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

Example 86 with Parameter

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

the class RandomWalkIntegerSetSizeWeightedOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    double d = xo.getDoubleAttribute(WINDOW_SIZE);
    if (d != Math.floor(d)) {
        throw new XMLParseException("The window size of a " + RANDOM_WALK_INT_SET_SIZE_WGT_OP + " should be an integer");
    }
    double baseSetSize = xo.getDoubleAttribute(BASE_SET_SIZE);
    int windowSize = (int) d;
    Parameter parameter = (Parameter) xo.getChild(Parameter.class);
    MicrosatelliteSamplerTreeModel msatSampleTreeModel = (MicrosatelliteSamplerTreeModel) xo.getChild(MicrosatelliteSamplerTreeModel.class);
    return new RandomWalkIntegerSetSizeWeightedOperator(parameter, windowSize, weight, msatSampleTreeModel, baseSetSize);
}

Example 87 with Parameter

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

the class LeafTraitExtractorParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel model = (TreeModel) xo.getChild(TreeModel.class);
    final CompoundParameter allTraits = (CompoundParameter) xo.getChild(CompoundParameter.class);
    String taxonString = (String) xo.getAttribute(TreeModelParser.TAXON);
    final int leafIndex = model.getTaxonIndex(taxonString);
    if (leafIndex == -1) {
        throw new XMLParseException("Unable to find taxon '" + taxonString + "' in trees.");
    }
    final Parameter leafTrait = allTraits.getParameter(leafIndex);
    boolean setBounds = xo.getAttribute(SET_BOUNDS, true);
    if (setBounds) {
        Parameter.DefaultBounds bound = new Parameter.DefaultBounds(Double.MAX_VALUE, -Double.MAX_VALUE, leafTrait.getDimension());
        leafTrait.addBounds(bound);
    }
    return leafTrait;
}

Example 88 with Parameter

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

the class PeakAndDeclineModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(PEAK_VALUE);
    Parameter peakValueParam = (Parameter) cxo.getChild(Parameter.class);
    Parameter rParam;
    cxo = xo.getChild(SHAPE);
    rParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(PEAK_TIME);
    Parameter peakTimeParam = (Parameter) cxo.getChild(Parameter.class);
    return new PeakAndDeclineModel(peakValueParam, rParam, peakTimeParam, units);
}

Example 89 with Parameter

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

the class PiecewisePopulationModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject obj = xo.getChild(EPOCH_WIDTHS);
    double[] epochWidths = obj.getDoubleArrayAttribute(WIDTHS);
    if (xo.hasChildNamed(EPOCH_SIZES)) {
        Parameter epochSizes = (Parameter) xo.getElementFirstChild(EPOCH_SIZES);
        boolean isLinear = false;
        if (xo.hasAttribute(LINEAR)) {
            isLinear = xo.getBooleanAttribute(LINEAR);
        }
        return new PiecewisePopulationModel(PIECEWISE_POPULATION, epochSizes, epochWidths, isLinear, units);
    } else {
        Parameter populationSize = (Parameter) xo.getElementFirstChild(POPULATION_SIZE);
        Parameter growthRates = (Parameter) xo.getElementFirstChild(GROWTH_RATES);
        return new PiecewisePopulationModel(PIECEWISE_POPULATION, populationSize, growthRates, epochWidths, units);
    }
}

Example 90 with Parameter

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

the class PowerLawGrowthModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(N0);
    Parameter N0Param = (Parameter) cxo.getChild(Parameter.class);
    Parameter rParam;
    cxo = xo.getChild(POWER);
    rParam = (Parameter) cxo.getChild(Parameter.class);
    return new PowerLawGrowthModel(N0Param, rParam, units);
}