use of dr.inference.distribution.DistributionLikelihood in project beast-mcmc by beast-dev.
the class ModelSpecificPseudoPriorLikelihoodParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
DistributionLikelihood priorLikelihood = (DistributionLikelihood) xo.getElementFirstChild(PRIOR);
DistributionLikelihood pseudoPriorLikelihood = (DistributionLikelihood) xo.getElementFirstChild(PSEUDO_PRIOR);
Distribution prior = priorLikelihood.getDistribution();
Distribution pseudoPrior = pseudoPriorLikelihood.getDistribution();
Parameter modelIndicator = (Parameter) xo.getElementFirstChild(MODEL_INDICATOR);
int[] models = xo.getIntegerArrayAttribute(MODELS);
Parameter selectedVariable = (Parameter) xo.getElementFirstChild(SELECTED_VARIABLE);
ModelSpecificPseudoPriorLikelihood likelihood = new ModelSpecificPseudoPriorLikelihood(prior, pseudoPrior, modelIndicator, models);
likelihood.addData(selectedVariable);
return likelihood;
}
use of dr.inference.distribution.DistributionLikelihood in project beast-mcmc by beast-dev.
the class CompoundGaussianProcessParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
List<GaussianProcessRandomGenerator> gpList = new ArrayList<GaussianProcessRandomGenerator>();
List<Likelihood> likelihoodList = new ArrayList<Likelihood>();
List<Integer> copyList = new ArrayList<Integer>();
for (int i = 0; i < xo.getChildCount(); ++i) {
Object obj = xo.getChild(i);
GaussianProcessRandomGenerator gp = null;
Likelihood likelihood = null;
int copies = -1;
if (obj instanceof DistributionLikelihood) {
DistributionLikelihood dl = (DistributionLikelihood) obj;
if (!(dl.getDistribution() instanceof GaussianProcessRandomGenerator)) {
throw new XMLParseException("Not a Gaussian process");
}
likelihood = dl;
gp = (GaussianProcessRandomGenerator) dl.getDistribution();
copies = 0;
for (Attribute<double[]> datum : dl.getDataList()) {
// Double draw = (Double) gp.nextRandom();
// System.err.println("DL: " + datum.getAttributeName() + " " + datum.getAttributeValue().length + " " + "1");
copies += datum.getAttributeValue().length;
}
} else if (obj instanceof MultivariateDistributionLikelihood) {
MultivariateDistributionLikelihood mdl = (MultivariateDistributionLikelihood) obj;
if (!(mdl.getDistribution() instanceof GaussianProcessRandomGenerator)) {
throw new XMLParseException("Not a Gaussian process");
}
likelihood = mdl;
gp = (GaussianProcessRandomGenerator) mdl.getDistribution();
copies = 0;
double[] draw = (double[]) gp.nextRandom();
for (Attribute<double[]> datum : mdl.getDataList()) {
// System.err.println("ML: " + datum.getAttributeName() + " " + datum.getAttributeValue().length + " " + draw.length);
copies += datum.getAttributeValue().length / draw.length;
}
} else if (obj instanceof GaussianProcessRandomGenerator) {
gp = (GaussianProcessRandomGenerator) obj;
likelihood = gp.getLikelihood();
copies = 1;
} else {
throw new XMLParseException("Not a Gaussian process");
}
gpList.add(gp);
likelihoodList.add(likelihood);
copyList.add(copies);
}
// System.exit(-1);
return new CompoundGaussianProcess(gpList, likelihoodList, copyList);
}
use of dr.inference.distribution.DistributionLikelihood in project beast-mcmc by beast-dev.
the class DistributionLikelihoodParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final XMLObject cxo = xo.getChild(DISTRIBUTION);
ParametricDistributionModel model = (ParametricDistributionModel) cxo.getChild(ParametricDistributionModel.class);
DistributionLikelihood likelihood = new DistributionLikelihood(model);
XMLObject cxo1 = xo.getChild(DATA);
final int from = cxo1.getAttribute(FROM, -1);
int to = cxo1.getAttribute(TO, -1);
if (from >= 0 || to >= 0) {
if (to < 0) {
to = Integer.MAX_VALUE;
}
if (!(from >= 0 && to >= 0 && from < to)) {
throw new XMLParseException("ill formed from-to");
}
likelihood.setRange(from, to);
}
for (int j = 0; j < cxo1.getChildCount(); j++) {
if (cxo1.getChild(j) instanceof Statistic) {
likelihood.addData((Statistic) cxo1.getChild(j));
} else {
throw new XMLParseException("illegal element in " + cxo1.getName() + " element");
}
}
return likelihood;
}
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