statalign.mcmc
Class McmcMove

java.lang.Object
  statalign.mcmc.McmcMove

Direct Known Subclasses:

AlignmentMove, AlignmentMove, ContinuousPositiveParameterMove, LOCALTopologyMove, McmcCombinationMove, RotationOrTranslationMove, SilentIndelMove, SubstMove, TopologyMove

public abstract class McmcMove
extends java.lang.Object

Field Summary

boolean	acceptAllDuringFirstHalfBurnin
int	acceptanceCount
boolean	autoTune
boolean	lastMoveAccepted
int	lowCounts Number of times that the acceptance rate has been recorded as being below the minimum.
double	maxAcceptance
double	maxProposalWidthControlVariable
double	minAcceptance
boolean	moveProposed
java.lang.String	name
int	proposalCount
double	proposalWidthControlVariable
double	spanMultiplier

Constructor Summary

McmcMove()

Method Summary

double	acceptanceRate()
void	afterFirstHalfBurnin()
void	afterMove(java.lang.Object externalState)
abstract void	copyState(java.lang.Object externalState)
McmcModule	getOwner()
ParameterInterface	getParam()
long	getTime()
boolean	isParamChangeAccepted(double logProposalRatio)
abstract double	logPriorDensity(java.lang.Object externalState)
void	move(java.lang.Object externalState)
abstract double	proposal(java.lang.Object externalState)
abstract void	restoreState(java.lang.Object externalState)
abstract void	updateLikelihood(java.lang.Object externalState)

Methods inherited from class java.lang.Object

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

Field Detail

proposalCount

public int proposalCount

acceptanceCount

public int acceptanceCount

lastMoveAccepted

public boolean lastMoveAccepted

acceptAllDuringFirstHalfBurnin

public boolean acceptAllDuringFirstHalfBurnin

moveProposed

public boolean moveProposed

lowCounts

public int lowCounts

Number of times that the acceptance rate has been recorded as being below the minimum. If this count reaches a particular threshold (set in Utils), then during the burnin we will multiply the new likelihood by a constant less than unity in order to favour acceptance of the proposal, mainly for the purposes of forcing the chain to explore alternative topologies.

proposalWidthControlVariable

public double proposalWidthControlVariable

maxProposalWidthControlVariable

public double maxProposalWidthControlVariable

spanMultiplier

public double spanMultiplier

minAcceptance

public double minAcceptance

maxAcceptance

public double maxAcceptance

autoTune

public boolean autoTune

name

public java.lang.String name

Constructor Detail

McmcMove

public McmcMove()

Method Detail

getOwner

public McmcModule getOwner()

getParam

public ParameterInterface getParam()

getTime

public long getTime()

acceptanceRate

public double acceptanceRate()

copyState

public abstract void copyState(java.lang.Object externalState)

proposal

public abstract double proposal(java.lang.Object externalState)

logPriorDensity

public abstract double logPriorDensity(java.lang.Object externalState)

updateLikelihood

public abstract void updateLikelihood(java.lang.Object externalState)

restoreState

public abstract void restoreState(java.lang.Object externalState)

afterMove

public void afterMove(java.lang.Object externalState)

isParamChangeAccepted

public boolean isParamChangeAccepted(double logProposalRatio)

move

public void move(java.lang.Object externalState)

afterFirstHalfBurnin

public void afterFirstHalfBurnin()