Examples with BranchRateGradientForDiscreteTrait dr.evomodel.treedatalikelihood.discrete.BranchRateGradientForDiscreteTrait used on opensource projects

Example 1 with BranchRateGradientForDiscreteTrait

use of dr.evomodel.treedatalikelihood.discrete.BranchRateGradientForDiscreteTrait 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 BranchRateGradientForDiscreteTrait

use of dr.evomodel.treedatalikelihood.discrete.BranchRateGradientForDiscreteTrait in project beast-mcmc by beast-dev.

the class BranchRateGradientWrtIncrementsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    AutoCorrelatedGradientWrtIncrements priorProvider = (AutoCorrelatedGradientWrtIncrements) xo.getChild(AutoCorrelatedGradientWrtIncrements.class);
    GradientWrtParameterProvider rateProvider = (GradientWrtParameterProvider) xo.getChild(GradientWrtParameterProvider.class);
    if (!(rateProvider instanceof BranchRateGradient) && !(rateProvider instanceof BranchRateGradientForDiscreteTrait)) {
        throw new XMLParseException("Must provide a branch rate gradient");
    }
    return new BranchRateGradientWrtIncrements(rateProvider, priorProvider);
}