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);
}
new public static ModelTesterDiscrete GetInstance(string modelTesterNameAndArguments)
{
if (modelTesterNameAndArguments.StartsWith(ModelTesterDiscreteFisher.Name))
{
return(ModelTesterDiscreteFisher.GetInstance());
}
else if (modelTesterNameAndArguments.StartsWith(ModelTesterDiscreteConditional.Name))
{
string leafDistnName = modelTesterNameAndArguments.Substring(ModelTesterDiscreteConditional.Name.Length);
DistributionDiscreteBinary distn = DistributionDiscreteBinary.GetInstance(leafDistnName);
return(ModelTesterDiscreteConditional.GetInstance(distn));
}
else if (modelTesterNameAndArguments.StartsWith(ModelTesterDiscreteJoint.Name))
{
string altDistnName = modelTesterNameAndArguments.Substring(ModelTesterDiscreteJoint.Name.Length);
DistributionDiscreteBinary nullDistn = DistributionDiscreteBinary.GetInstance("Repulsion"); // leafDistn doesn't matter
DistributionDiscreteJointBinary altDistn = DistributionDiscreteJointBinary.GetInstance(altDistnName);
return(ModelTesterDiscreteJoint.GetInstance(nullDistn, altDistn));
}
else
{
throw new ArgumentException(String.Format("{0} does not start with a valid ModelTesterDiscrete name.", modelTesterNameAndArguments));
}
}
