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

Example 1 with OnePhaseModel

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

the class LinearBiasTest method testLinearBiasModel.

public void testLinearBiasModel() {
    for (Instance test : all) {
        OnePhaseModel subModel = test.getSubModel();
        Microsatellite microsat = (Microsatellite) subModel.getDataType();
        Parameter biasLinear = new Parameter.Default(1, test.getBiasLinearParam());
        Parameter biasConstant = new Parameter.Default(1, test.getBiasConstantParam());
        LinearBiasModel lbm = new LinearBiasModel(microsat, null, subModel, biasConstant, biasLinear, test.isLogistics(), false, false);
        lbm.computeStationaryDistribution();
        double[] statDist = lbm.getStationaryDistribution();
        final double[] expectedStatDist = test.getExpectedPi();
        for (int k = 0; k < statDist.length; ++k) {
            assertEquals(statDist[k], expectedStatDist[k], 1e-10);
        }
        int stateCount = microsat.getStateCount();
        double[] mat = new double[stateCount * stateCount];
        lbm.getTransitionProbabilities(test.getDistance(), mat);
        final double[] result = test.getExpectedResult();
        int k;
        for (k = 0; k < mat.length; ++k) {
            assertEquals(result[k], mat[k], 5e-9);
        //System.out.print(" " + (mat[k] - result[k]));
        }
        k = 0;
        for (int i = 0; i < microsat.getStateCount(); i++) {
            for (int j = 0; j < microsat.getStateCount(); j++) {
                assertEquals(result[k++], lbm.getOneTransitionProbabilityEntry(test.getDistance(), i, j), 5e-9);
            }
        }
        for (int j = 0; j < microsat.getStateCount(); j++) {
            double[] colTransitionProb = lbm.getColTransitionProbabilities(test.getDistance(), j);
            for (int i = 0; i < microsat.getStateCount(); i++) {
                assertEquals(result[i * microsat.getStateCount() + j], colTransitionProb[i], 5e-9);
            }
        }
        for (int i = 0; i < microsat.getStateCount(); i++) {
            double[] rowTransitionProb = lbm.getRowTransitionProbabilities(test.getDistance(), i);
            for (int j = 0; j < microsat.getStateCount(); j++) {
                assertEquals(result[i * microsat.getStateCount() + j], rowTransitionProb[j], 5e-9);
            }
        }
    }
}

Example 2 with OnePhaseModel

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

the class TwoPhaseModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    OnePhaseModel subModel = (OnePhaseModel) xo.getElementFirstChild(SUBMODEL);
    Microsatellite dataType = (Microsatellite) xo.getChild(Microsatellite.class);
    Parameter.Default geoParam = (Parameter.Default) xo.getElementFirstChild(GEO_PARAM);
    Parameter paramP = (Parameter) xo.getElementFirstChild(ONEPHASEPR_PARAM);
    Parameter limitE = null;
    if (xo.hasChildNamed(TRANS_PARAM)) {
        limitE = (Parameter) xo.getElementFirstChild(TRANS_PARAM);
    }
    boolean estimateSubmodelParams = xo.getAttribute(ESTIMATE_SUBMODEL_PARAMS, false);
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    return new TwoPhaseModel(dataType, freqModel, subModel, paramP, geoParam, limitE, estimateSubmodelParams);
}

Example 3 with OnePhaseModel

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

the class LinearBiasModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    OnePhaseModel subModel = (OnePhaseModel) xo.getElementFirstChild(SUBMODEL);
    Microsatellite dataType = (Microsatellite) subModel.getDataType();
    Parameter biasConst = null;
    if (xo.hasChildNamed(BIAS_CONSTANT)) {
        biasConst = (Parameter) xo.getElementFirstChild(BIAS_CONSTANT);
    }
    Parameter biasLin = null;
    if (xo.hasChildNamed(BIAS_LINEAR)) {
        biasLin = (Parameter) xo.getElementFirstChild(BIAS_LINEAR);
    }
    //get FrequencyModel
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    boolean estimateSubmodelParams = false;
    if (xo.hasAttribute(ESTIMATE_SUBMODEL_PARAMS)) {
        estimateSubmodelParams = xo.getBooleanAttribute(ESTIMATE_SUBMODEL_PARAMS);
    }
    System.out.println("Is estimating submodel parameter(s): " + estimateSubmodelParams);
    boolean logistics = false;
    if (xo.hasAttribute(LOGISTICS)) {
        logistics = xo.getBooleanAttribute(LOGISTICS);
    }
    System.out.println("Using logistic regression: " + logistics);
    boolean isSubmodel = false;
    if (xo.hasAttribute(IS_SUBMODEL)) {
        isSubmodel = xo.getBooleanAttribute(IS_SUBMODEL);
    }
    System.out.println("Is a submodel: " + isSubmodel);
    return new LinearBiasModel(dataType, freqModel, subModel, biasConst, biasLin, logistics, estimateSubmodelParams, isSubmodel);
}

Example 4 with OnePhaseModel

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

the class TwoPhaseModelTest method testTwoPhaseModel.

public void testTwoPhaseModel() {
    for (Instance test : all) {
        OnePhaseModel subModel = test.getSubModel();
        Microsatellite microsat = (Microsatellite) subModel.getDataType();
        Parameter pParam = new Parameter.Default(test.getPParam());
        Parameter mParam = new Parameter.Default(test.getMParam());
        TwoPhaseModel tpm = new TwoPhaseModel(microsat, null, subModel, pParam, mParam, null, false);
        int k;
        tpm.computeStationaryDistribution();
        double[] statDist = tpm.getStationaryDistribution();
        final double[] expectedStatDist = test.getPi();
        for (k = 0; k < statDist.length; ++k) {
            assertEquals(statDist[k], expectedStatDist[k], 1e-10);
        }
        int stateCount = microsat.getStateCount();
        double[] mat = new double[stateCount * stateCount];
        tpm.getTransitionProbabilities(test.getDistance(), mat);
        final double[] result = test.getExpectedResult();
        for (k = 0; k < mat.length; ++k) {
            assertEquals(result[k], mat[k], 5e-9);
        //System.out.print(" " + (mat[k]));// - result[k]));
        }
        k = 0;
        for (int i = 0; i < microsat.getStateCount(); i++) {
            for (int j = 0; j < microsat.getStateCount(); j++) {
                assertEquals(result[k++], tpm.getOneTransitionProbabilityEntry(test.getDistance(), i, j), 1e-10);
            }
        }
        for (int j = 0; j < microsat.getStateCount(); j++) {
            double[] colTransitionProb = tpm.getColTransitionProbabilities(test.getDistance(), j);
            for (int i = 0; i < microsat.getStateCount(); i++) {
                assertEquals(result[i * microsat.getStateCount() + j], colTransitionProb[i], 1e-10);
            }
        }
        for (int i = 0; i < microsat.getStateCount(); i++) {
            double[] rowTransitionProb = tpm.getRowTransitionProbabilities(test.getDistance(), i);
            for (int j = 0; j < microsat.getStateCount(); j++) {
                assertEquals(result[i * microsat.getStateCount() + j], rowTransitionProb[j], 1e-10);
            }
        }
    }
}