init.enumerate_parsimony is used in function enumerate_parsimony,
and initialize the correct data structure.
init.enumerate_parsimony(phy, clusters, pos)Input tree.
a vector representing the group of each tip.
A list of size nNode + ntaxa, as described above.
This function returns a list with nNodes + 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 nNodes + ntaxa, with entry i set to k, and all the others to NA.