geogebra.common.kernel.statistics.AlgoTTestPaired.java Source code

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Here is the source code for geogebra.common.kernel.statistics.AlgoTTestPaired.java

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/* 
GeoGebra - Dynamic Mathematics for Everyone
http://www.geogebra.org
    
This file is part of GeoGebra.
    
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.
    
 */

package geogebra.common.kernel.statistics;

import geogebra.common.kernel.Construction;
import geogebra.common.kernel.algos.AlgoElement;
import geogebra.common.kernel.arithmetic.NumberValue;
import geogebra.common.kernel.commands.Commands;
import geogebra.common.kernel.geos.GeoElement;
import geogebra.common.kernel.geos.GeoList;
import geogebra.common.kernel.geos.GeoNumeric;
import geogebra.common.kernel.geos.GeoText;
import geogebra.common.util.StringUtil;

import org.apache.commons.math.MathException;
import org.apache.commons.math.stat.inference.TTestImpl;

/**
 * Performs a paired t-test.
 * 
 * 
 * @author G. Sturr
 */
public class AlgoTTestPaired extends AlgoElement {

    private GeoList geoList0, geoList1; // input
    private GeoText tail; // input
    private GeoList result; // output
    private TTestImpl tTestImpl;
    private double[] val0, val1;

    public AlgoTTestPaired(Construction cons, String label, GeoList geoList0, GeoList geoList1, GeoText tail) {
        super(cons);
        this.geoList0 = geoList0;
        this.geoList1 = geoList1;
        this.tail = tail;
        result = new GeoList(cons);
        setInputOutput(); // for AlgoElement

        compute();
        result.setLabel(label);
    }

    @Override
    public Commands getClassName() {
        return Commands.TTestPaired;
    }

    @Override
    protected void setInputOutput() {

        input = new GeoElement[3];
        input[0] = geoList0;
        input[1] = geoList1;
        input[2] = tail;

        setOnlyOutput(result);
        setDependencies(); // done by AlgoElement
    }

    public GeoList getResult() {
        return result;
    }

    private double adjustedPValue(double p, double testStatistic) {

        // two sided test
        if (StringUtil.isNotEqual(tail.getTextString()))
            return p;

        // one sided test
        else if ((tail.getTextString().equals(">") && testStatistic > 0)
                || (tail.getTextString().equals("<") && testStatistic < 0))
            return p / 2;
        else
            return 1 - p / 2;
    }

    @Override
    public final void compute() {

        if (!(StringUtil.isInequality(tail.getTextString()))) {
            result.setUndefined();
            return;
        }

        double p, testStat;

        // sample data input

        int size = geoList0.size();
        if (!geoList1.isDefined() || geoList1.size() != size) {
            result.setUndefined();
            return;
        }

        // create number value arrays
        val0 = new double[size];
        val1 = new double[size];
        GeoElement geo0, geo1;
        NumberValue num0, num1;

        for (int i = 0; i < size; i++) {
            geo0 = geoList0.get(i);
            geo1 = geoList1.get(i);
            if (geo0 instanceof NumberValue && geo1 instanceof NumberValue) {
                num0 = (NumberValue) geo0;
                num1 = (NumberValue) geo1;
                val0[i] = num0.getDouble();
                val1[i] = num1.getDouble();

            } else {
                result.setUndefined();
                return;
            }
        }

        try {

            // get the test statistic and p
            if (tTestImpl == null)
                tTestImpl = new TTestImpl();
            testStat = tTestImpl.pairedT(val0, val1);
            p = tTestImpl.pairedTTest(val0, val1);
            testStat = tTestImpl.pairedT(val0, val1);
            p = adjustedPValue(p, testStat);

            // put these results into the output list
            result.clear();
            result.add(new GeoNumeric(cons, p));
            result.add(new GeoNumeric(cons, testStat));

        } catch (IllegalArgumentException e) {
            e.printStackTrace();
        } catch (MathException e) {
            e.printStackTrace();
        }

    }

    // TODO Consider locusequability

}