equivalent_shifts_edges {PhylogeneticEM}

Find all the equivalent shift edges allocations.

Description

equivalent_shifts_edges uses function enumerate_parsimony to find all the shifts positions that are equivalent to a given one.

Usage

equivalent_shifts_edges(
  phylo,
  shifts_edges,
  part.list = enumerate_tips_under_edges(phylo)
)

Arguments

phylo

a phylogenetic tree, class phylo.

shifts_edges

a vector of shifts positions on the edges of the tree.

part.list

(optional) list of partition of the tree, result of function enumerate_tips_under_edges.

Details

This function is uses functions enumerate_parsimony for the actual computation of equivalent regimes, clusters_from_shifts for the clustering of the tips induced by the original set of shifts given, and allocate_shifts_from_regimes to convert back a parametrization in term of regimes to a parametrization in term of shifts.

Value

a matrix with as many columns as equivalent allocation, each column representing a possible parsimonious allocation of shifts on the tree.

See Also

equivalent_shifts, enumerate_parsimony