What I did for my summer vacation

Been a while since I wrote on here. I’ve been meaning to, but I’ve also been home with my entire family on months of quarantine. Such is life.

This summer, I only put two things on my docket: finish my NSF CAREER submission, and finish a preprint. I’ve managed to do both, and then some. Let’s take a peek at some new stuff in the lab.

Graeme Lloyd and I have a new paper on interpreting the posterior sample in Bayesian paleo phylogenetics. The code and data are here, along with some talk slides where I discuss the manuscript. We used treespace visualizations in RWTY to look at the distribution of treespace metrics across the posterior sample. In the paper we make the argument, hopefully convincingly, that the posterior sample has more information than a mean or median of the distribution might capture. We also provide some comparisons with the most parsimonious set of trees and discuss how and why summary trees of parsimony sets can be misleading.

It was my privilege to be involved in this collaboration on active learning and inclusive teaching online. Ecology and evolution are among the least diverse fields of study. In this manuscript, we intend to provide some basic definitions for common terms and concepts around active learning and inclusive teaching. This is very much a baby steps manuscript, and I hope everyone who looks at it will find a couple things they can do to make their classroom a more equitable and engaging place this coming semester.

Rachel Warnock and I had this paper accepted. We were both in a position of beginning to teach MS students about the work that we do, particularly with the fossilized birth-death model. We both found ourselves in need of a good, strong, explanation of the model and its underprinnings that could be read by a student who is new to this research. So we wrote one. We’re hoping this is a nice jumping off point for new students, but also a good catch-up review for people who might be more familiar with the concepts, but missed bits about how they fit together for analysis.

A nice companion is this published tutorial with Tracy Heath & co. In this tutorial, we provide a clear and simplified FBD analysis that pretty much anyone should be able to follow along with. Something that is very cool is that this tutorial appeared in a book that is entirely free and open source. It’s an incredible effort!

And lastly, this preprint with Davey Wright and Pete Wagner. Something that is very tricky about the FBD is that there are some parameters for which you might have little intuition. Speciation or extinction in your group, for example. It’s also a complex model, with submodels for parts of the data. We show some tractable ways to engage in finding the best model and rigorously testing for fit.

For my summer vacation, I got a lot done. But here’s the thing: I had my kids home. My husband was working from home. It was chaos. I worked with people who are kind. I worked with people who listen and exercise patience. I exercised more patience. I wasn’t perfect. I said “No” pretty much constantly to anything that didn’t make me feel genuinely excited and charged up. Things are about to kick off again for the semester, but that’s my mindset: do what you love and the rest follows

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