Examples with Parameter dr.inference.model.Parameter used on opensource projects

Example 71 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class AsymQuadModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Microsatellite microsatellite = (Microsatellite) xo.getChild(Microsatellite.class);
    Parameter expanConst = processModelParameter(xo, EXPANSION_CONSTANT);
    Parameter expanLin = processModelParameter(xo, EXPANSION_LIN);
    Parameter expanQuad = processModelParameter(xo, EXPANSION_QUAD);
    Parameter contractConst = processModelParameter(xo, CONTRACTION_CONSTANT);
    Parameter contractLin = processModelParameter(xo, CONTRACTION_LIN);
    Parameter contractQuad = processModelParameter(xo, CONTRACTION_QUAD);
    //get FrequencyModel
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    boolean isSubmodel = xo.getAttribute(IS_SUBMODEL, false);
    return new AsymmetricQuadraticModel(microsatellite, freqModel, expanConst, expanLin, expanQuad, contractConst, contractLin, contractQuad, isSubmodel);
}

Example 72 with Parameter

use of dr.inference.model.Parameter 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 73 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class TKF91ModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter lengthDistParameter = (Parameter) xo.getElementFirstChild(TKF91_LENGTH_DIST);
    Parameter deathParameter = (Parameter) xo.getElementFirstChild(DEATH_RATE);
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    return new TKF91Model(lengthDistParameter, deathParameter, units);
}

Example 74 with Parameter

use of dr.inference.model.Parameter in project beast-mcmc by beast-dev.

the class DiscretizedLociRatesParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final boolean normalize = xo.getAttribute(NORMALIZE, false);
    final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_MEAN_LOCI_RATE_TO, Double.NaN);
    final int categoryCount = xo.getIntegerAttribute(CATEGORY_COUNT);
    CompoundParameter lociRates = (CompoundParameter) xo.getElementFirstChild(LOCI_RATES);
    Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
    ParametricDistributionModel distributionModel = (ParametricDistributionModel) xo.getElementFirstChild(DISTRIBUTION);
    Logger.getLogger("dr.evomodel").info("Using discretized loci rates model.");
    Logger.getLogger("dr.evomodel").info("Number of categories: " + categoryCount);
    Logger.getLogger("dr.evomodel").info("  parametric model = " + distributionModel.getModelName());
    if (normalize) {
        Logger.getLogger("dr.evomodel").info("   mean rate is normalized to " + normalizeBranchRateTo);
    }
    return new DiscretizedLociRates(lociRates, rateCategoryParameter, distributionModel, normalize, normalizeBranchRateTo, categoryCount);
}

Example 75 with Parameter

use of dr.inference.model.Parameter 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);
}