R: Extraction of the actual number of solutions.

extract.parsimonyNumber {PhylogeneticEM} | R Documentation

## Extraction of the actual number of solutions.

### Description

`extract.parsimonyNumber` takes the two matrices computed by `parsimonyNumber`, and compute the actual number of parsimonious solution for any subtree starting from a given node.

### Usage

    ## S3 method for class 'parsimonyNumber'
    extract(x, node = attr(x$nbrReconstructions,
      "ntaxa") + 1, what = c("number", "cost"), ...)

### Arguments

`x` | an object of class "`parsimonyNumber`", result of function `parsimonyNumber`.
`node` | the root node of the subtree. By default, the root of the tree.
`what` | the quantity to retrieve. Either "number" for the number of solutions, or "cost" for the minimal cost of a solution. Default to "number".
`...` | unused

### Details

The parsimonious solutions are the one with the minimum number of shifts (that are given by matrix costReconstructions). This function sums the number of solutions (given in matrix nbrReconstructions) that have the minimum number of shifts.

### Value

An integer giving the number of equivalent parsimonious solutions.

### See Also

`parsimonyNumber`

[Package PhylogeneticEM version 1.1.0 Index]