Michael Landis

summer updates

02 Jun 2013

Evolution 2013 was very enjoyable, though exhausting (my classmates and I carpooled and camped). To share some of my “paperless” research, such as my Evolution talk, I created a Figshare account.

I received some great feedback about BayArea at the conference, both from empiricists and theorists. Designing new models is the next part, which is driving force behind increasing the number of areas per analysis. As an aside, I updated BayArea to fix a problem for proposing histories for small numbers of areas (N < 10). Thanks to Julien Vieu for mentioning the problem.

Also, I updated creepy-jerk (continuous character evolution using Lévy processes) to improve performance for computing the compound Poisson process with normally distributed jumps. While doing this, I modified the code to produce a FigTree-compatible output file that indicates the size and polarity of jumps on the phylogeny (using the posterior of sampled jumps and the signal-to-noise ratio divided by the square root of the branch length).

creepy-jerk posterior jumps

Looks nice, I think!