Add Coalescent Lag to Transmission Distances

Augments a transmission distance matrix with stochastic coalescent distances to simulate the divergence between a transmission tree and a gene tree.

Usage

add_coalescent_distance(pairwise_dist, theta)

Arguments

pairwise_dist

A symmetric numeric matrix of transmission distances.

theta

Numeric. The population size parameter (mean of the coalescent distance).

Value

A symmetric numeric matrix where each entry $(i, j)$ is the sum of the transmission distance and a simulated coalescent lag.