SIR Animation Example

Downloadable Source Code

The code below produces an animation of an SIR epidemic:

You may need to install additional software for this to work and modify extra_args appropriately. The commands below work on a mac with ffmpeg installed. The commands below also show an alternate way to specify the position of nodes passing pos through fast_SIR to be used when generating the simulation_investigation object.

import networkx as nx
import EoN
import matplotlib.pyplot as plt
G = nx.grid_2d_graph(100,100) #each node is (u,v) where 0<=u,v<=99
#we'll initially infect those near the middle
initial_infections = [(u,v) for (u,v) in G if 45<u<55 and 45<v<55]
pos = {node:node for node in G}
sim_kwargs = {'pos': pos}
sim = EoN.fast_SIR(G, 2.0, 1.0, initial_infecteds = initial_infections,
               tmax = 40, return_full_data=True, sim_kwargs = sim_kwargs)

ani=sim.animate(ts_plots=['I', 'SIR'], node_size = 4)'SIR_2dgrid.mp4', fps=5, extra_args=['-vcodec', 'libx264'])