statalign.base.mcmc
Class LOCALTopologyMove

java.lang.Object
  statalign.mcmc.McmcMove
      statalign.base.mcmc.LOCALTopologyMove

public class LOCALTopologyMove
extends McmcMove

Field Summary

int	nTopologyChanges

Fields inherited from class statalign.mcmc.McmcMove

acceptAllDuringFirstHalfBurnin, acceptanceCount, autoTune, lastMoveAccepted, lowCounts, maxAcceptance, maxProposalWidthControlVariable, minAcceptance, moveProposed, name, proposalCount, proposalWidthControlVariable, spanMultiplier

Constructor Summary

LOCALTopologyMove(McmcModule m, PriorDistribution<java.lang.Double> pr, double propVar, double _fastSwapProb, java.lang.String n)

Method Summary

void	afterMove(java.lang.Object externalState)
void	copyState(java.lang.Object externalState)
double	logPriorDensity(java.lang.Object externalState)
double	proposal(java.lang.Object externalState)
void	restoreState(java.lang.Object externalState)
double	setEdges(double a, double b, double c) Sets the three edges affected by the LOCAL move (nephew, parent and uncle) to the specified values.
void	updateLikelihood(java.lang.Object externalState)

Methods inherited from class statalign.mcmc.McmcMove

acceptanceRate, afterFirstHalfBurnin, getOwner, getParam, getTime, isParamChangeAccepted, move

Methods inherited from class java.lang.Object

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

Field Detail

nTopologyChanges

public int nTopologyChanges

Constructor Detail

LOCALTopologyMove

public LOCALTopologyMove(McmcModule m,
                         PriorDistribution<java.lang.Double> pr,
                         double propVar,
                         double _fastSwapProb,
                         java.lang.String n)

Method Detail

setEdges

public double setEdges(double a,
                       double b,
                       double c)

Sets the three edges affected by the LOCAL move (nephew, parent and uncle) to the specified values. If any of the values are less than minEdgeLength then the change is not made, invalidProposal is set to true, and negative infinity is returned.

Parameters:

a - The edge length for the nephew

b - The edge length for the parent

c - The edge length for the uncle

Returns:

The log ratio of new versus old prior densities.

copyState

public void copyState(java.lang.Object externalState)

Specified by:

copyState in class McmcMove

proposal

public double proposal(java.lang.Object externalState)

Specified by:

proposal in class McmcMove

logPriorDensity

public double logPriorDensity(java.lang.Object externalState)

Specified by:

logPriorDensity in class McmcMove

updateLikelihood

public void updateLikelihood(java.lang.Object externalState)

Specified by:

updateLikelihood in class McmcMove

restoreState

public void restoreState(java.lang.Object externalState)

Specified by:

restoreState in class McmcMove

afterMove

public void afterMove(java.lang.Object externalState)

Overrides:

afterMove in class McmcMove