Examples with RandomWalkOperator dr.inference.operators.RandomWalkOperator used on opensource projects

Example 1 with RandomWalkOperator

use of dr.inference.operators.RandomWalkOperator in project beast-mcmc by beast-dev.

the class RandomWalkOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    CoercionMode mode = CoercionMode.parseMode(xo);
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    double windowSize = xo.getDoubleAttribute(WINDOW_SIZE);
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    Double lower = null;
    Double upper = null;
    if (xo.hasAttribute(LOWER)) {
        lower = xo.getDoubleAttribute(LOWER);
    }
    if (xo.hasAttribute(UPPER)) {
        upper = xo.getDoubleAttribute(UPPER);
    }
    if (lower != null || upper != null) {
        throw new XMLParseException("Do not provide lower/upper bounds on for a RandomWalkOperator; set these values are parameter bounds");
    }
    RandomWalkOperator.BoundaryCondition condition = RandomWalkOperator.BoundaryCondition.valueOf(xo.getAttribute(BOUNDARY_CONDITION, RandomWalkOperator.BoundaryCondition.reflecting.name()));
    if (condition == RandomWalkOperator.BoundaryCondition.logit) {
        final Bounds<Double> bounds = parameter.getBounds();
        final int dim = parameter.getDimension();
        boolean boundsSet = true;
        for (int i = 0; i < dim; ++i) {
            if (bounds.getLowerLimit(i) == null || Double.isInfinite(bounds.getLowerLimit(i))) {
                boundsSet = false;
            }
            if (bounds.getUpperLimit(i) == null || Double.isInfinite(bounds.getUpperLimit(i))) {
                boundsSet = false;
            }
        }
        if (!boundsSet) {
            throw new XMLParseException("The logit transformed RandomWalkOperator cannot be used on a parameter without bounds.");
        }
    }
    if (xo.hasChildNamed(UPDATE_INDEX)) {
        XMLObject cxo = xo.getChild(UPDATE_INDEX);
        Parameter updateIndex = (Parameter) cxo.getChild(Parameter.class);
        if (updateIndex.getDimension() != parameter.getDimension())
            throw new RuntimeException("Parameter to update and missing indices must have the same dimension");
        return new RandomWalkOperator(parameter, updateIndex, windowSize, condition, weight, mode, lower, upper);
    }
    return new RandomWalkOperator(parameter, null, windowSize, condition, weight, mode, lower, upper);
}

Example 2 with RandomWalkOperator

use of dr.inference.operators.RandomWalkOperator in project beast-mcmc by beast-dev.

the class RandomWalkOperatorTest method testRandomWalkOperator.

public void testRandomWalkOperator() {
    Parameter parameter = new Parameter.Default("test", 0.5, 0.0, 1.0);
    RandomWalkOperator rwo = new RandomWalkOperator(parameter, 1.0, RandomWalkOperator.BoundaryCondition.reflecting, 1.0, CoercionMode.COERCION_OFF);
    double test1 = rwo.reflectValue(8.7654321, 3.14159265, Double.POSITIVE_INFINITY);
    double test2 = rwo.reflectValue(8.7654321, Double.NEGATIVE_INFINITY, 3.14159265);
    double test3 = rwo.reflectValue(1.2345678, 3.14159265, 2.0 * 3.14159265);
    double test4 = rwo.reflectValue(12345678.987654321, 3.14159265, 2.0 * 3.14159265);
    double test1b = rwo.reflectValueLoop(8.7654321, 3.14159265, Double.POSITIVE_INFINITY);
    double test2b = rwo.reflectValueLoop(8.7654321, Double.NEGATIVE_INFINITY, 3.14159265);
    double test3b = rwo.reflectValueLoop(1.2345678, 3.14159265, 2.0 * 3.14159265);
    double test4b = rwo.reflectValueLoop(12345678.987654321, 3.14159265, 2.0 * 3.14159265);
    assertEquals(test1, test1b);
    assertEquals(test2, test2b);
    assertEquals(test3, test3b);
    assertTrue(Math.abs(test4 - test4b) < 0.001);
}