Evolution

Recology is 1 yr old…

December 23, 2011 | 0 Comments

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...
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My talk on doing phylogenetics in R

November 18, 2011 | 0 Comments

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.  ...
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Phylogenetic community structure: PGLMMs

October 13, 2011 | 0 Comments

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...
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GLMM Hell

July 7, 2011 | 0 Comments

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...
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Comparison of functions for comparative phylogenetics

May 11, 2011 | 0 Comments

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...
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Phylometa from R: Randomization via Tip Shuffle

April 16, 2011 | 0 Comments

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...
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Phenotypic selection analysis in R

February 24, 2011 | 0 Comments

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...
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Troubling news for the teaching of evolution

February 9, 2011 | 0 Comments

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...
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