Phylogenetic control with OU
This is a little tutorial on how to analyze the dependency between two binary traits using phylogenetic control with the Ornstein-Uhlenbeck (OU) model, using R and Stan. I also included a Stan-implementation of the Pagel-Meade style phylogenetic comparative method.
You can cite this work as: Gerhard Jäger, 2025, Running a Phylogenetic OU Regression with R and Stan, 
, https://profgerhard.de/OU_logistic_example/phylogenetic_OU_regression.html