Welcome to Epidemics on Networks’s documentation!

EoN (Epidemics on Networks) is a Python module that provides tools to study the spread of SIS and SIR diseases in networks.

Distributed under MIT license. See license.txt for full details.

Highlights

EoN is based on the book

Mathematics of Epidemics on Networks: from Exact to Approximate Models

EoN is built on top of NetworkX. Its repository is on github. EoN’s tools fall into two broad categories:

  • Stochastic simulation of SIS and SIR disease
    • Event-based simulation
      • much faster than traditional Gillespie simulation
      • allows weighted graphs
      • allows non-Markovian dynamics
    • Gillespie algorithms for Markovian dynamics
      • lots of effort to optimize these (making the unweighted version comparable to the event-based simulation)
      • The weighted version is slower, but still reasonably fast.
    • discrete-time (synchronous update) models
    • tools for visualizing and animating simulated epidemics.
  • Numerical solvers for ODE models
    • pair approximation models
    • effective degree models
    • edge-based compartmental models

There is also support for producing figures and animations and other detailed investigation of simulations.