My talk on doing phylogenetics in R

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.  I know phyloch has function mrbayes, but can't … Continue reading

Use case: combining taxize and rgbif

Sure thing….this is just the sort of thing for which rOpenSci is being built. A colleague of mine recently saw our packages in development and thought, “Hey, that could totally make my life easier.”   What was made easier you ask?   This was his situation: He had a list of ca. … Continue reading

Two-sex demographic models in R

Tom Miller (a prof here at Rice) and Brian Inouye have a paper out in Ecology (paper, appendices) that confronts two-sex models of dispersal with empirical data.They conducted the first confrontation of two-sex demographic models with empirical data on lab populations of bean beetles … Continue reading

New food web dataset

So, there is a new food web dataset out that was put in Ecological Archives here, and I thought I would play with it. The food web is from Otago Harbour, an intertidal mudflat ecosystem in New Zealand. The web contains 180 nodes, with 1,924 links. Fun stuff...igraph, default layout plotigraph, … Continue reading