PhylogeneticEM (version 1.0.0)

partitionsNumber: Number of different models

Description

partitionsNumber computes the number of different models with a given number of shifts K. It is also the number of colorings of the tips to the tree in npart = K + 1 colors.

Usage

partitionsNumber(phylo, npart)

Arguments

phylo

a phylogenetic tree of class phylo.

npart

the numbers of partitions (colors) allowed at the tips. This is the number of shifts plus one (npart = K + 1).

Value

an object of class partitionsNumber. This is made of a matrix with (Nnodes + ntaxa) rows and (2*npart) columns. Each column contains two vectors: for k=1:npart it contains the number of partitions with k groups compatible with the tree and the shift process; and for k=(npart+1):2*npart, it contains the number of "marqued" partitions with (k-npart) groups compatible with the tree and the shift process. The actual number can be extracted with function extract.partitionsNumber (see examples below).

See Also

extract.partitionsNumber, parsimonyNumber, equivalent_shifts

Examples

npart <- 8 # number of colors at the tips allowed
tree <- read.tree(text="(A,(A,(A,A,A),A,A));") # a tree with polytomies
plot(tree)
parts_num <- partitionsNumber(tree, npart)
parts_num

## Number of possible colorings of the tips in npart colors
extract(parts_num)

## Get all the solutions for colorings with 1 to nparts colors
extract(parts_num, npart = 1:npart)

## Number of possible colorings of the tips in npart colors
## For the sub-tree starting at node 17
extract(parts_num, node = 10)

## Number of possible colorings of the tips in npart colors
## with one marked color
extract(parts_num, marqued = TRUE)