Java tutorial
/* * Java Statistics. A java library providing power/sample size estimation for * the general linear model. * * Copyright (C) 2015 Regents of the University of Colorado. * * 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 2 * 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, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package edu.ucdenver.bios.power; import java.io.File; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; import edu.cudenver.bios.power.GLMMPower; import junit.framework.TestCase; import org.apache.commons.math3.linear.Array2DRowRealMatrix; import org.apache.commons.math3.linear.RealMatrix; import edu.cudenver.bios.matrix.FixedRandomMatrix; import edu.cudenver.bios.matrix.MatrixUtils; import edu.cudenver.bios.matrix.OrthogonalPolynomialContrastCollection; import edu.cudenver.bios.matrix.OrthogonalPolynomials; import edu.cudenver.bios.power.glmm.GLMMTestFactory; import edu.cudenver.bios.power.parameters.GLMMPowerParameters; import edu.cudenver.bios.power.test.PowerChecker; import edu.cudenver.bios.power.test.ValidationReportBuilder; import edu.cudenver.bios.utils.Factor; import org.junit.Before; import org.junit.Test; import static org.junit.Assert.assertTrue; /** * Unit test for polynomial trends in U matrix * with comparison against simulation and SAS output. * Based on example 7 from POWERLIB (Johnson et al., 2009) * @author Sarah Kreidler * */ public class ConditionalOrthogonalPolynomial3FactorTest { private static final String DATA_FILE = "TestConditionalOrthogonalPolynomial3Factor.xml"; private static final String TITLE = "GLMM(F) Example 8. Power for tests of polynomial " + "trend for multiple between and within subject factors using 3-way orthogonal polynomial contrasts"; private StringBuffer matrixAltStringBuffer = new StringBuffer(); private static final double TOLERANCE = 0.000001; private PowerChecker checker; private static DecimalFormat ShortNumber = new DecimalFormat("#0.0000"); // groups for factors A,B, and C double[] dataA = { 1, 2, 3 }; String nameA = "A"; Factor factorA = new Factor(nameA, dataA); double[] dataB = { 1, 2, 3 }; String nameB = "B"; Factor factorB = new Factor(nameB, dataB); double[] dataC = { 1, 2, 3 }; String nameC = "C"; Factor factorC = new Factor(nameC, dataC); // times for factors D, E, and F double[] dataD = { 1, 2, 3 }; String nameD = "D"; Factor factorD = new Factor(nameD, dataD); double[] dataE = { 1, 2, 3 }; String nameE = "E"; Factor factorE = new Factor(nameE, dataE); double[] dataF = { 1, 2, 3 }; String nameF = "F"; Factor factorF = new Factor(nameF, dataF); @Before public void setUp() { List<GLMMPower> sasPowers = Utils.readSasPowers(DATA_FILE); checker = new PowerChecker(sasPowers, false); } /** * Test GLMM(F) with 1,2, and 3 Factor polynomial * contrasts in C and U matrices */ @Test public void testOneToThreeFactorPolynomialContrasts() { // set up the matrices GLMMPowerParameters params = buildInputsWithoutContrasts(); // run over all tests boolean first = true; for (GLMMTestFactory.Test test : GLMMTestFactory.Test.values()) { params.clearTestList(); params.addTest(test); // calculate all of the 3 factor polynomial contrasts ArrayList<Factor> withinFactorList = new ArrayList<Factor>(); withinFactorList.add(factorD); withinFactorList.add(factorE); withinFactorList.add(factorF); ArrayList<Factor> betweenFactorList = new