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

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Woe betide those who summon the Galactic Coelacanth

A couple of years ago I had an existential crisis when I realized that, in the time one of my papers had been in review (almost 8 months!), I could nearly have physically created an entirely new human being in my body, if I had so chosen. Thus began the saddest game in the universe that I like to play when I submit a paper: “What kind of animal could have been gestated in the time this paper has been in review?”. And this became an even better running joke when one of my colleagues had a highly unusual review experience that lasted for several years, which completely exhausted the gestation times of real animals.

My amazing and lovely sister saw us talking about this on Facebook and went ahead and wrote an R script that tells you exactly what kind of animal you could have birthed while waiting for reviewer comments. And because I am always forgetting to save this amazing piece of code, I’ve gotten permission from Jessica to post it here for posterity. My sincere apologies to anyone who gets the Space Whale, and my deepest condolences to anyone who is graced by the presence of the Galactic Coelacanth. 

Click here for the R script!

Updated 30 June 2015: If you don’t have R, you can also download a text file to see the code!