So You Want to Make a Time-Calibrated Phylogenetic Tree

Are you a palaeontologist interested in incorporating phylogenetic comparative methods into your research? Would you like to increase your toolkit of hypothesis-testing analyses for fossil-related questions? There’s a pretty good chance you’re going to need a time-calibrated phylogenetic tree. And to get one, you’re going to need to try your hand at R.

If you’re new to R programming or phylogenetic comparative methods, it can seem like a pretty steep uphill battle to learn some of these techniques, especially if you don’t feel like you got a great grounding in programming or statistics as an undergrad. Nevertheless, there are great resources out there for learning the basics of moving around in R (I like this one but I also just google things a lot), and good resources on phylogenetic comparative methods and statistical methods in biology. Today I’m going to do my best to make a bit of a tutorial for an important R package, paleotree (David Bapst), which will make magical time-calibrated trees for you that you can then use for all kinds of wonderful analyses. Continue reading