Examples with Parameter dr.inference.model.Parameter used on opensource projects

Example 11 with Parameter

use of dr.inference.model.Parameter 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 12 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class EllipticalSliceOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final Parameter variable = (Parameter) xo.getChild(Parameter.class);
    boolean drawByRowTemp = false;
    if (xo.hasAttribute(DRAW_BY_ROW))
        drawByRowTemp = xo.getBooleanAttribute(DRAW_BY_ROW);
    final boolean drawByRow = drawByRowTemp;
    boolean signal = xo.getAttribute(SIGNAL_CONSTITUENT_PARAMETERS, true);
    if (!signal && !(variable instanceof CompoundParameter))
        signal = true;
    double bracketAngle = xo.getAttribute(BRACKET_ANGLE, 0.0);
    boolean translationInvariant = xo.getAttribute(TRANSLATION_INVARIANT, false);
    boolean rotationInvariant = xo.getAttribute(ROTATION_INVARIANT, false);
    GaussianProcessRandomGenerator gaussianProcess = (GaussianProcessRandomGenerator) xo.getChild(GaussianProcessRandomGenerator.class);
    if (gaussianProcess == null) {
        final MultivariateDistributionLikelihood likelihood = (MultivariateDistributionLikelihood) xo.getChild(MultivariateDistributionLikelihood.class);
        if (!(likelihood.getDistribution() instanceof GaussianProcessRandomGenerator)) {
            throw new XMLParseException("Elliptical slice sampling only works for multivariate normally distributed random variables");
        }
        if (likelihood.getDistribution() instanceof MultivariateNormalDistribution)
            gaussianProcess = (MultivariateNormalDistribution) likelihood.getDistribution();
        if (likelihood.getDistribution() instanceof MultivariateNormalDistributionModel)
            gaussianProcess = (MultivariateNormalDistributionModel) likelihood.getDistribution();
    }
    EllipticalSliceOperator operator = new EllipticalSliceOperator(variable, gaussianProcess, drawByRow, signal, bracketAngle, translationInvariant, rotationInvariant);
    operator.setWeight(weight);
    return operator;
}

Example 13 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class SwapOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    double weight = xo.getDoubleAttribute("weight");
    int size = xo.getIntegerAttribute("size");
    boolean autoOptimize = xo.getBooleanAttribute("autoOptimize");
    if (autoOptimize)
        throw new XMLParseException("swapOperator can't be optimized!");
    System.out.println("Creating swap operator for parameter " + parameter.getParameterName() + " (weight=" + weight + ")");
    SwapOperator so = new SwapOperator(parameter, size);
    so.setWeight(weight);
    return so;
}

Example 14 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class UniformOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    if (parameter.getDimension() == 0) {
        throw new XMLParseException("parameter with 0 dimension.");
    }
    Double lower = null;
    Double upper = null;
    if (xo.hasAttribute(LOWER)) {
        lower = xo.getDoubleAttribute(LOWER);
    }
    if (xo.hasAttribute(UPPER)) {
        upper = xo.getDoubleAttribute(UPPER);
    }
    return new UniformOperator(parameter, weight, lower, upper);
}

Example 15 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class MultipleRandomWalkIntegerOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    double w = xo.getDoubleAttribute(RandomWalkIntegerOperatorParser.WINDOW_SIZE);
    if (w != Math.floor(w)) {
        throw new XMLParseException("The window size of a randomWalkIntegerOperator should be an integer");
    }
    double s = xo.getDoubleAttribute(SAMPLE_SIZE);
    if (s != Math.floor(s)) {
        throw new XMLParseException("The window size of a randomWalkIntegerOperator should be an integer");
    }
    int windowSize = (int) w;
    int sampleSize = (int) s;
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    return new MultipleRandomWalkIntegerOperator(parameter, windowSize, sampleSize, weight);
}