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<=p<=nclus)*Inf (where Inf * 0 = 0)