smile.clustering.linkage

Class UPGMALinkage

java.lang.Object

smile.clustering.linkage.Linkage

smile.clustering.linkage.UPGMALinkage

public class UPGMALinkage
extends Linkage

Unweighted Pair Group Method with Arithmetic mean (also known as average linkage). The distance between two clusters is the mean distance between all possible pairs of nodes in the two clusters.

In bioinformatics, UPGMA is used for the creation of phenetic trees (phenograms). UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-regarded method for inferring relationships unless this assumption has been tested and justified for the data set being used.

Constructor Summary

Constructors

Constructor and Description
UPGMALinkage(double[][] proximity) Constructor.

Method Summary

Modifier and Type	Method and Description
void	merge(int i, int j) Merge two clusters into one and update the proximity matrix.
java.lang.String	toString()

Methods inherited from class smile.clustering.linkage.Linkage

d, size

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

UPGMALinkage

public UPGMALinkage(double[][] proximity)

Constructor.

Parameters:

proximity - the proximity matrix to store the distance measure of dissimilarity. To save space, we only need the lower half of matrix.

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

merge

public void merge(int i,
                  int j)

Description copied from class: Linkage

Merge two clusters into one and update the proximity matrix.

Specified by:

merge in class Linkage

Parameters:

i - cluster id.

j - cluster id.