This repository contains code for analyses from "Horseshoe-Based Bayesian Nonparametric Estimation of Effective Population Size Trajectories" (Faulkner et al. 2019). In particular, in the Rev directory we include code for implementing coalescent models with horseshoe Markov random field (HSMRF) and Gaussian Markov random field (GMRF) priors for the effective population sizes in the RevBayes computing language. Descriptions of the files are contained in the README file in the Rev directory. The development branch of the fork of RevBayes available at: https://github.com/afmagee/revbayes. RevBayes should be compiled from this source to run any tests or analyses contained in this repository. In the BEAST directory we include code for implementing the Bayesian Skyline and Skyride models in the program BEAST. A copy of the BEAST software can be found at http://beast.community.
Faulkner, JR, AF Magee, B Shapiro, and VN Minin. 2019. Horseshoe-based Bayesian nonparametric estimation of effective population Size trajectories. Preprint arXiv:1808.04401v2 [stat.ME]