecology no...

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc.Please comment if you have code for doing bayesian phylogenetic inference in R.  ...

So, I've blogged about this topic before, way back on 5 Jan this year.Matt Helmus, a postdoc in the Wootton lab at the University of Chicago, published a paper with Anthony Ives in Ecological Monographs this year (abstract here).  The paper addres...

There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systemat...

I have been starting to analyze some data I have of repeated counts of salamanders from 5 plots over 4 years. I am trying to develop a predictive model of salamander nighttime surface activity as a function of weather variables. The repeated counting l...

With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell's functions), I was simply interested in which functions to use in cases where multiple functions exis...

I wrote earlier about some code I wrote for running Phylometa (software to do phylogenetic meta-analysis) from R.I have been concerned about what exactly is the right penalty for including phylogeny in a meta-analysis. E.g.: AIC is calculated from Q in...

Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.Get the code and example files here: http://wp.me/PRT1F-2vGet phylocom here: http:/...

I have up to recently always done my phenotypic selection analyses in SAS. I finally got some code I think works to do everything SAS would do. Feedback much appreciated!########################Selection analyses#############################install.pac...

A recent survey reported in Science ("Defeating Creationism in the Courtroom, but not in the Classroom"),  suggests that high school teachers are not teaching evolution to the fullest extent, say, that grammar is being taught in the English c...