ArrayList<Factor>(); betweenFactorList.add(factorA); betweenFactorList.add(factorB); betweenFactorList.add(factorC); OrthogonalPolynomialContrastCollection withinSubjectContrasts = OrthogonalPolynomials .withinSubjectContrast(withinFactorList); OrthogonalPolynomialContrastCollection betweenSubjectContrasts = OrthogonalPolynomials .betweenSubjectContrast(betweenFactorList); // run power for 1 factor contrasts RealMatrix U = withinSubjectContrasts.getMainEffectContrast(factorD).getContrastMatrix(); RealMatrix C = betweenSubjectContrasts.getMainEffectContrast(factorA).getContrastMatrix(); RealMatrix thetaNull = MatrixUtils.getRealMatrixWithFilledValue(C.getRowDimension(), U.getColumnDimension(), 0); params.setWithinSubjectContrast(U); params.setBetweenSubjectContrast(new FixedRandomMatrix(C.getData(), null, true)); params.setTheta(thetaNull); checker.checkPower(params); if (first) { matrixAltStringBuffer .append("\\newpage\\textbf{Contrasts for the test of the A x D interaction}\n\n"); appendMatrix("\\mathbf{C}'", C.transpose()); appendMatrix("\\mathbf{U}", U); } // run power for 2 factor contrasts ArrayList<Factor> intFactors = new ArrayList<Factor>(); intFactors.add(factorD); intFactors.add(factorE); U = withinSubjectContrasts.getInteractionContrast(intFactors).getContrastMatrix(); intFactors.clear(); intFactors.add(factorA); intFactors.add(factorB); C = betweenSubjectContrasts.getInteractionContrast(intFactors).getContrastMatrix(); thetaNull = MatrixUtils.getRealMatrixWithFilledValue(C.getRowDimension(), U.getColumnDimension(), 0); params.setWithinSubjectContrast(U); params.setBetweenSubjectContrast(new FixedRandomMatrix(C.getData(), null, true)); params.setTheta(thetaNull); checker.checkPower(params); if (first) { matrixAltStringBuffer .append("\\newpage\\textbf{Contrasts for the test of the A x B x D x E interaction}\n\n"); appendMatrix("\\mathbf{C}'", C.transpose()); appendMatrix("\\mathbf{U}", U); } // run power for 3 factor contrasts intFactors.clear(); intFactors.add(factorD); intFactors.add(factorE); intFactors.add(factorF); U = withinSubjectContrasts.getInteractionContrast(intFactors).getContrastMatrix(); intFactors.clear(); intFactors.add(factorA); intFactors.add(factorB); intFactors.add(factorC); C = betweenSubjectContrasts.getInteractionContrast(intFactors).getContrastMatrix(); thetaNull = MatrixUtils.getRealMatrixWithFilledValue(C.getRowDimension(), U.getColumnDimension(), 0); params.setWithinSubjectContrast(U); params.setBetweenSubjectContrast(new FixedRandomMatrix(C.getData(), null, true)); params.setTheta(thetaNull); checker.checkPower(params); if (first) { matrixAltStringBuffer.append( "\\newpage\\textbf{Contrasts for the test of the A x B x C x D x E x F interaction}\n\n"); appendMatrix("\\mathbf{C}'", C.transpose()); appendMatrix("\\mathbf{U}", U); first = false; } } // output the results // we reset the tests to include all params.clearTestList(); for (GLMMTestFactory.Test test : GLMMTestFactory.Test.values()) { params.addTest(test); } ValidationReportBuilder reportBuilder = new ValidationReportBuilder(); reportBuilder.createValidationReportAsStdout(checker, TITLE, false); assertTrue("results outside tolerance: " + TOLERANCE, checker.isSASDeviationBelowTolerance(TOLERANCE)); } /** * Sets up the basic X, beta matrices for each of the tests. The individual * tests create different contrast matrices * @return */ private GLMMPowerParameters buildInputsWithoutContrasts() { int Q = dataD.length * dataE.length * dataF.length; int P = dataA.length * dataB.length * dataC.length; // build the inputs GLMMPowerParameters params = new GLMMPowerParameters(); // add alpha values - bonferroni corrected for 6 comparisons params.addAlpha(0.05); // build the design matrix params.setDesignEssence(org.apache.commons.math3.linear.MatrixUtils.createRealIdentityMatrix(Q)); // add a concise representation of the design matrix to the alt matrix string matrixAltStringBuffer.append("\\begin{eqnarray*}\n"); matrixAltStringBuffer.append("\\underset{\\left(" + Q + "\\times" + Q + "\\right)}{\\text{Es}\\left(\\mathbf{X}\\right)} & = & I_{" + Q + "}\n"); matrixAltStringBuffer.append("\\end{eqnarray*}\n"); // build beta matrix RealMatrix beta = MatrixUtils.getRealMatrixWithFilledValue(Q, P, 0); beta.setEntry(0, 0, 1); params.setBeta(new FixedRandomMatrix(beta.getData(), null, false)); // add latex to represent matrix matrixAltStringBuffer.append("\\begin{eqnarray*}\n"); matrixAltStringBuffer.append("\\underset{\\left(" + Q + "\\times" + P + "\\right)}{\\mathbf{B}} & = & " + "\\begin{bmatrix}1 & 0 & \\ldots & 0\\\\\n" + "0 & & & \\vdots\\\\\n" + "\\vdots & & & \\vdots\\\\\n" + "0 & \\ldots & \\ldots & 0\n" + "\\end{bmatrix}\n"); matrixAltStringBuffer.append("\\end{eqnarray*}\n"); // add beta scale values params.addBetaScale(9); params.addBetaScale(18); params.addBetaScale(27); // build theta null matrix double[][] theta0 = { { 0, 0, 0, 0 } }; params.setTheta(new Array2DRowRealMatrix(theta0)); matrixAltStringBuffer.append("\\begin{eqnarray*}\n"); matrixAltStringBuffer .append("\\underset{\\left(" + 1 + "\\times" + 4 + "\\right)}{\\mathbf{\\Theta}_{0}} & = & " + "\\begin{bmatrix}0 & 0 & 0 & 0\n" + "\\end{bmatrix}\n"); matrixAltStringBuffer.append("\\end{eqnarray*}\n"); // build sigma matrix RealMatrix sigma = org.apache.commons.math3.linear.MatrixUtils.createRealIdentityMatrix(P); for (int i = 0; i < P; i++) sigma.setEntry(i, i, i + 1); params.setSigmaError(sigma); // add sigma scale values params.addSigmaScale(1); matrixAltStringBuffer.append("\\begin{eqnarray*}\n"); matrixAltStringBuffer.append("\\underset{\\left(" + P + "\\times" + P + "\\right)}{\\mathbf{\\Sigma}_{E}} & = & " + "\\begin{bmatrix}1 & 2 & 3 & \\ldots & " + P + "\n" + "\\end{bmatrix} \\times I_{" + P + "}\n"); matrixAltStringBuffer.append("\\end{eqnarray*}\n"); // add sample size multipliers for (int perGroupN = 2; perGroupN <= 12; perGroupN += 2) params.addSampleSize(perGroupN); //params.addSampleSize(2); return params; } /** * Write a matrix in latex * @param section * @param name * @param matrix */ private void appendMatrix(String name, RealMatrix matrix) { matrixAltStringBuffer.append("\\begin{eqnarray*}\n"); // add name label matrixAltStringBuffer.append("\\underset{\\left(" + matrix.getRowDimension() + "\\times" + matrix.getColumnDimension() + "\\right)}{" + name + "} & = & \\begin{bmatrix}"); for (int r = 0; r < matrix.getRowDimension(); r++) { boolean first = true; for (int c = 0; c < matrix.getColumnDimension(); c++) { if (!first) { matrixAltStringBuffer.append(" & "); } matrixAltStringBuffer.append(ShortNumber.format(matrix.getEntry(r, c))); if (first) { first = false; } } matrixAltStringBuffer.append("\\protect\\\\\n"); } matrixAltStringBuffer.append("\\end{bmatrix}\n"); matrixAltStringBuffer.append("\\end{eqnarray*}\n"); if (matrix.getColumnDimension() > 10) { matrixAltStringBuffer.append("\\normalsize\n"); } } }