McmcMove.java

package statalign.mcmc;

import statalign.base.Utils;

public abstract class McmcMove {

	protected McmcModule owner;
	public McmcModule getOwner() {
		return owner;
	}
	protected PriorDistribution<? extends Object> prior;
	
	protected ParameterInterface param;
	public ParameterInterface getParam() {
		return param;
	}
	
	public int proposalCount = 0;
	public int acceptanceCount = 0;
	public boolean lastMoveAccepted = false;
	protected double lastLogProposalRatio;
	public boolean acceptAllDuringFirstHalfBurnin = false;
	public boolean printableParam = false;
	public boolean moveProposed = false;
	/** 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. 
	 */ 
	public int lowCounts = 0;
	
	public double proposalWidthControlVariable = 1.0;
	public double minProposalWidthControlVariable = 0.0;
	public double maxProposalWidthControlVariable = Double.POSITIVE_INFINITY;
	public double spanMultiplier = Utils.SPAN_MULTIPLIER;
	public double minAcceptance = Utils.MIN_ACCEPTANCE;
	public double maxAcceptance = Utils.MAX_ACCEPTANCE;
	public boolean autoTune = true;
	public boolean inCombination = false;
	// TODO Add constructor fields for specifying the above two
	// variables.
	
	public String name;
	private long time = 0;
	
	public String getNameString() { return name; }
	public String getParameterString() { return ""; };
	
	public long getTime() {
		return time;
	}
	public double acceptanceRate() {
		return (double) acceptanceCount / (double) proposalCount;
	}
	
	public abstract void copyState(Object externalState);
	public abstract double proposal(Object externalState); 
	// Modifies variables and returns logProposalRatio
	
	public abstract double logPriorDensity(Object externalState);
	public abstract void updateLikelihood(Object externalState); 
	public abstract void restoreState(Object externalState);
	public void afterMove(Object externalState) { }

	public boolean isParamChangeAccepted(double logProposalRatio) {
		return getOwner().isParamChangeAccepted(logProposalRatio,this);
	}
	
	public void move(Object externalState) {
		if (Utils.DEBUG) System.out.println("Executing move:\""+name+"\"");
		time -= System.currentTimeMillis();
		proposalCount++;
		moveProposed = true;
		copyState(externalState);
		double logProposalRatio = -logPriorDensity(externalState);
		logProposalRatio += proposal(externalState); 
		logProposalRatio += logPriorDensity(externalState);
		lastLogProposalRatio = logProposalRatio;
		if (logProposalRatio != Double.NEGATIVE_INFINITY) {
			updateLikelihood(externalState);
		}
		if(isParamChangeAccepted(logProposalRatio)) {
			acceptanceCount++;
			lastMoveAccepted = true;
		}
		else {
			lastMoveAccepted = false;
			restoreState(externalState);
		}
		afterMove(externalState);
		time += System.currentTimeMillis();
	}
	public void afterFirstHalfBurnin() { }
	public void afterBurnin() { }
	
	/**  
	 * Can be optionally defined in order to print move info at end of MCMC run.
	 */
	public void printInfo() { }
}