org.drugepi.hdps.ZBiasCalculator.java Source code

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Here is the source code for org.drugepi.hdps.ZBiasCalculator.java

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/* 
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/. 
 */
package org.drugepi.hdps;

import java.util.*;

import org.apache.commons.math.stat.descriptive.rank.Percentile;
import org.drugepi.hdps.storage.HdpsVariable;
import org.drugepi.hdps.storage.comparators.*;

public class ZBiasCalculator {
    public static void scoreVariables(List<HdpsVariable> variableList) {
        // copy variables list
        List<HdpsVariable> expSortVariableList = new ArrayList<HdpsVariable>();
        List<HdpsVariable> outcomeSortVariableList = new ArrayList<HdpsVariable>();

        for (HdpsVariable var : variableList) {
            var.zBiasScore = 0;

            if ((var.expAssocRankingVariable != HdpsVariable.INVALID)
                    && (var.outcomeAssocRankingVariable != HdpsVariable.INVALID)) {
                expSortVariableList.add(var);
                outcomeSortVariableList.add(var);
            }
        }

        // sort variables by exposure association (strongest first) 
        Collections.sort(expSortVariableList, new HdpsVariableReverseExposureAssociationComparator());

        // sort variables by outcome association (weakest first) 
        Collections.sort(outcomeSortVariableList, new HdpsVariableReverseOutcomeAssociationComparator());
        Collections.reverse(outcomeSortVariableList);

        // create an array of outcome strengths
        double[] outcomeStrengths = new double[outcomeSortVariableList.size()];
        for (int i = 0; i < outcomeStrengths.length; i++)
            outcomeStrengths[i] = outcomeSortVariableList.get(i).outcomeAssocRankingVariable;

        // array that will store breaks between deciles
        // find the median of outcome strength 
        Percentile pctile = new Percentile();

        // Find quintiles 1 through 5 of outcome weakness
        // AMONG the weakest half of the variables.
        // List is sorted strongest first, so the weakest variables 
        // will be at the end
        // quintile 1 = weakest 
        // don't use startsOfQuintile[0]

        double median = pctile.evaluate(outcomeStrengths, 50.0);
        int searchCeiling = Arrays.binarySearch(outcomeStrengths, median);
        if (searchCeiling < 0)
            searchCeiling = -(searchCeiling + 1);

        int startsOfQuintile[] = new int[7];

        for (int quintile = 1; quintile <= 5; quintile++) {
            // find the probability that *begins* this quintile
            double p = (quintile - 1) * 20;
            if (p > 0) {
                double quintileStartP = pctile.evaluate(outcomeStrengths, 0, searchCeiling, (quintile - 1) * 20);

                startsOfQuintile[quintile] = Arrays.binarySearch(outcomeStrengths, quintileStartP);
                if (startsOfQuintile[quintile] < 0)
                    startsOfQuintile[quintile] = -(startsOfQuintile[quintile] + 1);
            } else
                startsOfQuintile[quintile] = 0;
        }
        startsOfQuintile[6] = searchCeiling;

        // score the variables, BUT make quintile 5 the weakest
        for (int quintile = 1; quintile <= 5; quintile++) {
            for (int i = startsOfQuintile[quintile]; i < startsOfQuintile[quintile + 1]; i++) {
                HdpsVariable v = outcomeSortVariableList.get(i);
                v.zBiasScore = 6 - quintile;
            }
        }

        //      for (HdpsVariable v: outcomeSortVariableList) {
        //         System.out.printf("%s    %1.4f    %d\n", v.varName, v.outcomeAssocRankingVariable, v.zBiasScore);
        //      }
    }
}