HSMRF

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts. Code for our work developing and characterizing the HSMRF priors for birth-death processes. 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.