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

Example 76 with Parameter

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

the class SingleTipObservationProcessParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter mu = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.DEATH_RATE);
    Parameter lam = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.IMMIGRATION_RATE);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    PatternList patterns = (PatternList) xo.getChild(PatternList.class);
    Taxon sourceTaxon = (Taxon) xo.getChild(Taxon.class);
    SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    Logger.getLogger("dr.evomodel.MSSD").info("Creating SingleTipObservationProcess model. All traits are assumed extant in " + sourceTaxon.getId() + "Initial mu = " + mu.getParameterValue(0) + " initial lam = " + lam.getParameterValue(0));
    return new SingleTipObservationProcess(treeModel, patterns, siteModel, branchRateModel, mu, lam, sourceTaxon);
}

Example 77 with Parameter

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

the class BifractionalDiffusionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(ALPHA_PARAMETER);
    Parameter alpha = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(BETA_PARAMETER);
    Parameter beta = (Parameter) cxo.getChild(Parameter.class);
    return new BifractionalDiffusionModel(alpha, beta);
}

Example 78 with Parameter

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

the class MarkovJumpsTreeLikelihoodParser method parseAllChildren.

public static int parseAllChildren(XMLObject xo, MarkovJumpsRegisterAcceptor acceptor, int stateCount, String jumpTag, MarkovJumpsType type, boolean scaleRewards) throws XMLParseException {
    int registersFound = 0;
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object obj = xo.getChild(i);
        if (obj instanceof Parameter) {
            Parameter registerParameter = (Parameter) obj;
            if (type == MarkovJumpsType.COUNTS && registerParameter.getDimension() != stateCount * stateCount) {
                if (registerParameter.getDimension() == 1) {
                    // if the dimension hasn't been set then default to counting all jumps
                    registerParameter.setDimension(stateCount * stateCount);
                    for (int j = 0; j < stateCount; j++) {
                        for (int k = 0; k < stateCount; k++) {
                            registerParameter.setParameterValueQuietly((j * stateCount) + k, (j == k ? 0.0 : 1.0));
                        }
                    }
                } else {
                    throw new XMLParseException("Markov Jumps register parameter " + registerParameter.getId() + " is of the wrong dimension");
                }
            }
            if (type == MarkovJumpsType.REWARDS && registerParameter.getDimension() != stateCount) {
                if (registerParameter.getDimension() == 1) {
                    // if the dimension hasn't been set then default to getting rewards for all states
                    registerParameter.setDimension(stateCount);
                    for (int j = 0; j < stateCount; j++) {
                        registerParameter.setParameterValueQuietly(j, 1.0);
                    }
                } else {
                    throw new XMLParseException("Markov Rewards register parameter " + registerParameter.getId() + " is of the wrong dimension");
                }
            }
            if (registerParameter.getId() == null) {
                registerParameter.setId(jumpTag + (registersFound + 1));
            }
            acceptor.addRegister(registerParameter, type, scaleRewards);
            registersFound++;
        }
    }
    return registersFound;
}

Example 79 with Parameter

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

the class SampleNonActiveGibbsOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    XMLObject cxo = xo.getChild(DISTRIBUTION);
    ParametricDistributionModel distribution = (ParametricDistributionModel) cxo.getChild(ParametricDistributionModel.class);
    cxo = xo.getChild(DATA_PARAMETER);
    Parameter data = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(INDICATOR_PARAMETER);
    Parameter indicators = (Parameter) cxo.getChild(Parameter.class);
    return new SampleNonActiveGibbsOperator(distribution, data, indicators, weight);
}

Example 80 with Parameter

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

the class DataFromTreeTipsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeTraitParserUtilities utilities = new TreeTraitParserUtilities();
    String traitName = (String) xo.getAttribute(TreeTraitParserUtilities.TRAIT_NAME);
    MultivariateTraitTree treeModel = (MultivariateTraitTree) xo.getChild(MultivariateTraitTree.class);
    TreeTraitParserUtilities.TraitsAndMissingIndices returnValue = utilities.parseTraitsFromTaxonAttributes(xo, traitName, treeModel, true);
    MatrixParameter dataParameter = MatrixParameter.recast(returnValue.traitParameter.getId(), returnValue.traitParameter);
    if (xo.hasChildNamed(TreeTraitParserUtilities.MISSING)) {
        Parameter missing = (Parameter) xo.getChild(TreeTraitParserUtilities.MISSING).getChild(Parameter.class);
        missing.setDimension(dataParameter.getDimension());
        for (int i = 0; i < missing.getDimension(); i++) {
            if (returnValue.missingIndices.contains(i)) {
                missing.setParameterValue(i, 1);
            } else {
                missing.setParameterValue(i, 0);
            }
        }
    }
    return dataParameter;
}