Joint and conditional Entropy in Java

// --------------------------------------------------------------------------------------------------------------------
// <copyright file="EntropyExample.java" company="Bayes Server">
//   Copyright (C) Bayes Server.  All rights reserved.
// </copyright>
// --------------------------------------------------------------------------------------------------------------------

package com.bayesserver.examples;

import com.bayesserver.*;
import com.bayesserver.inference.*;
import com.bayesserver.statistics.*;

import javax.xml.stream.XMLStreamException;
import java.io.IOException;
import java.util.ArrayList;

public class EntropyExample {

    public static void main(String[] args) throws IOException, XMLStreamException, InconsistentEvidenceException {

        Network network = new Network();

        // TODO download the network from the Bayes Server User Interface (or Bayes Server Online)
        // and adjust the following path
        network.load("Asia.bayes");

        Variable visitToAsia = network.getVariables().get("Visit to Asia", true);
        Variable hasLungCancer = network.getVariables().get("Has Lung Cancer", true);
        Variable tuberculosisOrCancer = network.getVariables().get("Tuberculosis or Cancer", true);
        Variable smoker = network.getVariables().get("Smoker", true);
        Variable hasTuberculosis = network.getVariables().get("Has Tuberculosis", true);
        Variable dyspnea = network.getVariables().get("Dyspnea", true);
        Variable xRayResult = network.getVariables().get("XRay Result", true);
        Variable hasBronchitis = network.getVariables().get("Has Bronchitis", true);


        InferenceFactory factory = new RelevanceTreeInferenceFactory();
        Inference inf = factory.createInferenceEngine(network);
        QueryOptions qopt = factory.createQueryOptions();
        QueryOutput qout = factory.createQueryOutput();

        // Set evidence, if any
        inf.getEvidence().setState(smoker.getStates().get("True", true));


        Table queryJoint = new Table(hasBronchitis, dyspnea);

        inf.getQueryDistributions().add(queryJoint);

        inf.query(qopt, qout);

        double jointEntropyGivenSmokerTrue = Entropy.calculate(queryJoint, LogarithmBase.NATURAL);

        ArrayList<VariableContext> conditionOn = new ArrayList<VariableContext>();
        conditionOn.add(queryJoint.getSortedVariables().get(queryJoint.getSortedVariables().indexOf(hasBronchitis)));
        double conditionalEntropyGivenSmokerTrue = Entropy.calculate(queryJoint, conditionOn, LogarithmBase.NATURAL);

        System.out.println(String.format("H(Has Bronchitis, Dyspnea | Smoker = True) = %s NATS", jointEntropyGivenSmokerTrue));
        System.out.println(String.format("H(Has Bronchitis | Dyspnea, Smoker = True) = %s NATS", conditionalEntropyGivenSmokerTrue));

        //  Expected output

        //  H(Has Bronchitis, Dyspnea | Smoker = True) = 1.14347590829214 NATS
        //  H(Has Bronchitis | Dyspnea, Smoker = True) = 0.470464241282886 NATS

    }
}