parsimonyCost {PhylogeneticEM}

Minimal number of shifts needed to get a clustering.

Description

parsimonyCost is an implementation of the Sankoff algorithm, when the cost of transition between two state is always one. It is used in functions parsimonyNumber and enumerate_parsimony to count or enumerate all the parsimonious solutions given one clustering of the tips.

Usage

parsimonyCost(phylo, clusters = rep(1, length(phylo$tip.label)))

Arguments

phylo

a phylogenetic tree, class phylo.

clusters

the vector of the clusters of the tips. (Default to all the tips in a single group).

Value

An S3 class "parsimonyCost" containing a (ntaxa + Nnode) x (nclus) matrix of the total number of shifts needed to get the clustering, if starting from a node in state k. The cost can be extract from any subtree with function extract.parsimonyCost.

See Also

extract.parsimonyCost, parsimonyNumber, enumerate_parsimony, partitionsNumber, equivalent_shifts

Examples

tree <- read.tree(text="(((1,1),2),2);")
plot(tree); nodelabels()
clusters <- c(1, 1, 2, 2)
costs <- parsimonyCost(tree, clusters)
costs

## Extract the parsimony cost at the root
extract(costs)

## Extract the cost for the sub-tree below node 7
extract(costs, 7)