network-epi

This is the accompanying repo for: Multi-scale Local Network Structure Critically Impacts Epidemic Spread and Interventions

It contains functions for performing SIR and SEIR simulations with a neighbor quarantining policy. We model stochastic simulations using a Discrete Event Simulation that only tracks updates in node states.

The other notable computation is for computing the Network Community Profile (NCP) for both seeded PageRank and epidemic simulations.

Usage

See juypter notebooks in the examples/ directory for examples of code usage.

Citations

Scripts have citations where the code is based on the work of others. If you believe some portion requires a citation, please bring this to our attention. Some notable portions of code that deserve mentioning are:

1. Computing the NCP from seeded PageRank solution vectors
2. Code for producing HexBins

The first is mostly code that I modifed from David Gleich (https://github.com/dgleich). The second was modified from https://github.com/RalphAS/HexBinPlots.jl for the missed sets computation.

Data Sources

For sources of data, please see the accompanying paper for appropriate citations.