Examples with ArbitrarySubstitutionParameterBranchModel dr.evomodel.branchmodel.ArbitrarySubstitutionParameterBranchModel used on opensource projects

Example 1 with ArbitrarySubstitutionParameterBranchModel

use of dr.evomodel.branchmodel.ArbitrarySubstitutionParameterBranchModel in project beast-mcmc by beast-dev.

the class LocationScaleGradientParser method parseTreeDataLikelihood.

private GradientWrtParameterProvider parseTreeDataLikelihood(XMLObject xo, TreeDataLikelihood treeDataLikelihood, String traitName, boolean useHessian) throws XMLParseException {
    BranchRateModel branchRateModel = treeDataLikelihood.getBranchRateModel();
    DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate();
    if (delegate instanceof ContinuousDataLikelihoodDelegate) {
        throw new XMLParseException("Not yet implemented! ");
    } else if (delegate instanceof BeagleDataLikelihoodDelegate) {
        BeagleDataLikelihoodDelegate beagleData = (BeagleDataLikelihoodDelegate) delegate;
        BranchModel branchModel = beagleData.getBranchModel();
        if (branchRateModel instanceof DefaultBranchRateModel || branchRateModel instanceof ArbitraryBranchRates) {
            if (xo.hasChildNamed(LOCATION)) {
                BranchSpecificFixedEffects location = parseLocation(xo);
                return new LocationGradient(traitName, treeDataLikelihood, beagleData, location, useHessian);
            } else if (xo.hasChildNamed(SCALE)) {
                Parameter scale = (Parameter) xo.getElementFirstChild(SCALE);
                return new ScaleGradient(traitName, treeDataLikelihood, beagleData, scale, useHessian);
            } else {
                throw new XMLParseException("Poorly formed");
            }
        } else if (branchModel instanceof ArbitrarySubstitutionParameterBranchModel) {
            BranchParameter branchParameter = (BranchParameter) xo.getChild(BranchParameter.class);
            if (xo.hasChildNamed(LOCATION)) {
                BranchSpecificFixedEffects location = parseLocation(xo);
                return new BranchSubstitutionParameterLocationGradient(traitName, treeDataLikelihood, beagleData, branchParameter, useHessian, location);
            } else if (xo.hasChildNamed(SCALE)) {
                Parameter scale = (Parameter) xo.getElementFirstChild(SCALE);
                return new BranchSubstitutionParameterScaleGradient(traitName, treeDataLikelihood, beagleData, branchParameter, scale, useHessian);
            } else {
                throw new XMLParseException("Not yet implemented.");
            }
        } else {
            throw new XMLParseException("Only implemented for an arbitrary rates model");
        }
    } else {
        throw new XMLParseException("Unknown likelihood delegate type");
    }
}

Example 2 with ArbitrarySubstitutionParameterBranchModel

use of dr.evomodel.branchmodel.ArbitrarySubstitutionParameterBranchModel in project beast-mcmc by beast-dev.

the class ArbitrarySubstitutionParameterBranchModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing branch-specific substitution parameter branch model.");
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    if (!(substitutionModel instanceof ParameterReplaceableSubstitutionModel)) {
        throw new RuntimeException("The substitution model is not parameter replaceable!");
    }
    XMLObject cxo = xo.getChild(BRANCH_SPECIFIC_PARAMETER);
    // XMLObject dxo = xo.getChild(SINGLE_RATE);
    BranchSpecificSubstitutionModelProvider substitutionModelProvider;
    ArbitrarySubstitutionParameterBranchModel branchParameterModel;
    // assert (dxo.getChildCount() == cxo.getChildCount());
    List<Parameter> oldParameters = new ArrayList<Parameter>();
    List<BranchParameter> parameterList = new ArrayList<BranchParameter>();
    for (int i = 0; i < cxo.getChildCount(); i++) {
        // Parameter rootParameter = (Parameter) dxo.getChild(i);
        // ArbitraryBranchRates branchRateModel = (ArbitraryBranchRates) cxo.getChild(i);
        // BranchParameter branchParameter = new BranchParameter("branchSpecific.substitution.parameter",
        // tree,
        // branchRateModel,
        // rootParameter);
        // branchParameter.setId("branchSpecific." + rootParameter.getId());
        // parameterList.add(branchParameter);
        // xo.setNativeObject(branchParameter);
        BranchParameter branchParameter = (BranchParameter) cxo.getChild(i);
        parameterList.add(branchParameter);
        oldParameters.add(branchParameter.getRootParameter());
    }
    List<SubstitutionModel> substitutionModelList = new ArrayList<SubstitutionModel>();
    ParameterReplaceableSubstitutionModel rootSubstitutionModel = (ParameterReplaceableSubstitutionModel) substitutionModel;
    // List<Parameter> oldParameters = parseParameters(dxo);
    // List<Parameter> branchParameters = parseParameters(cxo);
    final int parameterCount = parameterList.size();
    int v = 0;
    for (int nodeNum = 0; nodeNum < tree.getNodeCount(); ++nodeNum) {
        NodeRef node = tree.getNode(nodeNum);
        ParameterReplaceableSubstitutionModel branchSubstitutionModel = (ParameterReplaceableSubstitutionModel) substitutionModel;
        List<Parameter> newParameters = new ArrayList<Parameter>();
        if (tree.isRoot(node)) {
            for (int i = 0; i < parameterCount; i++) {
                BranchParameter branchParameter = parameterList.get(i);
                newParameters.add(branchParameter.getRootParameter());
            }
        } else {
            for (int i = 0; i < parameterCount; i++) {
                BranchParameter branchParameter = parameterList.get(i);
                newParameters.add(branchParameter.getParameter(v));
            }
            v++;
        }
        branchSubstitutionModel = branchSubstitutionModel.factory(oldParameters, newParameters);
        substitutionModelList.add(branchSubstitutionModel);
    }
    substitutionModelProvider = new BranchSpecificSubstitutionModelProvider.Default(substitutionModelList, tree);
    branchParameterModel = new ArbitrarySubstitutionParameterBranchModel(ARBITRARY_SUBSTITUTION_PARAMETER_BRANCH_MODEL, substitutionModelProvider, parameterList, tree);
    return branchParameterModel;
}