statalign.mcmc
Class McmcModule

java.lang.Object
  statalign.mcmc.McmcModule

Direct Known Subclasses:

CoreMcmcModule, ModelExtension

public abstract class McmcModule
extends java.lang.Object

Generic class for a group of McmcMove objects. Each ModelExtension is an instance of this class, as is the CoreMcmcModule

Author:

herman

Field Summary

double	curLogLike Current log-likelihood contribution
boolean	printExtraInfo

Constructor Summary

McmcModule()

Method Summary

void	addMcmcMove(McmcMove m, int weight)
void	addMcmcMove(McmcMove m, int weight, int increment)
void	afterFirstHalfBurnin()
void	afterSampling()
void	beforeSampling(Tree tree) Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated.
double	getLogLike()
java.lang.String	getMcmcInfo()
McmcMove	getMcmcMove(java.lang.String name)
java.util.List<McmcMove>	getMcmcMoves()
int	getParamChangeWeight()
void	incrementWeights()
boolean	isFirstHalfBurnin()
boolean	isParamChangeAccepted(double logProposalRatio, McmcMove m)
abstract double	logLikeFactor(Tree tree) This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space.
double	logPrior(Tree tree) This should return the log of the total prior calculated for the model parameters.
void	modifyProposalWidths()
boolean	proposeParamChange(Tree tree)
void	setAllMovesNotProposed()
void	setLogLike(double ll)
void	setMcmc(Mcmc m)
void	setWeight(java.lang.String name, int weight)
void	zeroAllMoveCounts()

Methods inherited from class java.lang.Object

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

Field Detail

printExtraInfo

public boolean printExtraInfo

curLogLike

public double curLogLike

Current log-likelihood contribution

Constructor Detail

McmcModule

public McmcModule()

Method Detail

setMcmc

public void setMcmc(Mcmc m)

isFirstHalfBurnin

public boolean isFirstHalfBurnin()

getParamChangeWeight

public int getParamChangeWeight()

setWeight

public void setWeight(java.lang.String name,
                      int weight)

addMcmcMove

public void addMcmcMove(McmcMove m,
                        int weight)

addMcmcMove

public void addMcmcMove(McmcMove m,
                        int weight,
                        int increment)

getMcmcMoves

public java.util.List<McmcMove> getMcmcMoves()

setAllMovesNotProposed

public void setAllMovesNotProposed()

zeroAllMoveCounts

public void zeroAllMoveCounts()

getMcmcMove

public McmcMove getMcmcMove(java.lang.String name)

getMcmcInfo

public java.lang.String getMcmcInfo()

beforeSampling

public void beforeSampling(Tree tree)

Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated. Override to initialise data structures etc.

Parameters:

tree - the starting tree

afterSampling

public void afterSampling()

logLikeFactor

public abstract double logLikeFactor(Tree tree)

This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space. Normally it will be called once at the initialisation of the MCMC process and from then on once in each MCMC step, when proposing any change. In debug mode, will be called more often (including after proposed changes) to ensure consistency.

Parameters:

tree - current tree

Returns:

log of model extension likelihood, conditional on current tree, alignment and params

getLogLike

public double getLogLike()

setLogLike

public void setLogLike(double ll)

logPrior

public double logPrior(Tree tree)

This should return the log of the total prior calculated for the model parameters. It is only used in parallel mode when proposing swaps between chains. By default returns 0.

proposeParamChange

public boolean proposeParamChange(Tree tree)

modifyProposalWidths

public void modifyProposalWidths()

isParamChangeAccepted

public boolean isParamChangeAccepted(double logProposalRatio,
                                     McmcMove m)

incrementWeights

public void incrementWeights()

afterFirstHalfBurnin

public void afterFirstHalfBurnin()