Examples with SubstitutionModel dr.evomodel.substmodel.SubstitutionModel used on opensource projects

Example 21 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class RandomBranchModel method setup.

// END: Constructor
private void setup() {
    DataType dataType = baseSubstitutionModel.getDataType();
    FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
    Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa());
    substitutionModels = new LinkedList<SubstitutionModel>();
    branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();
    int branchClass = 0;
    for (NodeRef node : treeModel.getNodes()) {
        if (!treeModel.isRoot(node)) {
            double nodeHeight = treeModel.getNodeHeight(node);
            double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
            double time = 0.5 * (parentHeight + nodeHeight);
            double baseOmega = baseSubstitutionModel.getOmega();
            double fixed = baseOmega * time;
            // Math.exp((random.nextGaussian() * stdev + mean));
            double epsilon = (Math.log(1 - random.nextDouble()) / (-rate));
            double value = fixed + epsilon;
            Parameter omegaParameter = new Parameter.Default("omega", 1, value);
            GY94CodonModel gy94 = new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel);
            substitutionModels.add(gy94);
            branchAssignmentMap.put(node, branchClass);
            branchClass++;
        }
    // END: root check
    }
// END: nodes loop
}

Example 22 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel 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;
}

Example 23 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class GammaSiteModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String msg = "";
    SubstitutionModel substitutionModel = null;
    double muWeight = 1.0;
    Parameter muParam = null;
    if (xo.hasChildNamed(SUBSTITUTION_RATE)) {
        muParam = (Parameter) xo.getElementFirstChild(SUBSTITUTION_RATE);
        msg += "\n  with initial substitution rate = " + muParam.getParameterValue(0);
    } else if (xo.hasChildNamed(MUTATION_RATE)) {
        muParam = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
        msg += "\n  with initial substitution rate = " + muParam.getParameterValue(0);
    } else if (xo.hasChildNamed(RELATIVE_RATE)) {
        XMLObject cxo = xo.getChild(RELATIVE_RATE);
        muParam = (Parameter) cxo.getChild(Parameter.class);
        msg += "\n  with initial relative rate = " + muParam.getParameterValue(0);
        if (cxo.hasAttribute(WEIGHT)) {
            muWeight = cxo.getDoubleAttribute(WEIGHT);
            msg += " with weight: " + muWeight;
        }
    }
    Parameter shapeParam = null;
    int catCount = 4;
    if (xo.hasChildNamed(GAMMA_SHAPE)) {
        XMLObject cxo = xo.getChild(GAMMA_SHAPE);
        catCount = cxo.getIntegerAttribute(GAMMA_CATEGORIES);
        shapeParam = (Parameter) cxo.getChild(Parameter.class);
        msg += "\n  " + catCount + " category discrete gamma with initial shape = " + shapeParam.getParameterValue(0);
    }
    Parameter invarParam = null;
    if (xo.hasChildNamed(PROPORTION_INVARIANT)) {
        invarParam = (Parameter) xo.getElementFirstChild(PROPORTION_INVARIANT);
        msg += "\n  initial proportion of invariant sites = " + invarParam.getParameterValue(0);
    }
    if (msg.length() > 0) {
        Logger.getLogger("dr.evomodel").info("\nCreating site rate model: " + msg);
    } else {
        Logger.getLogger("dr.evomodel").info("\nCreating site rate model.");
    }
    GammaSiteRateModel siteRateModel = new GammaSiteRateModel(SITE_MODEL, muParam, muWeight, shapeParam, catCount, invarParam);
    if (xo.hasChildNamed(SUBSTITUTION_MODEL)) {
        // System.err.println("Doing the substitution model stuff");
        // set this to pass it along to the OldTreeLikelihoodParser...
        substitutionModel = (SubstitutionModel) xo.getElementFirstChild(SUBSTITUTION_MODEL);
        siteRateModel.setSubstitutionModel(substitutionModel);
    }
    return siteRateModel;
}

Example 24 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class SubstitutionModelDelegate method updateSubstitutionModels.

// END: getStateFrequencies
@Override
public void updateSubstitutionModels(Beagle beagle, boolean flipBuffers) {
    for (int i = 0; i < eigenCount; i++) {
        if (flipBuffers) {
            eigenBufferHelper.flipOffset(i);
        }
        SubstitutionModel substitutionModel = substitutionModelList.get(i);
        EigenDecomposition ed = substitutionModel.getEigenDecomposition();
        beagle.setEigenDecomposition(eigenBufferHelper.getOffsetIndex(i), ed.getEigenVectors(), ed.getInverseEigenVectors(), ed.getEigenValues());
    }
}

Example 25 with SubstitutionModel

use of dr.evomodel.substmodel.SubstitutionModel in project beast-mcmc by beast-dev.

the class EpochBranchModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing multi-epoch branch model.");
    MutableTreeModel treeModel = (MutableTreeModel) xo.getChild(MutableTreeModel.class);
    SubstitutionModel ancestralSubstitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    List<Epoch> epochs = new ArrayList<Epoch>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            if (xoc.getName().equals(EPOCH)) {
                Parameter tt = null;
                if (xoc.hasAttribute(TRANSITION_TIME)) {
                    double t = xoc.getAttribute(TRANSITION_TIME, 0.0);
                    tt = new Parameter.Default(1, t);
                }
                SubstitutionModel s = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                if (xoc.hasChildNamed(TRANSITION_TIME)) {
                    if (tt != null) {
                        throw new XMLParseException("An epoch cannot have a transitionTime attribute and a parameter");
                    }
                    tt = (Parameter) xoc.getElementFirstChild(TRANSITION_TIME);
                }
                epochs.add(new Epoch(s, tt));
            }
        }
    }
    Collections.sort(epochs);
    List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
    CompoundParameter transitionTimes = new CompoundParameter("epochTimes");
    for (Epoch epoch : epochs) {
        substitutionModels.add(epoch.substitutionModel);
        transitionTimes.addParameter(epoch.timeParameter);
    }
    substitutionModels.add(ancestralSubstitutionModel);
    return new EpochBranchModel(treeModel, substitutionModels, transitionTimes);
}