protected override double ComputeLLR(ModelScorer modelScorer, PhyloTree phyloTree, StringBuilder stringBuilder, double targetMarginal, double predictorMarginal,
Converter <Leaf, SufficientStatistics> predictorDistributionClassFunction, Converter <Leaf, SufficientStatistics> targetDistributionClassFunction)
{
Converter <Leaf, SufficientStatistics> LeafToJointDistributionClass =
CreateAlternativeSufficientStatisticsMap(predictorDistributionClassFunction, targetDistributionClassFunction);
double logLikelihoodIndependentModel, logLikelihoodJointModel;
Score scoreIndTarget, scoreIndPredictor, scoreJoint;
MessageInitializer messageInitializer;
// first score the target.
NullModelDistribution.EmpiricalEquilibrium = targetMarginal;
messageInitializer = modelScorer.CreateMessageInitializer(predictorDistributionClassFunction, targetDistributionClassFunction, NullModelDistribution);
scoreIndTarget = modelScorer.ScoreModel(messageInitializer, false);
NullModelDistribution.EmpiricalEquilibrium = predictorMarginal;
messageInitializer = modelScorer.CreateMessageInitializer(targetDistributionClassFunction, predictorDistributionClassFunction, NullModelDistribution);
scoreIndPredictor = modelScorer.ScoreModel(messageInitializer, false);
DistributionDiscreteJointBinary jointDistn = (DistributionDiscreteJointBinary)AlternativeModelDistribution;
jointDistn.SetInitialParams(scoreIndPredictor.OptimizationParameters, scoreIndTarget.OptimizationParameters);
messageInitializer = modelScorer.CreateMessageInitializer(null, LeafToJointDistributionClass, jointDistn);
scoreJoint = modelScorer.ScoreModel(messageInitializer, false);
logLikelihoodIndependentModel = scoreIndTarget.Loglikelihood + scoreIndPredictor.Loglikelihood;
logLikelihoodJointModel = scoreJoint.Loglikelihood;
stringBuilder.Append(SpecialFunctions.CreateTabString(scoreIndPredictor.ToString(NullModelDistribution), scoreIndTarget.ToString(NullModelDistribution),
logLikelihoodIndependentModel, scoreJoint.ToString(jointDistn), ""));
double diff = logLikelihoodJointModel - logLikelihoodIndependentModel;
return(diff);
}
