PhylogeneticEM (version 1.0.0)

init.parsimonyCost: Initialization for parsimonyCost.

Description

init.parsimonyCost initialize a (ntaxa + nNodes) x (nclus) matrix with NAs everywhere, except for the tips.

Usage

init.parsimonyCost(phy, clusters)

Arguments

clusters

the vector of the clusters of the tips.

phylo

a phylogenetic tree, class phylo.

Value

A (ntaxa + nNodes)x(nclus) matrix, with ntaxa first lines initialized as described.

Details

At a tip i in state k, the line-vector is initialized as follow : (1 - Ind(k=p)_1