package dr.evomodel.antigenic.phyloClustering.MCMCOperators;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.inference.operators.AbstractCoercableOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.MCMCOperator;
import dr.inference.operators.OperatorUtils;
import dr.math.MathUtils;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLObjectParser;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
public class muPrecisionInactiveMuOperator extends AbstractCoercableOperator {
private Parameter muPrecision = null;
private MatrixParameter mu = null;
private Parameter indicators = null;
private double scaleFactor;
private Parameter muMean = null;
public muPrecisionInactiveMuOperator(double weight, MatrixParameter mu, Parameter muPrec, double scale, Parameter indicators, Parameter muMean){
super(CoercionMode.COERCION_ON);
setWeight(weight);
this.mu = mu;
this.muPrecision = muPrec;
this.scaleFactor = scale;
this.indicators = indicators;
this.muMean = muMean;
}
public double doOperation() {
final double scale = (scaleFactor + (MathUtils.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
double original_muPrec_Val = muPrecision.getParameterValue(0);
double new_muPrec_Val = scale * original_muPrec_Val;
muPrecision.setParameterValue(0, new_muPrec_Val);
for(int i=0; i < mu.getColumnDimension(); i++){
//only change the inactive mus
if(indicators.getParameterValue(i) == 0){
for(int j=0; j < 2; j++){
if(j==0){
double translatedValue = (mu.getParameter(i).getParameterValue(j) - muMean.getParameterValue(0) );
double newValue = translatedValue * Math.sqrt( original_muPrec_Val/new_muPrec_Val) + muMean.getParameterValue(0);
mu.getParameter(i).setParameterValue(j, newValue);
}
else{
double oldValue = mu.getParameter(i).getParameterValue(j);
double newValue = oldValue * Math.sqrt( original_muPrec_Val/new_muPrec_Val);
mu.getParameter(i).setParameterValue(j, newValue);
}
}
}
}
double logq = -Math.log(scale);
return logq;
}
//copied from the original ScaleOperator
public double getCoercableParameter() {
return Math.log(1.0 / scaleFactor - 1.0);
}
//copied from the original ScaleOperator
public void setCoercableParameter(double value) {
scaleFactor = 1.0 / (Math.exp(value) + 1.0);
}
//copied from the original ScaleOperator
public double getRawParameter() {
return scaleFactor;
}
//copied from the original ScaleOperator
public double getTargetAcceptanceProbability() {
return 0.234;
}
//copied from the original ScaleOperator
public final String getPerformanceSuggestion() {
double prob = MCMCOperator.Utils.getAcceptanceProbability(this);
double targetProb = getTargetAcceptanceProbability();
dr.util.NumberFormatter formatter = new dr.util.NumberFormatter(5);
double sf = OperatorUtils.optimizeScaleFactor(scaleFactor, prob, targetProb);
if (prob < getMinimumGoodAcceptanceLevel()) {
return "Try setting scaleFactor to about " + formatter.format(sf);
} else if (prob > getMaximumGoodAcceptanceLevel()) {
return "Try setting scaleFactor to about " + formatter.format(sf);
} else return "";
}
public final static String CLASSNAME = "muPrecisionInactiveMuOperator";
public final String getOperatorName() {
return CLASSNAME;
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public final static String MU = "mu";
public final static String MUPREC = "muPrec";
public final static String SCALE = "scaleFactor";
public final static String MUMEAN = "muMean";
public final static String INDICATORS = "indicators";
public String getParserName() {
return CLASSNAME;
}
/* (non-Javadoc)
* @see dr.xml.AbstractXMLObjectParser#parseXMLObject(dr.xml.XMLObject)
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
double scale = xo.getDoubleAttribute(SCALE);
XMLObject cxo = xo.getChild(MU);
MatrixParameter mu = (MatrixParameter) cxo.getChild(MatrixParameter.class);
cxo = xo.getChild(MUPREC);
Parameter muPrec = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(INDICATORS);
Parameter indicators = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(MUMEAN);
Parameter muMean = (Parameter) cxo.getChild(Parameter.class);
return new muPrecisionInactiveMuOperator(weight, mu, muPrec, scale, indicators, muMean);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "changes serum drift and make sure the first dimension of the active drifted mus stay the same";
}
public Class getReturnType() {
return muPrecisionInactiveMuOperator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newDoubleRule(SCALE),
new ElementRule(MU, Parameter.class),
new ElementRule(MUPREC, Parameter.class),
new ElementRule(INDICATORS, Parameter.class),
new ElementRule(MUMEAN, Parameter.class)
};
};
public int getStepCount() {
return 1;
}
}