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

Example 1 with SubstitutionModel

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

the class testGammaSiteBMA method testGammaSiteBMA.

public void testGammaSiteBMA() {
    for (Instance test : all) {
        SubstitutionModel substModel = test.getSubstModel();
        Parameter mu = new Parameter.Default(test.getMu());
        Parameter logitInvar = new Parameter.Default(test.getLogitInvar());
        Parameter logShape = new Parameter.Default(test.getLogShape());
        int catCount = test.getCategoryCount();
        Variable<Integer> modelChoose = test.getModelChoose();
        GammaSiteBMA gammaSiteBMA = new GammaSiteBMA(substModel, mu, logitInvar, logShape, catCount, modelChoose);
        double[] catRates = gammaSiteBMA.getCategoryRates();
        double[] expectedCatRates = test.getCategoryRates();
        for (int i = 0; i < catRates.length; i++) {
            assertEquals(catRates[i], expectedCatRates[i], 8e-10);
        }
        double[] catProps = gammaSiteBMA.getCategoryProportions();
        double[] expectedCatProps = test.getCategoryProportions();
        for (int i = 0; i < catProps.length; i++) {
            assertEquals(catProps[i], expectedCatProps[i], 1e-10);
        }
    }
}

Example 2 with SubstitutionModel

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

the class MultivariateOUModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    Parameter effectParameter = (Parameter) ((XMLObject) xo.getChild(DATA)).getChild(Parameter.class);
    Parameter timesParameter = (Parameter) ((XMLObject) xo.getChild(TIME)).getChild(Parameter.class);
    Parameter designParameter = (Parameter) ((XMLObject) xo.getChild(DESIGN)).getChild(Parameter.class);
    MatrixParameter gammaParameter = (MatrixParameter) xo.getChild(MatrixParameter.class);
    if (effectParameter.getDimension() != timesParameter.getDimension() || effectParameter.getDimension() != designParameter.getDimension()) {
        //				System.err.println("dim(design) "+designParameter.getDimension());
        throw new XMLParseException("dim(" + effectParameter.getStatisticName() + ") != dim(" + timesParameter.getStatisticName() + ") != dim(" + designParameter.getStatisticName() + ") in " + xo.getName() + " element");
    }
    MultivariateOUModel glm = new MultivariateOUModel(substitutionModel, effectParameter, gammaParameter, timesParameter.getParameterValues(), designParameter.getParameterValues());
    addIndependentParameters(xo, glm, effectParameter);
    return glm;
}

Example 3 with SubstitutionModel

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

the class SubstitutionEpochModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = null;
    FrequencyModel freqModel = null;
    List<SubstitutionModel> modelList = new ArrayList<SubstitutionModel>();
    XMLObject cxo = xo.getChild(MODELS);
    for (int i = 0; i < cxo.getChildCount(); i++) {
        SubstitutionModel model = (SubstitutionModel) cxo.getChild(i);
        if (dataType == null) {
            dataType = model.getDataType();
        } else if (dataType != model.getDataType())
            throw new XMLParseException("Substitution models across epoches must use the same data type.");
        if (freqModel == null) {
            freqModel = model.getFrequencyModel();
        } else if (freqModel != model.getFrequencyModel())
            throw new XMLParseException("Substitution models across epoches must currently use the same frequency model.\nHarass Marc to fix this.");
        modelList.add(model);
    }
    Parameter transitionTimes = (Parameter) xo.getChild(Parameter.class);
    if (transitionTimes.getDimension() != modelList.size() - 1) {
        throw new XMLParseException("# of transition times must equal # of substitution models - 1\n" + transitionTimes.getDimension() + "\n" + modelList.size());
    }
    return new SubstitutionEpochModel(SUBSTITUTION_EPOCH_MODEL, modelList, transitionTimes, dataType, freqModel);
}

Example 4 with SubstitutionModel

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

the class SampleStateAndCategoryModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(MUTATION_RATE);
    Parameter muParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(CATEGORY_PARAMETER);
    Parameter catParam = (Parameter) cxo.getChild(Parameter.class);
    Vector subModels = new Vector();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof SubstitutionModel) {
            subModels.addElement(xo.getChild(i));
        }
    }
    return new SampleStateAndCategoryModel(muParam, catParam, subModels);
}

Example 5 with SubstitutionModel

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

the class GammaSiteBMAParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getElementFirstChild(SUBSTITUTION_MODEL);
    Parameter muParam = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
    Parameter logitInvar = (Parameter) xo.getElementFirstChild(LOGIT_PROPORTION_INVARIANT);
    final XMLObject cxo = xo.getChild(LOG_GAMMA_SHAPE);
    Parameter logShape = (Parameter) cxo.getChild(Parameter.class);
    int catCount = cxo.getIntegerAttribute(GAMMA_CATEGORIES);
    Variable<Integer> modelChoose = (Variable<Integer>) xo.getElementFirstChild(MODEL_CHOOSE);
    return new GammaSiteBMA(substitutionModel, muParam, logitInvar, logShape, catCount, modelChoose);
}