branchTransitions: Compute transitions per branch

In ndukler/epiAllele: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

Description

Compute the number of expected transitions per branch between states based on the marginal joint probabilities

Arguments

obj	rateModel object
subset	The site indices for which should be summed over to compute the total number of expected transitions (NOT IMPLEMENTED)
ncores	Number of cores to use

Value

A 3-dimensional vectors where the first index is the branch, the second is the state of the parent, and the third is the state of the child. The entries are the exprected number of transitions on that branch for the corresponding parent and child states.

ndukler/epiAllele documentation built on May 5, 2019, 4:50 p.m.