de.lmu.ifi.dbs.elki.distance.distancefunction

Class BrayCurtisDistanceFunction

java.lang.Object

de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractPrimitiveDistanceFunction<NumberVector>

de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractNumberVectorDistanceFunction

de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractSpatialDistanceFunction

de.lmu.ifi.dbs.elki.distance.distancefunction.BrayCurtisDistanceFunction

All Implemented Interfaces:

DistanceFunction<NumberVector>, NumberVectorDistanceFunction<NumberVector>, PrimitiveDistanceFunction<NumberVector>, SpatialPrimitiveDistanceFunction<NumberVector>

@Alias(value={"bray-curtis","braycurtis","sorensen","dice","sorensen-dice"})
@Reference(authors="J. R. Bray and J. T. Curtis",
           title="An ordination of the upland forest communities of southern Wisconsin",
           booktitle="Ecological monographs 27.4",
           url="http://dx.doi.org/10.2307/1942268")
public class BrayCurtisDistanceFunction
extends AbstractSpatialDistanceFunction

Bray-Curtis distance function / Sørensen–Dice coefficient for continuous spaces. Reference:

J. R. Bray and J. T. Curtis
An ordination of the upland forest communities of southern Wisconsin
Ecological monographs 27.4

Also:

T. Sørensen
A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons
Kongelige Danske Videnskabernes Selskab 5 (4)

and:

L. R. Dice
Measures of the Amount of Ecologic Association Between Species
Ecology 26 (3)

Note: we modified the usual definition of Bray-Curtis for use with negative values. In essence, this function is defined as: ManhattanDistance(v1, v2) / (ManhattanNorm(v1) + ManhattanNorm(v2)) This obviously limits the usefulness of this distance function for cases where this kind of normalization is desired. In particular in low dimensional data it should be used with care. TODO: add a version optimized for sparse vectors / binary data.

Since:

0.4.0

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BrayCurtisDistanceFunction.Parameterizer Parameterization class.

Field Summary

Fields

Modifier and Type	Field and Description
static BrayCurtisDistanceFunction	STATIC_CONTINUOUS Static instance.

Constructor Summary

Constructors

Constructor and Description
BrayCurtisDistanceFunction() Deprecated. Use STATIC_CONTINUOUS instance instead.

Method Summary

Methods

Modifier and Type	Method and Description
double	distance(NumberVector v1, NumberVector v2) Computes the distance between two given DatabaseObjects according to this distance function.
double	minDist(SpatialComparable mbr1, SpatialComparable mbr2) Computes the distance between the two given MBRs according to this distance function.
(package private) static void	secondReference() Dummy method, just to attach a second reference.
(package private) static void	thirdReference() Dummy method, just to attach a third reference.

Methods inherited from class de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractSpatialDistanceFunction

instantiate

Methods inherited from class de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractNumberVectorDistanceFunction

dimensionality, dimensionality, dimensionality, dimensionality, getInputTypeRestriction

Methods inherited from class de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractPrimitiveDistanceFunction

isMetric, isSymmetric

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.lmu.ifi.dbs.elki.distance.distancefunction.PrimitiveDistanceFunction

getInputTypeRestriction

Methods inherited from interface de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction

isMetric, isSymmetric

Field Detail

STATIC_CONTINUOUS

public static final BrayCurtisDistanceFunction STATIC_CONTINUOUS

Static instance.

Constructor Detail

BrayCurtisDistanceFunction

@Deprecated
public BrayCurtisDistanceFunction()

Deprecated. Use STATIC_CONTINUOUS instance instead.

Constructor.

Method Detail

secondReference

@Reference(authors="T. S\u00f8rensen",
           title="A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons",
           booktitle="Kongelige Danske Videnskabernes Selskab 5 (4)")
static void secondReference()

Dummy method, just to attach a second reference.

thirdReference

@Reference(authors="L. R. Dice",
           title="Measures of the Amount of Ecologic Association Between Species",
           booktitle="Ecology 26 (3)")
static void thirdReference()

Dummy method, just to attach a third reference.

distance

public double distance(NumberVector v1,
              NumberVector v2)

Description copied from interface: PrimitiveDistanceFunction

Computes the distance between two given DatabaseObjects according to this distance function.

Specified by:

distance in interface NumberVectorDistanceFunction<NumberVector>

Specified by:

distance in interface PrimitiveDistanceFunction<NumberVector>

Specified by:

distance in class AbstractPrimitiveDistanceFunction<NumberVector>

Parameters:

v1 - first DatabaseObject

v2 - second DatabaseObject

Returns:

the distance between two given DatabaseObjects according to this distance function

minDist

public double minDist(SpatialComparable mbr1,
             SpatialComparable mbr2)

Description copied from interface: SpatialPrimitiveDistanceFunction

Computes the distance between the two given MBRs according to this distance function.

Parameters:

mbr1 - the first MBR object

mbr2 - the second MBR object

Returns:

the distance between the two given MBRs according to this distance function