Stars
Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components. Ordinary differential equations (ODEs), stochastic differential equat…
This repository is an implementation of the TimTam likelihood as a BEAST2 package.
Phylodynamics for partially observed Markov processes in Julia
Infectious disease models (Python and R) from Keeling and Rohani (2007)
Inference and modeling for partially observed Markov process (POMP) models
Agent-Based Simulation of Viral Evolution powered by a Sparse Haplotype Representation
STATS 700 Fall 2025. Topics in Applied Statistics: Phylodynamic Inference
Symbolic programming for the next generation of numerical software
Half day phylodynamics workshop at KEMRI
Phylogeographic inference with structured coalescent models
MERS-CoV spillover at the camel-human interface
R package for statistical inference using panelPOMPs (panel Partially Observed Markov Processes)
Some useful Mathematica add-on packages
Supporting code and data for Frontiers MS "Red blood cell dynamics during malaria infection violate the assumptions of mathematical models of infection dynamics"
Supporting code and data for King, Lin, & Ionides (2026) "Exact Phylodynamic Likelihood via Structured Markov Genealogy Processes"
Supporting material for Bjørnstad, Viboud, Grenfell, King (2020) "Comparison of alternative models of human movement and the spread of disease"
A repository of abbreviations for references, e.g., for conferences, journals, institutes, etc.
Desktop app for managing BibTeX and BibLaTeX (.bib) libraries
Software for maximum likelihood estimation of ARIMA models