Phylogeny and associated weighted network graph for a simulated epidemic.

<p>Branch colour indicates on which island transmission and evolution takes place, while tip label colour indicates cluster membership based on snipping the WPGMA dendrogram at height 0.0071. Only islands with at least one infected vertex are displayed. Vertex and edge colours are matched with tip label and branch colours, respectively. A white vertex with a teal frame is infected, but undiagnosed. A white vertex with frame color matching that of the island is uninfected.</p

Estimates of island recovery for epidemics on type C sexual contact networks, measured with the adjusted Rand Index (ARI).

<p>Fig A indicates the mean ARI across cutpoints for the different cluster definitions applied to epidemics simulated on unweighted networks. In Fig B, we show corresponding results for weighted networks with between-island transmission rate equal to 25% the within-island transmission rate. In Fig C, each curve gives mean island recovery rates across between-tip distance percentile requirements in Def. 3 for networks with between-island transmission rates 25%, 50%, 75%, or 100% the within-island transmission rate. Fig D gives the optimal ARIs across between-island transmission rates. Each curve represents the maximum achieved mean island recovery under a different cluster definition. For example, the values at bridge weight 0.25 are the suprema in Fig B, as well as the supremum of the red curve in Fig C. Def. 1-4 correspond to the methods for cluster detection described in the Methods section.</p

A simple undirected interconnected-islands network, representing subjects living in three different islands, corresponding to cities.

<p>The graph was randomly-generated. It has three islands of of size 15, and the connection probability of any two vertices within an island is 0.6. There are two edges, called “bridges”, between any two islands. The label within each vertex indicates in which city the subject lives.</p

Phylogeny and associated unweighted network graph for a simulated epidemic.

<p>Branch colour indicates on which island transmission and evolution takes place, while tip label colour indicates cluster membership based on snipping the WPGMA dendrogram at height 0.007. Only islands with at least one infected vertex are displayed. Vertex and edge colours are matched with tip label and branch colours, respectively. A white vertex with a teal frame is infected, but undiagnosed. A white vertex with frame color matching that of the island is uninfected.</p