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‚Äôs 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.