init.enumerate_parsimony: Initialization for the enumeration of parsimonious solutions.
In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

init.enumerate_parsimony

R Documentation

Initialization for the enumeration of parsimonious solutions.

Description

init.enumerate_parsimony is used in function enumerate_parsimony, and initialize the correct data structure.

Usage

init.enumerate_parsimony(phy, clusters, pos)

Arguments

`phy`	Input tree.
`clusters`	a vector representing the group of each tip.

Details

This function returns a list with Nnode + ntaxa entries. Entries corresponding to the tips are initialized with a list of nclus matrices. For tip i of group k, all matrices are set to NULL, except for the kth, set to a vector of size Nnode + ntaxa, with entry i set to k, and all the others to NA.