Calculate the probability of a phylogenetic tree given a transmission tree

Calculate the probability of a phylogenetic tree given a transmission tree

probPTreeGivenTTree(ctree, neg, w = integer(0))

Arguments

ctree

Combined phylogenetic/transmission tree

neg

Within-host coalescent rate

w

Vector of hosts for which to calculate the probability, or nothing for all

Value

Probability of phylogeny given transmission tree