Cophenetic {DECIPHER} | R Documentation

## Compute cophenetic distances on dendrogram objects

### Description

Calculates the matrix of cophenetic distances represented by a dendrogram object.

### Usage

    Cophenetic(x)

### Arguments

`x` | A dendrogram object.

### Details

The cophenetic distance between two observations is defined as the branch length separating them on a dendrogram. This function differs from the `cophenetic` function in that it does not assume the tree is ultrametric and outputs the branch length separating pairs of observations rather than the height of their merger. A dendrogram that better preserves a distance matrix will show higher correlation between the distance matrix and it cophenetic distances.

### Value

An object of class 'dist'.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`IdClusters`

### Examples

    fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
    dna <- readDNAStringSet(fas)
    d1 <- DistanceMatrix(dna, type="dist")
    dend <- IdClusters(d1, method="NJ", type="dendrogram")
    d2 <- Cophenetic(dend)
    cor(d1, d2)

[Package DECIPHER version 2.16.1 Index]