Java tutorial
/* 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 org.apache.commons.math.MathException; import org.apache.commons.math.distribution.ChiSquaredDistribution; import org.apache.commons.math.distribution.ChiSquaredDistributionImpl; /** * Performs a chi square Goodness of Fit test or Test of Independence. * * * @author G. Sturr */ public class AlgoChiSquaredTest extends AlgoElement { private GeoList geoList1, geoList2; // input private GeoList result; // output private double p, testStat; private ChiSquaredDistribution chisquared = null; public AlgoChiSquaredTest(Construction cons, String label, GeoList geoList) { this(cons, geoList, null); result.setLabel(label); } public AlgoChiSquaredTest(Construction cons, String label, GeoList geoList, GeoList geoList2) { this(cons, geoList, geoList2); result.setLabel(label); } public AlgoChiSquaredTest(Construction cons, GeoList geoList, GeoList geoList2) { super(cons); this.geoList1 = geoList; this.geoList2 = geoList2; result = new GeoList(cons); setInputOutput(); // for AlgoElement compute(); } @Override public Commands getClassName() { return Commands.ChiSquaredTest; } @Override protected void setInputOutput() { if (geoList2 == null) { input = new GeoElement[1]; input[0] = geoList1; } else { input = new GeoElement[2]; input[0] = geoList1; input[1] = geoList2; } setOnlyOutput(result); setDependencies(); // done by AlgoElement } public GeoList getResult() { return result; } /** * @param df * degree of freedom * @return implementation of ChiSquaredDistribution for given degree of * freedom */ ChiSquaredDistribution getChiSquaredDistribution(double df) { if (chisquared == null || chisquared.getDegreesOfFreedom() != df) chisquared = new ChiSquaredDistributionImpl(df); return chisquared; } @Override public final void compute() { int df; int rows = geoList1.size(); int columns = 0; if (!geoList1.isDefined() || rows < 2) { result.setUndefined(); return; } if (geoList2 != null) { if (!geoList2.isDefined() || geoList2.size() != rows) { result.setUndefined(); return; } } double[][] observed = null; double[][] expected = null; double[][] diff = null; // store observed and expected values in arrays // Three cases must be handled: // 1) <List of Observed, List of Expected> (the GOF test) // 2) <Matrix of Observed, Matrix of Expected> // 3) <Matrix of Observed>, here we compute the expected counts based on // the hypothesis of independence: // expected count = row sum * column sum / grand total) // if list1 is not a matrix, then we have the two list case if (!geoList1.isMatrix()) { if (geoList2 == null) { result.setUndefined(); return; } columns = 1; df = rows - 1; observed = new double[rows][columns]; expected = new double[rows][columns]; for (int i = 0; i < rows; i++) { GeoElement geo = geoList1.get(i); GeoElement geo2 = geoList2.get(i); if (geo instanceof NumberValue && geo2 instanceof NumberValue) { observed[i][0] = ((NumberValue) geo).getDouble(); expected[i][0] = ((NumberValue) geo2).getDouble(); } else { result.setUndefined(); return; } } } else { // list1 is matrix columns = ((GeoList) geoList1.get(0)).size(); observed = new double[rows][columns]; expected = new double[rows][columns]; df = (columns - 1) * (rows - 1); for (int i = 0; i < rows; i++) { for (int j = 0; j < columns; j++) { // get observed values GeoElement geo = ((GeoList) geoList1.get(i)).get(j); if (geo instanceof NumberValue) { observed[i][j] = ((NumberValue) geo).getDouble(); } else { result.setUndefined(); return; } // get expected values if list2 exists (it must be a matrix) if (geoList2 != null) { GeoElement geo2 = ((GeoList) geoList2.get(i)).get(j); if (geo2 instanceof NumberValue) { expected[i][j] = ((NumberValue) geo2).getDouble(); } else { result.setUndefined(); return; } } } } // compute expected values if list2 is not given if (geoList2 == null) { double[] columnSum = new double[columns]; for (int j = 0; j < columns; j++) { columnSum[j] = 0; } double[] rowSum = new double[rows]; for (int i = 0; i < rows; i++) { rowSum[i] = 0; } double total = 0; for (int i = 0; i < rows; i++) { for (int j = 0; j < columns; j++) { rowSum[i] += observed[i][j]; columnSum[j] += observed[i][j]; total += observed[i][j]; } } for (int i = 0; i < rows; i++) { for (int j = 0; j < columns; j++) { expected[i][j] = rowSum[i] * columnSum[j] / total; } } } } // compute test statistic and chi-square contributions diff = new double[rows][columns]; testStat = 0; for (int i = 0; i < rows; i++) { for (int j = 0; j < columns; j++) { diff[i][j] = (observed[i][j] - expected[i][j]) * (observed[i][j] - expected[i][j]) / expected[i][j]; testStat += diff[i][j]; } } try { double leftArea = getChiSquaredDistribution(df).cumulativeProbability(testStat); p = 1 - leftArea; } catch (IllegalArgumentException e) { result.setUndefined(); e.printStackTrace(); } catch (MathException e) { result.setUndefined(); e.printStackTrace(); } // put results into the output list result.clear(); result.add(new GeoNumeric(cons, p)); result.add(new GeoNumeric(cons, testStat)); } // TODO Consider locusequability }