pal.statistics

Class ShimodairaHasegawaStatistics

java.lang.Object

pal.statistics.ShimodairaHasegawaStatistics

All Implemented Interfaces:

TopologyTestEngine.StatisticsHandler

public class ShimodairaHasegawaStatistics
extends java.lang.Object
implements TopologyTestEngine.StatisticsHandler

Title: ShimodairaHasegawaStatistics

Description:The Statistics Handler for the ShimodairaHasegawa test

Version:

1.0

Author:

Matthew Goode

Constructor Summary

Constructors

Constructor and Description
ShimodairaHasegawaStatistics()

Method Summary

Methods

Modifier and Type	Method and Description
double[]	getOriginalTestStatistics(double[] originalOptimisedLogLikelihoods, int numberOfTopologies)
double[]	getPValues(double[] originalOptimisedLogLikelihoods, double[][] replicateLogLikelihoods, int numberOfReplicates, int numberOfTopologies) The pValue in this case represents the alpha value ( CI 1-alpha) when topology becomes significantly different from the ML topology (or stops being not significantly different)

Methods inherited from class java.lang.Object

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

Constructor Detail

ShimodairaHasegawaStatistics

public ShimodairaHasegawaStatistics()

Method Detail

getOriginalTestStatistics

public double[] getOriginalTestStatistics(double[] originalOptimisedLogLikelihoods,
                                 int numberOfTopologies)

Specified by:

getOriginalTestStatistics in interface TopologyTestEngine.StatisticsHandler

getPValues

public double[] getPValues(double[] originalOptimisedLogLikelihoods,
                  double[][] replicateLogLikelihoods,
                  int numberOfReplicates,
                  int numberOfTopologies)

The pValue in this case represents the alpha value ( CI 1-alpha) when topology becomes significantly different from the ML topology (or stops being not significantly different)

Specified by:

getPValues in interface TopologyTestEngine.StatisticsHandler

Parameters:

originalOptimisedLogLikelihoods - stored as [topology]

replicateLogLikelihoods - store as [replicate][topology]

numberOfTopologies - the number of topologies

numberOfReplicates - the number of replicates

Returns:

the pValue array