Examples with IntegratedFactorAnalysisLikelihood dr.evomodel.treedatalikelihood.continuous.IntegratedFactorAnalysisLikelihood used on opensource projects

Example 1 with IntegratedFactorAnalysisLikelihood

use of dr.evomodel.treedatalikelihood.continuous.IntegratedFactorAnalysisLikelihood in project beast-mcmc by beast-dev.

the class LoadingsGibbsOperatorParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    // Get XML attributes
    double weight = xo.getDoubleAttribute(WEIGHT);
    boolean randomScan = xo.getAttribute(RANDOM_SCAN, true);
    int numThreads = xo.getAttribute(NUM_THREADS, 4);
    boolean multiThreaded = xo.getAttribute(MULTI_THREADED, false);
    boolean useNewMode = xo.getAttribute(MODE, false);
    // Get main objects
    LatentFactorModel LFM = (LatentFactorModel) xo.getChild(LatentFactorModel.class);
    // TODO The next 3 lines are not necessary, nor in XML rules
    MatrixParameterInterface loadings = null;
    if (xo.getChild(MatrixParameterInterface.class) != null) {
        loadings = (MatrixParameterInterface) xo.getChild(MatrixParameterInterface.class);
    }
    // Get priors
    DistributionLikelihood prior = (DistributionLikelihood) xo.getChild(DistributionLikelihood.class);
    MomentDistributionModel prior2 = (MomentDistributionModel) xo.getChild(MomentDistributionModel.class);
    DistributionLikelihood cutoffPrior = null;
    if (xo.hasChildNamed(CUTOFF_PRIOR)) {
        cutoffPrior = (DistributionLikelihood) xo.getChild(CUTOFF_PRIOR).getChild(DistributionLikelihood.class);
    }
    DistributionLikelihood WorkingPrior = null;
    if (xo.getChild(WORKING_PRIOR) != null) {
        WorkingPrior = (DistributionLikelihood) xo.getChild(WORKING_PRIOR).getChild(DistributionLikelihood.class);
    }
    // Dispatch
    if (prior != null) {
        if (useNewMode) {
            final FactorAnalysisOperatorAdaptor adaptor;
            if (LFM != null) {
                adaptor = new FactorAnalysisOperatorAdaptor.SampledFactors(LFM);
            } else {
                IntegratedFactorAnalysisLikelihood integratedLikelihood = (IntegratedFactorAnalysisLikelihood) xo.getChild(IntegratedFactorAnalysisLikelihood.class);
                TreeDataLikelihood treeLikelihood = (TreeDataLikelihood) xo.getChild(TreeDataLikelihood.class);
                adaptor = new FactorAnalysisOperatorAdaptor.IntegratedFactors(integratedLikelihood, treeLikelihood);
            }
            NewLoadingsGibbsOperator.ConstrainedSampler sampler = NewLoadingsGibbsOperator.ConstrainedSampler.parse(xo.getAttribute(CONSTRAINT, NewLoadingsGibbsOperator.ConstrainedSampler.NONE.getName()));
            return new NewLoadingsGibbsOperator(adaptor, prior, weight, randomScan, WorkingPrior, multiThreaded, numThreads, sampler);
        } else {
            // return new LoadingsGibbsOperator(LFM, prior, weight, randomScan, WorkingPrior, multiThreaded, numThreads);
            return null;
        }
    } else {
        return new LoadingsGibbsTruncatedOperator(LFM, prior2, weight, randomScan, loadings, cutoffPrior);
    }
}