This project aims to collate mathematical models of infectious disease transmission, with implementations in R, Python, and Julia.

Categories of models include:

- Simple deterministic models using ordinary differential equations
- Standard compartmental models
- Non-exponential distributions of infectious periods
- Delay differential equations
- Method of stages
- Infection-age models

- Simple stochastic models
- Gillespie’s stochastic simulation algorithm
- Discrete time
- Stochastic differential equations

- Models with time-varying parameters
- Spatial models
- Network models
- Pair approximations
- Edge based models

- Applications to specific disease systems

Interactive notebooks are linked from the text, and can be found here.