Code and data - The Occurrence Birth-Death Diffusion Process: Unraveling Diversification Histories with Fossils and Heterogeneous Rates

Overview

This project introduces the Occurrence Birth-Death Diffusion (OBDD) model and applies it to study the diversification dynamics of cetaceans. It builds on the Tapestree.jl framework.

Directory Structure and Description

OBDD_illustration_figure.Rmd: Code for producing Figure 1

Figure_augmented_tree.py: Code for producing Figure 2

Calibration/: Model validation

.jl files: Julia scripts

.submit files: HTcondor cluster submission files

datasets_calibration/: simulated datasets

outputs/: MCMC trace files

Cetacea/: Diversification analyses

.jl files: Julia scripts

.submit files: HTcondor cluster submission files

outputs/: MCMC trace files