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

Class BrayCurtisDistanceFunction

java.lang.Object

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

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

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

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

All Implemented Interfaces:

DistanceFunction<NumberVector<?>,DoubleDistance>, NumberVectorDistanceFunction<DoubleDistance>, PrimitiveDistanceFunction<NumberVector<?>,DoubleDistance>, PrimitiveDoubleDistanceFunction<NumberVector<?>>, SpatialPrimitiveDistanceFunction<NumberVector<?>,DoubleDistance>, SpatialPrimitiveDoubleDistanceFunction<NumberVector<?>>, Parameterizable

@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 AbstractSpatialDoubleDistanceFunction

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.

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	doubleDistance(NumberVector<?> v1, NumberVector<?> v2) Computes the distance between two given Objects according to this distance function.
double	doubleMinDist(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.AbstractSpatialDoubleDistanceFunction

instantiate, minDist

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

dimensionality, dimensionality, dimensionality, dimensionality, distance, getDistanceFactory, 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

distance, getInputTypeRestriction

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

getDistanceFactory, 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.

doubleDistance

public double doubleDistance(NumberVector<?> v1,
                    NumberVector<?> v2)

Description copied from interface: PrimitiveDoubleDistanceFunction

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

Parameters:

v1 - first Object

v2 - second Object

Returns:

the distance between two given Objects according to this distance function

doubleMinDist

public double doubleMinDist(SpatialComparable mbr1,
                   SpatialComparable mbr2)

Description copied from interface: SpatialPrimitiveDoubleDistanceFunction

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