package dr.inference.operators; import dr.inference.model.Parameter; import dr.inference.model.Variable; import dr.inferencexml.operators.UniformIntegerOperatorParser; import dr.math.MathUtils; /** * A generic uniform sampler/operator for use with a multi-dimensional parameter. * * @author Alexei Drummond * @author Andrew Rambaut * @version $Id: UniformOperator.java,v 1.16 2005/06/14 10:40:34 rambaut Exp $ */ public class UniformIntegerOperator extends SimpleMCMCOperator { private final int howMany; public UniformIntegerOperator(Parameter parameter, int lower, int upper, double weight, int howMany) { this(parameter, weight, howMany); this.lower = lower; this.upper = upper; } public UniformIntegerOperator(Parameter parameter, int lower, int upper, double weight) { this(parameter, lower, upper, weight, 1); } public UniformIntegerOperator(Variable parameter, double weight, int howMany) { // Bounds.Staircase this.parameter = parameter; this.howMany = howMany; setWeight(weight); } /** * @return the parameter this operator acts on. */ public Parameter getParameter() { return (Parameter) parameter; } /** * @return the Variable this operator acts on. */ public Variable getVariable() { return parameter; } /** * change the parameter and return the hastings ratio. */ public final double doOperation() { for (int n = 0; n < howMany; ++n) { // do not worry about duplication, does not matter int index = MathUtils.nextInt(parameter.getSize()); if (parameter instanceof Parameter) { int newValue = MathUtils.nextInt(upper - lower + 1) + lower; // from 0 to n-1, n must > 0, ((Parameter) parameter).setParameterValue(index, newValue); } else { // Variable<Integer>, Bounds.Staircase int upper = ((Variable<Integer>) parameter).getBounds().getUpperLimit(index); int lower = ((Variable<Integer>) parameter).getBounds().getLowerLimit(index); int newValue = MathUtils.nextInt(upper - lower + 1) + lower; // from 0 to n-1, n must > 0, ((Variable<Integer>) parameter).setValue(index, newValue); } } return 0.0; } //MCMCOperator INTERFACE public final String getOperatorName() { return "uniformInteger(" + parameter.getId() + ")"; } public final void optimize(double targetProb) { throw new RuntimeException("This operator cannot be optimized!"); } public boolean isOptimizing() { return false; } public void setOptimizing(boolean opt) { throw new RuntimeException("This operator cannot be optimized!"); } public double getMinimumAcceptanceLevel() { return 0.1; } public double getMaximumAcceptanceLevel() { return 0.4; } public double getMinimumGoodAcceptanceLevel() { return 0.20; } public double getMaximumGoodAcceptanceLevel() { return 0.30; } public String getPerformanceSuggestion() { if (Utils.getAcceptanceProbability(this) < getMinimumAcceptanceLevel()) { return ""; } else if (Utils.getAcceptanceProbability(this) > getMaximumAcceptanceLevel()) { return ""; } else { return ""; } } public String toString() { return UniformIntegerOperatorParser.UNIFORM_INTEGER_OPERATOR + "(" + parameter.getId() + ")"; } //PRIVATE STUFF private Variable parameter = null; private int upper; private int lower; }