Examples with GeneralSubstitutionModel dr.oldevomodel.substmodel.GeneralSubstitutionModel used on opensource projects

Example 1 with GeneralSubstitutionModel

use of dr.oldevomodel.substmodel.GeneralSubstitutionModel in project beast-mcmc by beast-dev.

the class BinarySubstitutionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter ratesParameter;
    XMLObject cxo = xo.getChild(GeneralSubstitutionModelParser.FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    if (dataType != TwoStates.INSTANCE)
        throw new XMLParseException("Frequency model must have binary (two state) data type.");
    int relativeTo = 0;
    ratesParameter = new Parameter.Default(0);
    return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, relativeTo);
}

Example 2 with GeneralSubstitutionModel

use of dr.oldevomodel.substmodel.GeneralSubstitutionModel in project beast-mcmc by beast-dev.

the class LewisMkSubstitutionModelParser method parseXMLObject.

// public static XMLObjectParser PARSER=new LewisMkSubstitutionModelParser();
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    int k = dataType.getStateCount();
    System.err.println("Number of states " + k);
    Parameter ratesParameter;
    if (xo.hasAttribute(TOTAL_ORDER) && xo.getBooleanAttribute(TOTAL_ORDER)) {
        // TOTAL ORDERING OF THE STATES BASED ON DATATYPE
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 0);
        int j = k - 1;
        for (int i = 0; i < (k - 1) * k / 2; i = i + j + 1) {
            ratesParameter.setParameterValue(i, 1);
            j -= 1;
        }
    } else if (xo.hasChildNamed(ORDER)) {
        // USER-SPECIFIED ORDERING OF THE STATES
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 0);
        for (int i = 0; i < xo.getChildCount(); ++i) {
            if (xo.getChildName(i).equals(ORDER)) {
                cxo = (XMLObject) xo.getChild(i);
                if (cxo.getName().equals(ORDER)) {
                    int from = dataType.getState(cxo.getStringAttribute(STATE).charAt(0));
                    int to = dataType.getState(cxo.getStringAttribute(ADJACENT).charAt(0));
                    if (from > to) {
                        // SWAP: from should have the smaller state number
                        to += from;
                        from = to - from;
                        to -= from;
                    }
                    int ratesIndex = (from * (2 * k - 3) - from * from) / 2 + to - 1;
                    ratesParameter.setParameterValue(ratesIndex, 1);
                }
            }
        }
    } else {
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 1);
    }
    System.err.println(ratesParameter.toString());
    System.err.println("Infinitesimal matrix:");
    for (int i = 0; i < k; ++i) {
        for (int j = 0; j < k; ++j) {
            int from, to;
            if (i < j) {
                from = i;
                to = j;
            } else {
                from = j;
                to = i;
            }
            // This is right now!!! Thanks, Marc!
            int ratesIndex = (from * (2 * k - 3) - from * from) / 2 + to - 1;
            if (i != j)
                System.err.print(Double.toString(ratesParameter.getValue(ratesIndex)) + "\t(" + ratesIndex + ")\t");
            else
                System.err.print("-\t\t");
        }
        // newline
        System.err.println("");
    }
    System.err.println("");
    if (!checkConnected(ratesParameter.getValues(), k)) {
        throw (new XMLParseException("The state transitions form a disconnected graph! This model is not suited for this case."));
    }
    return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, 0);
}

Example 3 with GeneralSubstitutionModel

use of dr.oldevomodel.substmodel.GeneralSubstitutionModel in project beast-mcmc by beast-dev.

the class MkModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(GeneralSubstitutionModelParser.FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    int rateCount = ((dataType.getStateCount() - 1) * dataType.getStateCount()) / 2 - 1;
    Parameter ratesParameter = new Parameter.Default(rateCount, 1.0);
    Logger.getLogger("dr.evolution").info("Creating an Mk substitution model with data type: " + dataType.getType() + "on " + dataType.getStateCount() + " states.");
    int relativeTo = 1;
    return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, relativeTo);
}

Example 4 with GeneralSubstitutionModel

use of dr.oldevomodel.substmodel.GeneralSubstitutionModel in project beast-mcmc by beast-dev.

the class BinaryCovarionModelTest method testTransitionProbabilitiesUnequalBaseFreqsUnequalRateFreqsEqualRates.

public void testTransitionProbabilitiesUnequalBaseFreqsUnequalRateFreqsEqualRates() {
    // with alpha == 1, the transition probability should be the same as binary jukes cantor
    alpha.setParameterValue(0, 1.0);
    switchingRate.setParameterValue(0, 1.0);
    frequencies.setParameterValue(0, 0.25);
    frequencies.setParameterValue(1, 0.75);
    hiddenFrequencies.setParameterValue(0, 0.1);
    hiddenFrequencies.setParameterValue(1, 0.9);
    FrequencyModel freqModel = new FrequencyModel(TwoStates.INSTANCE, frequencies);
    GeneralSubstitutionModel modelToCompare = new GeneralSubstitutionModel(TwoStates.INSTANCE, freqModel, null, 0);
    model.setupMatrix();
    double[] matrix = new double[16];
    double[] m = new double[4];
    double[] pi = model.getFrequencyModel().getFrequencies();
    for (double distance = 0.01; distance <= 1.005; distance += 0.01) {
        model.getTransitionProbabilities(distance, matrix);
        modelToCompare.getTransitionProbabilities(distance, m);
        double pChange = (matrix[1] + matrix[3]) * pi[0] + (matrix[4] + matrix[6]) * pi[1] + (matrix[9] + matrix[11]) * pi[2] + (matrix[12] + matrix[14]) * pi[3];
        double pChange2 = m[1] * frequencies.getParameterValue(0) + m[2] * frequencies.getParameterValue(1);
        // System.out.println(distance + "\t" + pChange2 + "\t" + pChange);
        assertEquals(pChange2, pChange, 1e-14);
    }
}

Example 5 with GeneralSubstitutionModel

use of dr.oldevomodel.substmodel.GeneralSubstitutionModel in project beast-mcmc by beast-dev.

the class BinaryCovarionModelTest method testTransitionProbabilitiesUnequalBaseFreqsEqualRates.

public void testTransitionProbabilitiesUnequalBaseFreqsEqualRates() {
    // with alpha == 1, the transition probability should be the same as binary jukes cantor
    alpha.setParameterValue(0, 1.0);
    switchingRate.setParameterValue(0, 1.0);
    frequencies.setParameterValue(0, 0.25);
    frequencies.setParameterValue(1, 0.75);
    FrequencyModel freqModel = new FrequencyModel(TwoStates.INSTANCE, frequencies);
    GeneralSubstitutionModel modelToCompare = new GeneralSubstitutionModel(TwoStates.INSTANCE, freqModel, null, 0);
    model.setupMatrix();
    double[] matrix = new double[16];
    double[] m = new double[4];
    double[] pi = model.getFrequencyModel().getFrequencies();
    for (double distance = 0.01; distance <= 1.005; distance += 0.01) {
        model.getTransitionProbabilities(distance, matrix);
        modelToCompare.getTransitionProbabilities(distance, m);
        double pChange = (matrix[1] + matrix[3]) * pi[0] + (matrix[4] + matrix[6]) * pi[1] + (matrix[9] + matrix[11]) * pi[2] + (matrix[12] + matrix[14]) * pi[3];
        double pChange2 = m[1] * frequencies.getParameterValue(0) + m[2] * frequencies.getParameterValue(1);
        System.out.println(distance + "\t" + pChange2 + "\t" + pChange);
        assertEquals(pChange2, pChange, 1e-14);
    }
}