Collaboration diagram for broad.core.math.EmpiricalDistribution:

Public Member Functions
	EmpiricalDistribution (int numberOfBins, double min, double max)

	EmpiricalDistribution (int numberOfBins, double min, double max, boolean includeOutOfRange)

	EmpiricalDistribution (Collection< Double > vals, int numberOfBins)

double	getMax ()

double	getMin ()

int	getBinNumber ()

	EmpiricalDistribution (Collection< Double > vals)

	EmpiricalDistribution (Collection< Double > vals, int numberOfBins, boolean absVal)

	EmpiricalDistribution (double[] vals, int numberOfBins)

	EmpiricalDistribution (List< Double > vals, int numberOfBins)

	EmpiricalDistribution (double[] vals, int numberOfBins, double min, double max)

double	testGoodnessOfFit (EmpiricalDistribution other) throws IllegalArgumentException

double	chiSquareDistance (EmpiricalDistribution other) throws IllegalArgumentException, IOException

double	KLDivergence (EmpiricalDistribution other) throws IllegalArgumentException

double	KLDivergenceSym (EmpiricalDistribution other) throws IllegalArgumentException, IOException

	EmpiricalDistribution (InputStream is) throws IOException

	EmpiricalDistribution (File source) throws IOException

	EmpiricalDistribution (Matrix permutations, int numberOfBins)

void	add (double observation)

double	leftIntersect (EmpiricalDistribution other)

int	getBin (double value)

double	getBinMidPoint (int bin)

double	getBinStart (int bin)

double	getBinEnd (int bin)

double	rightIntersect (EmpiricalDistribution other)

double	getFirstIntersectLeftFromMedian (EmpiricalDistribution other)

double	getFirstIntersectRightFromMedian (EmpiricalDistribution other)

int	getTotalObservations ()

void	ensureNoEmptyBins ()

void	addPsuedocounts (double psuedocount)

double	getDensity (int bin)

double	getHistogram (int bin)

EmpiricalDistribution	getDistributionOfHistogramValues ()

double	getRawDensity (int bin)

double	getPercentOfValuesBetween (double leftBound, double rightBound)

double	getPercentOfValuesLargerThan (double value)

double	getMean ()

double	getStandardDeviation ()

double	getMedianOfAllDataValues ()

double	getQuantileOfBins (double probability)

double	getCumulativeProbability (double value)

int	getNumberOfValuesLargerThan (double value)

double	getKSStatistic (List< Double > observed)

double	getKSStatistic (double[] observed)

void	write (BufferedWriter bw) throws IOException

void	write (String save) throws IOException

void	addDistribution (EmpiricalDistribution other)

Collection< Double >	getAllDataValues ()

void	addAll (Collection< Double > values)

void	addAll (double[] values)

void	addAll (Matrix vals)

Map< Double, Double >	getCountByBinStart ()

double	getProbability (double size)

double	getPValue (double score)

double	getPValue (double score, double min)

int	numBins ()

double	getPValue2 (double score)

double	getZscore (double value)

Static Public Member Functions
static void	main (String[] args) throws Exception

static EmpiricalDistribution	getEmpiricalMaxStatisticDistribution (Collection< EmpiricalDistribution > distributions)

Static Public Attributes
static final String	USAGE

Constructor & Destructor Documentation

broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	int	numberOfBins,
		double	min,
		double	max
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	int	numberOfBins,
		double	min,
		double	max,
		boolean	includeOutOfRange
	)

broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	Collection< Double >	vals,
		int	numberOfBins
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution ( Collection< Double > vals )

broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	Collection< Double >	vals,
		int	numberOfBins,
		boolean	absVal
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	double[]	vals,
		int	numberOfBins
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	List< Double >	vals,
		int	numberOfBins
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	double[]	vals,
		int	numberOfBins,
		double	min,
		double	max
	)

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broad.core.math.EmpiricalDistribution.EmpiricalDistribution ( InputStream is ) throws IOException

broad.core.math.EmpiricalDistribution.EmpiricalDistribution ( File source ) throws IOException

broad.core.math.EmpiricalDistribution.EmpiricalDistribution	(	Matrix	permutations,
		int	numberOfBins
	)

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Member Function Documentation

void broad.core.math.EmpiricalDistribution.add ( double observation )

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void broad.core.math.EmpiricalDistribution.addAll ( Collection< Double > values )

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void broad.core.math.EmpiricalDistribution.addAll ( double[] values )

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void broad.core.math.EmpiricalDistribution.addAll ( Matrix vals )

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void broad.core.math.EmpiricalDistribution.addDistribution ( EmpiricalDistribution other )

void broad.core.math.EmpiricalDistribution.addPsuedocounts ( double psuedocount )

double broad.core.math.EmpiricalDistribution.chiSquareDistance ( EmpiricalDistribution other ) throws IllegalArgumentException, IOException

This function will calculate the chi square distance between this and other empirical distribution. A psuedocount of 1 is added to both distributions before calculating the statistic otherwise zeros will return a MathException

Author: skadri

Parameters

other

Returns

Exceptions

IllegalArgumentException
MathException

void broad.core.math.EmpiricalDistribution.ensureNoEmptyBins ( )

Collection<Double> broad.core.math.EmpiricalDistribution.getAllDataValues ( )

Get list of all the data values that contributed to the bins

Returns: List of all data values subject to same filters as the binned counts

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int broad.core.math.EmpiricalDistribution.getBin ( double value )

double broad.core.math.EmpiricalDistribution.getBinEnd ( int bin )

double broad.core.math.EmpiricalDistribution.getBinMidPoint ( int bin )

int broad.core.math.EmpiricalDistribution.getBinNumber ( )

double broad.core.math.EmpiricalDistribution.getBinStart ( int bin )

