Software

Open-Source Projects

paleobuddy: Flexible simulations of birth-death-sampling models

paleobuddy is an R package to simulate phylogenetic trees and fossil records. It allows for efficient simulation of a number of scenarios of interest for the validation of macroevolution software.

• Prioritizes computational efficiency in draws from complex birth-death-sampling distributions
• Written to allow for straightforward expansion by use of flexible forward-simulation framework
• Includes dependence on absolute age, species age, traits, and environmental variables for speciation, extinction, and fossil-sampling rate

Role: Maintainer | License: GPL | Current version: 1.1.0
🔗 View on GitHub or CRAN

RevBayes: Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language

RevBayes is a C++-based software to perform Bayesian phylogenetic analyses. It makes use of probabilistic graphical models and an interpreted language (Rev, similar to R) to maximize flexibility and modularity. In Spring and Summer of 2025, I was part of an NSF POSE grant to make RevBayes more accessible to users, improve its testing suite and website, and investigate the most effective ways to garner user feedback.

• C++ backend makes for efficient and flexible object-oriented framework
• Includes a plethora of models of inference for phylogenetic trees, macroevolutionary rates, biogrography, traits etc.
• Its focus on modularity and highly active community makes for a package that is constantly improving and expanding
• Robust tutorials can aid with nearly any analysis setup

Role: Contributor | License: GPL
🔗 View on GitHub