 • java.lang.Object
• All Implemented Interfaces:

@Reference(authors="R. R. Sokal, C. D. Michener",
title="A statistical method for evaluating systematic relationship",
booktitle="University of Kansas science bulletin 28",
url="https://archive.org/details/cbarchive_33927_astatisticalmethodforevaluatin1902",
bibkey="journals/kansas/SokalM1902")
@Priority(value=201)
extends java.lang.Object
Group-average linkage clustering method (UPGMA).

This is a good default linkage to use with hierarchical clustering, as it neither exhibits the single-link chaining effect, nor has the strong tendency of complete linkage to split large clusters. It is also easy to understand, and it can be used with arbitrary distances and similarity functions.

The distances of two clusters is defined as the between-group average distance of two points $a$ and $b$, one from each cluster. It should be noted that this is not the average distance within the resulting cluster, because it does not take within-cluster distances into account.

The distance of two clusters in this method is: $d_{\text{UPGMA}}(A,B)=\tfrac{1}{|A|\cdot|B|} \sum\nolimits_{a\in A}\sum\nolimits_{b\in B} d(a,b)$

For Lance-Williams, we can then obtain the following recursive definition: $d_{\text{UPGMA}}(A\cup B,C)=\tfrac{|A|}{|A|+|B|} d(A,C) + \tfrac{|B|}{|A|+|B|} d(B,C)$

While the method is also called "Unweighted Pair Group Method with Arithmetic mean", it uses weights in the Lance-Williams formulation that account for the cluster size. It is unweighted in the sense that every point keeps the same weight, whereas in WeightedAverageLinkage (WPGMA), the weight of points effectively depends on the depth in the cluster tree.

Reference:

R. R. Sokal, C. D. Michener
A statistical method for evaluating systematic relationship
University of Kansas science bulletin, 28, 1409-1438.

Since:
0.6.0
Author:
Erich Schubert
• Field Summary

Fields
Modifier and Type Field and Description
Static instance of class.
• Constructor Summary

Constructors
Constructor and Description
Deprecated.
use the static instance STATIC instead.
• Method Summary

All Methods
Modifier and Type Method and Description
double combine(int sizex, double dx, int sizey, double dy, int sizej, double dxy)
Compute combined linkage for two clusters.
• Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

initial, restore

• Constructor Detail

@Deprecated
Deprecated. use the static instance STATIC instead.
Constructor.
• Method Detail

• combine

public double combine(int sizex,
double dx,
int sizey,
double dy,
int sizej,
double dxy)
Description copied from interface: Linkage
Compute combined linkage for two clusters.
Specified by:
combine in interface Linkage
Parameters:
sizex - Size of first cluster x before merging
dx - Distance of cluster x to j before merging
sizey - Size of second cluster y before merging
dy - Distance of cluster y to j before merging
sizej - Size of candidate cluster j
dxy - Distance between clusters x and y before merging
Returns:
Combined distance