Package 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	Description
UPGMALinkage(double[][] proximity)	Constructor.
UPGMALinkage(int size, float[] proximity)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	merge(int i, int j)	Merges two clusters into one and update the proximity matrix.
static UPGMALinkage	of(double[][] data)	Computes the proximity and the linkage.
static <T> UPGMALinkage	of(T[] data, Distance<T> distance)	Computes the proximity and the linkage.
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 Details

UPGMALinkage

public UPGMALinkage(double[][] proximity)

Constructor.

Parameters:

proximity - the proximity matrix. Only the lower half will be referred.

UPGMALinkage

public UPGMALinkage(int size,
 float[] proximity)

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

Parameters:

size - the data size.

proximity - the 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 Details

of

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

Computes the proximity and the linkage.

Parameters:

data - the data points.

Returns:

the linkage.

of

public static <T> UPGMALinkage of(T[] data,
 Distance<T> distance)

Computes the proximity and the linkage.

Type Parameters:

T - the data type of points.

Parameters:

data - the data points.

distance - the distance function.

Returns:

the linkage.

toString

public String toString()

Overrides:

toString in class Object

merge

public void merge(int i,
 int j)

Description copied from class: Linkage

Merges two clusters into one and update the proximity matrix.

Specified by:

merge in class Linkage

Parameters:

i - cluster id.

j - cluster id.