org.drugis.mtc.summary.SummaryUtil.java Source code

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Here is the source code for org.drugis.mtc.summary.SummaryUtil.java

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/*
 * This file is part of the GeMTC software for MTC model generation and
 * analysis. GeMTC is distributed from http://drugis.org/gemtc.
 * Copyright (C) 2009-2012 Gert van Valkenhoef.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.drugis.mtc.summary;

import java.util.List;
import java.util.AbstractList;
import java.util.ArrayList;

import org.drugis.mtc.MCMCResults;
import org.drugis.mtc.Parameter;

import org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;

public class SummaryUtil {
    /**
     * A List view on one (parameter, chain) of the MCMCResults.
     */
    public static class ResultsView extends AbstractList<Double> {
        private final MCMCResults d_results;
        private final int d_param;
        private final int d_chain;

        public ResultsView(MCMCResults r, int p, int c) {
            d_results = r;
            d_param = p;
            d_chain = c;
        }

        @Override
        public int size() {
            return d_results.getNumberOfSamples();
        }

        @Override
        public Double get(int idx) {
            return d_results.getSample(d_param, d_chain, idx);
        }
    }

    /**
     * A view on the last half of the supplied list.
     */
    public static class LastHalfView extends AbstractList<Double> {
        private final List<Double> d_list;

        public LastHalfView(List<Double> list) {
            d_list = list;
        }

        @Override
        public int size() {
            return d_list.size() / 2;
        }

        @Override
        public Double get(int idx) {
            return d_list.get(size() + idx);
        }
    }

    /**
     * A view that concatenates the supplied lists.
     * All lists are assumed to be of equal length, and it is assumed that at least one list is supplied.
     */
    public static class ConcatenationView extends AbstractList<Double> {
        private final List<List<Double>> d_lists;

        public ConcatenationView(List<List<Double>> lists) {
            d_lists = lists;
        }

        @Override
        public int size() {
            return d_lists.size() * d_lists.get(0).size();
        }

        @Override
        public Double get(int idx) {
            int size = d_lists.get(0).size();
            return d_lists.get(idx / size).get(idx % size);
        }
    }

    public static double evaluate(StorelessUnivariateStatistic stat, List<Double> vals) {
        stat.clear();
        for (Double d : vals) {
            stat.increment(d);
        }
        return stat.getResult();
    }

    /**
     * Get the last 1/2 of the samples from each chain in results, for parameter.
     */
    public static List<Double> getAllChainsLastHalfSamples(MCMCResults results, Parameter parameter) {
        List<List<Double>> lists = new ArrayList<List<Double>>();
        for (int i = 0; i < results.getNumberOfChains(); ++i) {
            lists.add(getOneChainLastHalfSamples(results, parameter, i));
        }
        return new ConcatenationView(lists);
    }

    /**
     * Get the last 1/2 of the samples from one chain in results, for parameter.
     */
    public static List<Double> getOneChainLastHalfSamples(MCMCResults results, Parameter parameter, int c) {
        int p = results.findParameter(parameter);
        return new LastHalfView(new ResultsView(results, p, c));
    }
}