This repository contains code for analyses from "Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts" (Magee et al. 2019). In the directory 1_simulation_study is code for simulating a number of trees under a time-dependent birth-death process, inferring diversification rates under the HSMRF-based and GMRF-based models, and processing those results. In the directory 2_empirical_analyses is code for the empirical analyses presented in the manuscript. Both directories contain more extensive readme files.
Running any analyses in this repository requires an installation of RevBayes, version 1.0.11 or higher. Pre- and post-processing steps require R 3.4.4 or higher. All R scripts are designed to be called from the top level directory. Further requirements are discussed in the relevant readme files.