PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.

Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.

Bayesian inference of trait evolution under a “fossilized” Brownian motion.

A Julia interface to the Paleobiology Database (PBDB) data service.

Data and code for "The Cultural Macroevolution of Arcade Video Games: Innovation, Collaboration, and Collapse"

Data and analyses used in Moon & Stubbs, Communications Biology doi:10.1038/s42003-020-0779-6

Data, code & figures used to assess global patterns of potential thermal niche filling

Galapagos Islands Testudinidae Macroevolution (GITM)

Benchmarks Physics-Informed Neural ODEs vs. Fine-Tuned Foundation Models (Chronos) on Cenozoic fossil data. Includes a Random Forest analysis of the Lilliput Effect to test climate vs. taphonomy drivers. Results show Neural ODEs outperform generic Transformers (MSE 13.05) in reconstructing deep-time evolutionary history.

Paper - A novel function of banded stripes to prevent cannibalism in snake-eating snakes

Infer phylogeny parameters with Deep Learning.

Macroevolutionary analyses of the Monodoreae tribe (Annonaceae) 🧬🌳🌍

Supplementary R code for analyses in "Rates of passerine body plan evolution in time and space"

Supplementary code and data for "The paradox of predictability"

R scripts to explore global patterns of diversificatio and species richness of current and present-natural mammals

Exploring how changes on the adaptive landscape affect phenotypic evolution within lineages

This repository provides research data and source code for reproducing the computational analysis reported in the manuscript "Community-level functional stability in East African herbivores amid major environmental change"

Code and data to reproduce all analyses and figures in Hill et al 2023

R code and analysis for Bazzi et al. (2025)