Examples with LocalBranchRates dr.evomodel.branchratemodel.LocalBranchRates used on opensource projects

Example 1 with LocalBranchRates

use of dr.evomodel.branchratemodel.LocalBranchRates in project beast-mcmc by beast-dev.

the class BranchRateGradientParser method parseTreeDataLikelihood.

private GradientWrtParameterProvider parseTreeDataLikelihood(TreeDataLikelihood treeDataLikelihood, String traitName, boolean useHessian) throws XMLParseException {
    BranchRateModel branchRateModel = treeDataLikelihood.getBranchRateModel();
    if (branchRateModel instanceof DefaultBranchRateModel || branchRateModel instanceof ArbitraryBranchRates) {
        Parameter branchRates = null;
        if (branchRateModel instanceof ArbitraryBranchRates) {
            branchRates = ((ArbitraryBranchRates) branchRateModel).getRateParameter();
        }
        DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate();
        if (delegate instanceof ContinuousDataLikelihoodDelegate) {
            ContinuousDataLikelihoodDelegate continuousData = (ContinuousDataLikelihoodDelegate) delegate;
            return new BranchRateGradient(traitName, treeDataLikelihood, continuousData, branchRates);
        } else if (delegate instanceof BeagleDataLikelihoodDelegate) {
            BeagleDataLikelihoodDelegate beagleData = (BeagleDataLikelihoodDelegate) delegate;
            if (branchRateModel instanceof LocalBranchRates) {
                return new LocalBranchRateGradientForDiscreteTrait(traitName, treeDataLikelihood, beagleData, branchRates, useHessian);
            } else {
                return new BranchRateGradientForDiscreteTrait(traitName, treeDataLikelihood, beagleData, branchRates, useHessian);
            }
        } else {
            throw new XMLParseException("Unknown likelihood delegate type");
        }
    } else {
        throw new XMLParseException("Only implemented for an arbitrary rates model");
    }
}

Example 2 with LocalBranchRates

use of dr.evomodel.branchratemodel.LocalBranchRates in project beast-mcmc by beast-dev.

the class LocalBranchRatesParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    BranchRateTransform transform = (BranchRateTransform) xo.getChild(BranchRateTransform.class);
    if (transform == null) {
        transform = new BranchRateTransform.None();
    }
    Parameter multipllierParameter = (Parameter) xo.getChild(Parameter.class);
    final int numBranches = tree.getNodeCount() - 1;
    if (multipllierParameter.getDimension() != numBranches) {
        multipllierParameter.setDimension(numBranches);
    }
    return new LocalBranchRates(tree, multipllierParameter, transform);
}