R: Number of different models

partitionsNumber {PhylogeneticEM} | R Documentation

## 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 "marked" 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, marked = TRUE)

[Package PhylogeneticEM version 1.1.0 Index]