smile.clustering.linkage

Class WPGMALinkage

java.lang.Object

smile.clustering.linkage.Linkage

smile.clustering.linkage.WPGMALinkage

public class WPGMALinkage
extends Linkage

Weighted Pair Group Method with Arithmetic mean. WPGMA down-weights the largest group by giving equal weights to the two branches of the dendrogram that are about to fuse.

Note that the terms weighted and unweighted refer to the final result, not the math by which it is achieved. Thus the simple averaging in WPGMA produces a weighted result, and the proportional averaging in UPGMA produces an unweighted result.

Constructor Summary

Constructors

Constructor and Description
WPGMALinkage(double[][] proximity) Constructor.
WPGMALinkage(int size, float[] 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.
static WPGMALinkage	of(double[][] data) Given a set of data, computes the proximity and then the linkage.
static <T> WPGMALinkage	of(T[] data, smile.math.distance.Distance<T> distance) Given a set of data, computes the proximity and then the linkage.
java.lang.String	toString()

Methods inherited from class smile.clustering.linkage.Linkage

d, proximity, proximity, size

Methods inherited from class java.lang.Object

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

Constructor Detail

WPGMALinkage

public WPGMALinkage(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.

WPGMALinkage

public WPGMALinkage(int size,
                    float[] proximity)

Constructor. Initialize the linkage with the lower triangular proximity matrix.

Parameters:

size - the data size.

proximity - column-wise linearized proximity matrix that stores only the lower half. The length of proximity should be size * (size+1) / 2. To save space, Linkage will use this argument directly without copy. The elements may be modified.

Method Detail

of

public static WPGMALinkage of(double[][] data)

Given a set of data, computes the proximity and then the linkage.

of

public static <T> WPGMALinkage of(T[] data,
                                  smile.math.distance.Distance<T> distance)

Given a set of data, computes the proximity and then the linkage.

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.