Examples with BranchSpecificGradient dr.evomodel.treedatalikelihood.continuous.BranchSpecificGradient used on opensource projects

Example 1 with BranchSpecificGradient

use of dr.evomodel.treedatalikelihood.continuous.BranchSpecificGradient in project beast-mcmc by beast-dev.

the class AttenuationGradientParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String traitName = xo.getAttribute(TRAIT_NAME, DEFAULT_TRAIT_NAME);
    MatrixParameterInterface parameter = (MatrixParameterInterface) xo.getChild(MatrixParameterInterface.class);
    TreeDataLikelihood treeDataLikelihood = (TreeDataLikelihood) xo.getChild(TreeDataLikelihood.class);
    DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate();
    int dim = treeDataLikelihood.getDataLikelihoodDelegate().getTraitDim();
    Tree tree = treeDataLikelihood.getTree();
    ContinuousDataLikelihoodDelegate continuousData = (ContinuousDataLikelihoodDelegate) delegate;
    ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient traitGradient = new ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient(dim, tree, continuousData, new ArrayList<ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient.DerivationParameter>(Arrays.asList(ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient.DerivationParameter.WRT_DIAGONAL_SELECTION_STRENGTH)));
    BranchSpecificGradient branchSpecificGradient = new BranchSpecificGradient(traitName, treeDataLikelihood, continuousData, traitGradient, parameter);
    ParameterMode parameterMode = parseParameterMode(xo);
    return parameterMode.factory(branchSpecificGradient, treeDataLikelihood, parameter);
}

Example 2 with BranchSpecificGradient

use of dr.evomodel.treedatalikelihood.continuous.BranchSpecificGradient in project beast-mcmc by beast-dev.

the class DiffusionGradientParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String traitName = xo.getAttribute(TRAIT_NAME, DEFAULT_TRAIT_NAME);
    List<ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient.DerivationParameter> derivationParametersList = new ArrayList<ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient.DerivationParameter>();
    CompoundParameter compoundParameter = new CompoundParameter(null);
    List<GradientWrtParameterProvider> derivativeList = new ArrayList<GradientWrtParameterProvider>();
    List<AbstractDiffusionGradient> diffGradients = xo.getAllChildren(AbstractDiffusionGradient.class);
    if (diffGradients != null) {
        for (AbstractDiffusionGradient grad : diffGradients) {
            derivationParametersList.add(grad.getDerivationParameter());
            compoundParameter.addParameter(grad.getRawParameter());
            derivativeList.add(grad);
        }
    }
    CompoundGradient parametersGradients = new CompoundDerivative(derivativeList);
    // testSameModel(precisionGradient, attenuationGradient);
    TreeDataLikelihood treeDataLikelihood = ((TreeDataLikelihood) diffGradients.get(0).getLikelihood());
    DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate();
    int dim = treeDataLikelihood.getDataLikelihoodDelegate().getTraitDim();
    Tree tree = treeDataLikelihood.getTree();
    ContinuousDataLikelihoodDelegate continuousData = (ContinuousDataLikelihoodDelegate) delegate;
    ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient traitGradient = new ContinuousTraitGradientForBranch.ContinuousProcessParameterGradient(dim, tree, continuousData, derivationParametersList);
    BranchSpecificGradient branchSpecificGradient = new BranchSpecificGradient(traitName, treeDataLikelihood, continuousData, traitGradient, compoundParameter);
    return new DiffusionParametersGradient(branchSpecificGradient, parametersGradients);
}