Reconstructing contact network structure and cross-immunity patterns from multiple infection histories
Fig 3
Correlations between a matrix based on infection barcodes similarity and the network’s adjacency (top) or shortest path (bottom) matrices.
For simulated epidemics on clustered networks with 2 or 4 circulating genotypes and a variety of cross-immunity settings, we tested for correlations using p-values of two-sided Mantel tests with 104 permutations. For each setting, we re-sampled 20 times randomly 100, 50, 25, or 10% of the infected nodes and report the average p-value.