RevBayes & the universe

One of the interesting things about having a blog is that you can see what people are interested in, and when. This week, I can see a lot of traffic going to a couple of blog posts, Teaching Phylogenetics in the Cloud and Plan C. This is pretty common around the start of the semester – people are interested in trying new things in their teaching, and particularly using cloud technologies to improve access to compute resources.

I want to emphasize some new developments on this front. Jeremy Brown and I taught a workshop at the SSB2020 meetings on developing a hands-on classroom using RevBayes. Slides are here.

We covered three main things: Graphical models, and why they’re cool; how to build a graphical model; and some of the graphical interfaces that you might use to deliver RevBayes to your students. That last point is important – systematics isn’t a science isolation. To use phylogenetic methods, students need to understand statistics, they need to understand where their data come from, and what the biases in those data may be. Common tools like R and RStudio, or Python and the Jupyter notebook are often used for “data science.” Given the integrative nature of systematics as a discipline, doesn’t it make sense to make our tools interoperate more smoothly with a broader universe of tools for working with data?

We have some tools to help RevBayes play nicer with tools like RStudio and Jupyter. Michael Landis and Sebastian Frost developed a Jupyter Kernel for using Rev inside of Jupyter notebooks. Lately, David Bapst and I have been working on an RStudio interface. If you’re interested in any of these tools, please do see the install page for them, and give us feedback. A manuscript describing the classroom contexts for these tools is forthcoming; in the mean time, you might find interesting tidbits related in the paper described here.

If you were at the workshop, you ought to have received an email inviting you to take a survey on it, and inviting you to comment on the issue tracker for the RevKnitr repository. I’d like to extend that invite more widely – if you are teaching with RevBayes and would like to join the conversation with other educators, do feel free to open an issue on the RevKnitr issue tracker. It would be wonderful to have an active discussion on how to teach systematics expansively and inclusively.

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