com.analog.lyric.chimple.monkeys.ChimpDirichlet.java Source code

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Here is the source code for com.analog.lyric.chimple.monkeys.ChimpDirichlet.java

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/*******************************************************************************
*   Copyright 2013 Analog Devices Inc.
*
*   Licensed under the Apache License, Version 2.0 (the "License");
*   you may not use this file except in compliance with the License.
*   You may obtain a copy of the License at
*
*       http://www.apache.org/licenses/LICENSE-2.0
*
*   Unless required by applicable law or agreed to in writing, software
*   distributed under the License is distributed on an "AS IS" BASIS,
*   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
*   See the License for the specific language governing permissions and
*   limitations under the License.
********************************************************************************/

package com.analog.lyric.chimple.monkeys;

import org.apache.commons.math.special.Gamma;

import com.analog.lyric.chimple.MonkeyHandler;

public class ChimpDirichlet extends MonkeyBase {

    public ChimpDirichlet(MonkeyHandler handler) {
        super(handler);
    }

    @Override
    public Object generate(Object[] parameters) {
        double[] alphas = (double[]) parameters[0];
        return getRandom().nextDirichlet(alphas);
    }

    @Override
    public double calculateLogLikelihood(Object result, Object[] parameters) {
        double[] alphas = (double[]) parameters[0];
        double[] value = (double[]) result;

        double retval = 0;

        double sum = 0;
        for (int i = 0; i < alphas.length; i++) {
            retval -= (alphas[i] - 1) * Math.log(value[i]);
            retval += Gamma.logGamma(alphas[i]);
            sum += alphas[i];
        }

        retval -= Gamma.logGamma(sum);

        //result=sum(gammaln(alphas))-gammaln(sum(alphas))-sum((alphas-1).*log(value));

        return retval;
    }

    @Override
    public RegeneratorPair regenerate(Object oldVal, Object[] parameters) {
        double[] prev = (double[]) oldVal;

        int ii = 0;
        int jj = 0;

        while (ii == jj) {
            ii = getRandom().nextInt(prev.length);
            jj = getRandom().nextInt(prev.length);
        }

        double[] retval = prev.clone();

        double a = retval[ii];
        double b = retval[jj];
        double total = a + b;

        double ap = getRandom().nextDouble() * total;
        double bp = total - ap;

        retval[ii] = ap;
        retval[jj] = bp;

        return new RegeneratorPair(retval, 0);
    }

}