Examples with RandomWalkNodeHeightOperator dr.evomodel.operators.RandomWalkNodeHeightOperator used on opensource projects

Example 1 with RandomWalkNodeHeightOperator

use of dr.evomodel.operators.RandomWalkNodeHeightOperator in project beast-mcmc by beast-dev.

the class NodeHeightOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    OperatorType operatorType = OperatorType.UNIFORM;
    if (xo.hasAttribute(OPERATOR_TYPE)) {
        try {
            operatorType = OperatorType.valueOf(xo.getStringAttribute(OPERATOR_TYPE).trim().toUpperCase());
        } catch (IllegalArgumentException iae) {
            throw new XMLParseException("Unrecognised operator type attribute: " + xo.getStringAttribute(OPERATOR_TYPE));
        }
    }
    if (operatorType != OperatorType.UNIFORM) {
        AdaptationMode mode = AdaptationMode.parseMode(xo);
        double tuningParameter = 0.75;
        if (xo.hasAttribute(SIZE)) {
            tuningParameter = xo.getDoubleAttribute(SIZE);
            if (tuningParameter <= 0.0) {
                throw new XMLParseException("The UniformNodeHeightOperator size attribute must be positive and non-zero.");
            }
        }
        if (xo.hasAttribute(SCALE_FACTOR)) {
            tuningParameter = xo.getDoubleAttribute(SCALE_FACTOR);
            if (tuningParameter <= 0.0 || tuningParameter >= 1.0) {
                throw new XMLParseException("The UniformNodeHeightOperator scaleFactor attribute must be between 0 and 1.");
            }
        }
        final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234);
        if (targetAcceptance <= 0.0 || targetAcceptance >= 1.0) {
            throw new XMLParseException("Target acceptance probability has to lie in (0, 1)");
        }
        switch(operatorType) {
            case RANDOMWALK:
                return new RandomWalkNodeHeightOperator(treeModel, weight, tuningParameter, mode, targetAcceptance);
            case SCALEROOT:
            case SCALEALL:
                return new ScaleNodeHeightOperator(treeModel, weight, tuningParameter, operatorType, mode, targetAcceptance);
            default:
                throw new IllegalArgumentException("Unknown operator type");
        }
    }
    if (xo.hasAttribute(SIZE) || xo.hasAttribute(SCALE_FACTOR) || xo.hasAttribute(TARGET_ACCEPTANCE) || xo.hasAttribute(AdaptableMCMCOperator.AUTO_OPTIMIZE)) {
        throw new XMLParseException("Uniform node height operator does not take adaptable operator arguments");
    }
    return new UniformNodeHeightOperator(treeModel, weight);
}