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

Example 26 with FrequencyModel

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

the class LineageSpecificBranchModelParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    FrequencyModel rootFrequencyModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
    XMLObject cxo = xo.getChild(MODELS);
    for (int i = 0; i < cxo.getChildCount(); i++) {
        SubstitutionModel substModel = (SubstitutionModel) cxo.getChild(i);
        substitutionModels.add(substModel);
    }
    //END: models loop
    // TODO: check if categories numbering starts from zero
    Parameter categories = (Parameter) xo.getElementFirstChild(CATEGORIES);
    return new //provider, 
    LineageSpecificBranchModel(//provider, 
    treeModel, //provider, 
    rootFrequencyModel, //provider, 
    substitutionModels, categories);
}

Example 27 with FrequencyModel

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

the class HiddenMarkovRatesTest method testHiddenRates.

public void testHiddenRates() {
    final int index = 0;
    double[] freqs = getBinaryFreqs(index);
    FrequencyModel binaryFreqModel = new FrequencyModel(TwoStates.INSTANCE, freqs);
    int relativeTo = 0;
    Parameter ratesParameter = new Parameter.Default(0);
    GeneralSubstitutionModel binaryModel = new GeneralSubstitutionModel("binary", TwoStates.INSTANCE, binaryFreqModel, ratesParameter, relativeTo);
    UniformizedSubstitutionModel uSM = new UniformizedSubstitutionModel(binaryModel, MarkovJumpsType.REWARDS);
    uSM.setSaveCompleteHistory(true);
    double[] rewardRegister = new double[] { 0.0, 1.0 };
    uSM.setRegistration(rewardRegister);
    final double[] hkyFreqs = getHKYFreqs(index);
    FrequencyModel hkyFreqModel = new FrequencyModel(Nucleotides.INSTANCE, hkyFreqs);
    final double kappa = getKappa(index);
    final HKY hky = new HKY(kappa, hkyFreqModel);
    final double length = getLength(index);
    double[] resultCompleteHistory = new double[16];
    final int replicates = getNumberReplicates(index);
    double result = 0.0;
    for (int r = 0; r < replicates; ++r) {
        result += oneCompleteHistoryReplicate(resultCompleteHistory, hky, uSM, length);
    }
    result /= replicates;
    normalize(resultCompleteHistory, replicates);
    System.out.println("Averaged probabilities");
    System.out.println(result);
    System.out.println(new Vector(resultCompleteHistory));
    System.out.println();
    double[] intermediate = new double[16];
    hky.getTransitionProbabilities(result, intermediate);
    System.out.println("Intermediate using above average reward");
    System.out.println(result);
    System.out.println(new Vector(intermediate));
    System.out.println();
    double[] resultExpected = new double[16];
    UniformizedSubstitutionModel expectedUSM = new UniformizedSubstitutionModel(binaryModel, MarkovJumpsType.REWARDS, replicates);
    expectedUSM.setRegistration(rewardRegister);
    result = oneCompleteHistoryReplicate(resultExpected, hky, expectedUSM, length);
    System.out.println("Averaged reward");
    System.out.println(result);
    System.out.println(new Vector(resultExpected));
    System.out.println();
    double[] originalProbs = new double[16];
    hky.getTransitionProbabilities(length, originalProbs);
    System.out.println("Original probabilities");
    System.out.println(new Vector(originalProbs));
    System.out.println();
}

Example 28 with FrequencyModel

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

the class TN93Test method testTN93.

public void testTN93() {
    Parameter kappa1 = new Parameter.Default(5.0);
    Parameter kappa2 = new Parameter.Default(2.0);
    double[] pi = new double[] { 0.40, 0.20, 0.30, 0.10 };
    double time = 0.1;
    FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, pi);
    TN93 tn = new TN93(kappa1, kappa2, freqModel);
    EigenDecomposition decomp = tn.getEigenDecomposition();
    Vector eval = new Vector(decomp.getEigenValues());
    System.out.println("Eval = " + eval);
    double[] probs = new double[16];
    tn.getTransitionProbabilities(time, probs);
    System.out.println("new probs = " + new Vector(probs));
    // check against old implementation
    dr.oldevomodel.substmodel.FrequencyModel oldFreq = new dr.oldevomodel.substmodel.FrequencyModel(Nucleotides.INSTANCE, pi);
    dr.oldevomodel.substmodel.TN93 oldTN = new dr.oldevomodel.substmodel.TN93(kappa1, kappa2, oldFreq);
    double[] oldProbs = new double[16];
    oldTN.getTransitionProbabilities(time, oldProbs);
    System.out.println("old probs = " + new Vector(oldProbs));
    assertEquals(probs, oldProbs, 10E-6);
}

Example 29 with FrequencyModel

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

the class CompleteHistorySimulator method simulate.

// END: toString
/**
     * perform the actual sequence generation
     *
     * @return alignment containing randomly generated sequences for the nodes in the
     *         leaves of the tree
     */
public void simulate() {
    double[] lambda = new double[stateCount * stateCount];
    if (!branchSpecificLambda) {
        // Assumes a single generator for whole tree
        siteModel.getSubstitutionModel().getInfinitesimalMatrix(lambda);
    }
    NodeRef root = tree.getRoot();
    double[] categoryProbs = siteModel.getCategoryProportions();
    int[] category = new int[nReplications];
    for (int i = 0; i < nReplications; i++) {
        category[i] = MathUtils.randomChoicePDF(categoryProbs);
    }
    FrequencyModel frequencyModel = siteModel.getSubstitutionModel().getFrequencyModel();
    int[] seq = new int[nReplications];
    for (int i = 0; i < nReplications; i++) {
        seq[i] = MathUtils.randomChoicePDF(frequencyModel.getFrequencies());
    }
    setDataType(siteModel.getSubstitutionModel().getDataType());
    traverse(root, seq, category, this, lambda);
}

Example 30 with FrequencyModel

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

the class PartitionParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0) {
            throw new XMLParseException("Illegal 'from' attribute in patterns element");
        }
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from) {
            throw new XMLParseException("Illegal 'to' attribute in patterns element");
        }
    }
    if (every <= 0) {
        throw new XMLParseException("Illegal 'every' attribute in patterns element");
    }
    // END: every check
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    GammaSiteRateModel siteModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    Sequence rootSequence = (Sequence) xo.getChild(Sequence.class);
    BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (rateModel == null) {
        rateModel = new DefaultBranchRateModel();
    }
    BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
    if (branchModel == null) {
        SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
        branchModel = new HomogeneousBranchModel(substitutionModel);
    }
    Partition partition = new Partition(tree, branchModel, siteModel, rateModel, freqModel, from, to, every);
    if (rootSequence != null) {
        partition.setRootSequence(rootSequence);
    }
    return partition;
}