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SpreadingMapping

MATLAB code for simulating SIR processes on networks via weighted shortest paths.

Reference: Tolić, D., Kleineberg, K-K., & Antulov-Fantulin, N. (2018). Simulating SIR processes on networks using weighted shortest paths. Scientific Reports, 8, 6562. https://doi.org/10.1038/s41598-018-24648-w

Files

  • SIR_mapping.m — direct sampling, single realization
  • mcmc_sir_meanfield.m — rejection-free Gibbs sampler, mean-field variant
  • mcmc_sir_exact.m — rejection-free Gibbs sampler, exact variant with dynamical correlations
  • interventions.m — time-critical vaccination strategies (random, hubs, temporal); reproduces Fig. 7

Usage

D = SIR_mapping(A, N, E, beta, gamma, source);
samples = mcmc_sir_meanfield(A, beta, gamma, source, num_samples, burn_in, thin);
samples = mcmc_sir_exact(A, beta, gamma, source, num_samples, burn_in, thin);