Map<Double, Double> broad.core.math.EmpiricalDistribution.getCountByBinStart ( )

Get the distribution as a map

Returns: Map associating bin lower bound with number of values in the bin

double broad.core.math.EmpiricalDistribution.getCumulativeProbability ( double value )

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double broad.core.math.EmpiricalDistribution.getDensity ( int bin )

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EmpiricalDistribution broad.core.math.EmpiricalDistribution.getDistributionOfHistogramValues ( )

Get distribution of number of observations per bin

Returns: Distribution of number of observations per bin

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static EmpiricalDistribution broad.core.math.EmpiricalDistribution.getEmpiricalMaxStatisticDistribution ( Collection< EmpiricalDistribution > distributions )

static

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double broad.core.math.EmpiricalDistribution.getFirstIntersectLeftFromMedian ( EmpiricalDistribution other )

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double broad.core.math.EmpiricalDistribution.getFirstIntersectRightFromMedian ( EmpiricalDistribution other )

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double broad.core.math.EmpiricalDistribution.getHistogram ( int bin )

Get the total number of observations in the bin

Parameters

bin	Bin number

Returns

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double broad.core.math.EmpiricalDistribution.getKSStatistic ( List< Double > observed )

Compared a list of observed with this empirical distribution using the Kolmogorov Smirnov Test. Will be approximate since we don't store every value in this distribution.

Get signifiance with: 1 - new umontreal.iro.lecuyer.probdist.KolmogorovSmirnovDist().cdf(D, observed.size());

Parameters

observed List of observations

Returns: D statistic

NOTE: UNTESTED

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double broad.core.math.EmpiricalDistribution.getKSStatistic ( double[] observed )

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double broad.core.math.EmpiricalDistribution.getMax ( )

double broad.core.math.EmpiricalDistribution.getMean ( )

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double broad.core.math.EmpiricalDistribution.getMedianOfAllDataValues ( )

Get median of all data values including out of range

Returns: Median of all individual values including out of range or -99 if no data

double broad.core.math.EmpiricalDistribution.getMin ( )

int broad.core.math.EmpiricalDistribution.getNumberOfValuesLargerThan ( double value )

double broad.core.math.EmpiricalDistribution.getPercentOfValuesBetween	(	double	leftBound,
		double	rightBound
	)

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double broad.core.math.EmpiricalDistribution.getPercentOfValuesLargerThan ( double value )

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double broad.core.math.EmpiricalDistribution.getProbability ( double size )

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double broad.core.math.EmpiricalDistribution.getPValue ( double score )

double broad.core.math.EmpiricalDistribution.getPValue	(	double	score,
		double	min
	)

double broad.core.math.EmpiricalDistribution.getPValue2 ( double score )

P(x>Score)

Parameters

score

Returns

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double broad.core.math.EmpiricalDistribution.getQuantileOfBins ( double probability )

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double broad.core.math.EmpiricalDistribution.getRawDensity ( int bin )

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double broad.core.math.EmpiricalDistribution.getStandardDeviation ( )

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int broad.core.math.EmpiricalDistribution.getTotalObservations ( )

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double broad.core.math.EmpiricalDistribution.getZscore ( double value )

double broad.core.math.EmpiricalDistribution.KLDivergence ( EmpiricalDistribution other ) throws IllegalArgumentException

This function will calculate the KULLBACK-LIEBLER DIVERGENCE between this and other empirical distribution. MAKE SURE THAT GIBB'S INEQUALITY HOLDS. FOR THIS, ADD 1.0 AS PSUEDOCOUNTS (USE addPsuedocounts() FUNCTION)

Parameters

other

Returns

Exceptions

IllegalArgumentException
MathException

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double broad.core.math.EmpiricalDistribution.KLDivergenceSym ( EmpiricalDistribution other ) throws IllegalArgumentException, IOException

double broad.core.math.EmpiricalDistribution.leftIntersect ( EmpiricalDistribution other )

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static void broad.core.math.EmpiricalDistribution.main ( String[] args ) throws Exception

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int broad.core.math.EmpiricalDistribution.numBins ( )

Get the number of bins

Returns: The number of bins

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double broad.core.math.EmpiricalDistribution.rightIntersect ( EmpiricalDistribution other )

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double broad.core.math.EmpiricalDistribution.testGoodnessOfFit ( EmpiricalDistribution other ) throws IllegalArgumentException

This function will calculate the significance of the chi square statistic between this and other empirical distribution.

Parameters

other

Returns

Exceptions

IllegalArgumentException
MathException

void broad.core.math.EmpiricalDistribution.write ( BufferedWriter bw ) throws IOException

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void broad.core.math.EmpiricalDistribution.write ( String save ) throws IOException

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Member Data Documentation

final String broad.core.math.EmpiricalDistribution.USAGE

static

Initial value:

= "Usage: EmpiricDistribution TASK=<task_num> <task_args>\n" +
    "\tTasks:\n" +
    "\t\t1. Get empirical distribution -col <column to use 0 for the first one> [-in <Input file standard input is default> -out <output file, standard output by default> -separator <tab (\t) is default>]" +
    "\t\t\t -binNum <Number of bins, default is 200> -maxValue <Maximum value to consider> -minValue <Minimum value to consider>" +
    "\n\t2. Combine distributions -indir <directory> -suffix <suffix of distribution files to combine> -out <output file name defalut is standard out>" +
    "\n\t3. Get quantile -probability -in <Input distribution standard input is default>" +
    "\n"

The documentation for this class was generated from the following file:

java/broad/core/math/EmpiricalDistribution.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation