R: Cophenetic Matrix on Haplotype Networks

cophenetic.haploNet {pegas} | R Documentation

## Cophenetic Matrix on Haplotype Networks

### Description

This function calculates the cophenetic distance on a network. The output can be used to find nodes with short distances to most nodes.

### Usage

    ## S3 method for class 'haploNet'
    cophenetic(x)

### Arguments

`x` | an object of class `"haploNet"`.

### Details

The results of the function are likely to be approximate in most cases with reticulations in the network. In the case of MSTs, the results are exact.

### Value

a numeric matrix with colnames and rownames set to the labels of the network nodes.

### Author(s)

Emmanuel Paradis

### See Also

`cophenetic.phylo` in ape, `cophenetic` for the generic function

### Examples

    example(mst)
    coph <- cophenetic(r)
    rowSums(coph)

[Package pegas version 1.1 Index]