Java tutorial
/* * This file is part of ADDIS (Aggregate Data Drug Information System). * ADDIS is distributed from http://drugis.org/. * Copyright 2009 Gert van Valkenhoef, Tommi Tervonen. * Copyright 2010 Gert van Valkenhoef, Tommi Tervonen, Tijs Zwinkels, * Maarten Jacobs, Hanno Koeslag, Florin Schimbinschi, Ahmad Kamal, Daniel * Reid. * Copyright 2011 Gert van Valkenhoef, Ahmad Kamal, Daniel Reid, Florin * Schimbinschi. * Copyright 2012 Gert van Valkenhoef, Daniel Reid, Jol Kuiper, Wouter * Reckman. * Copyright 2013 Gert van Valkenhoef, Jol Kuiper. * * 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.addis.util.JSMAAintegration; import static org.junit.Assert.assertArrayEquals; import static org.junit.Assert.assertEquals; import java.io.FileNotFoundException; import java.io.IOException; import java.util.ArrayList; import java.util.List; import org.apache.commons.math3.linear.RealVector; import org.drugis.addis.entities.Domain; import org.drugis.addis.entities.DomainManager; import org.drugis.addis.entities.OutcomeMeasure; import org.drugis.addis.entities.analysis.MetaBenefitRiskAnalysis; import org.drugis.addis.gui.AddisMCMCPresentation; import org.drugis.addis.entities.treatment.TreatmentDefinition; import org.drugis.addis.presentation.MetaBenefitRiskPresentation; import org.drugis.addis.presentation.SMAAPresentation; import org.drugis.addis.util.EntityUtil; import org.drugis.common.threading.TaskUtil; import org.drugis.mtc.MCMCModel.ExtendSimulation; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; import fi.smaa.common.RandomUtil; import fi.smaa.jsmaa.model.Alternative; import fi.smaa.jsmaa.model.Criterion; import fi.smaa.jsmaa.model.CriterionMeasurement; import fi.smaa.jsmaa.model.GaussianMeasurement; import fi.smaa.jsmaa.model.PerCriterionMeasurements; import fi.smaa.jsmaa.model.RelativeGaussianCriterionMeasurement; import fi.smaa.jsmaa.model.RelativeLogitGaussianCriterionMeasurement; import fi.smaa.jsmaa.model.SMAAModel; import fi.smaa.jsmaa.simulator.SMAA2Simulation; /** * Test results of MetaBenefitRisk implementation against results of our published analysis. * This test calculates the MTC results in ADDIS using the underlying trial data. * @see <a href="http://drugis.org/network-br">network-br paper</a> */ public class NetworkBenefitRiskIT extends NetworkBenefitRiskTestBase { private static DomainManager d_domainManager; private static MetaBenefitRiskAnalysis d_br; private static MetaBenefitRiskPresentation d_brpm; private static SMAAModel d_model; @BeforeClass public static void setUp() throws IOException, InterruptedException { System.out.println("BeforeClass -- Running models"); d_domainManager = new DomainManager(); d_domainManager.loadXMLDomain(NetworkBenefitRiskIT.class.getResourceAsStream("network-br.addis"), 1); final Domain domain = d_domainManager.getDomain(); d_br = (MetaBenefitRiskAnalysis) domain.getBenefitRiskAnalyses().get(0); d_brpm = new MetaBenefitRiskPresentation(d_br, null); for (final AddisMCMCPresentation model : d_brpm.getWrappedModels()) { System.out.println("Running " + model); model.getModel().setSimulationIterations(100000); model.getModel().setExtendSimulation(ExtendSimulation.FINISH); TaskUtil.run(model.getModel().getActivityTask()); } // Build SMAA model SMAAPresentation<TreatmentDefinition, MetaBenefitRiskAnalysis> smaapm = d_brpm.getSMAAPresentation(); d_model = smaapm.getSMAAFactory().createSMAAModel(); } @AfterClass public static void cleanUp() { d_domainManager = null; d_br = null; d_brpm = null; d_model = null; } /** * Test SMAA using measurements derived using the internal MTC models. */ @Test public void testNetworkBRBaseline() { // Test results of underlying models verifyBaselineMeasurement(d_br, "HAM-D Responders", -0.17, 0.11); verifyBaselineMeasurement(d_br, "Diarrhea", -2.19, 0.21); verifyBaselineMeasurement(d_br, "Dizziness", -2.23, 0.61); verifyBaselineMeasurement(d_br, "Headache", -1.20, 0.29); verifyBaselineMeasurement(d_br, "Insomnia", -2.61, 0.19); verifyBaselineMeasurement(d_br, "Nausea", -2.02, 0.19); } @Test public void testNetworkBRRelativeEffects() throws FileNotFoundException, IOException, InterruptedException { List<Alternative> alternatives = new ArrayList<Alternative>(d_model.getAlternatives()); alternatives = movePlacebo(alternatives, findPlacebo(alternatives), 0); // The build* expect placebo first verifyRelativeEffects(d_brpm, d_model, "HAM-D Responders", buildHAMD(alternatives)); verifyRelativeEffects(d_brpm, d_model, "Diarrhea", buildDiarrhea(alternatives)); verifyRelativeEffects(d_brpm, d_model, "Dizziness", buildDizziness(alternatives)); verifyRelativeEffects(d_brpm, d_model, "Headache", buildHeadache(alternatives)); verifyRelativeEffects(d_brpm, d_model, "Insomnia", buildInsomnia(alternatives)); verifyRelativeEffects(d_brpm, d_model, "Nausea", buildNausea(alternatives)); } @Test public void testNetworkBRModel() throws InterruptedException { // Reorder criteria final List<Criterion> newCrit = new ArrayList<Criterion>(d_model.getCriteria()); final Criterion hamd = newCrit.remove(0); assertEquals("HAM-D Responders", hamd.getName()); newCrit.add(2, hamd); d_model.reorderCriteria(newCrit); // Run SMAA final RandomUtil random = RandomUtil.createWithRandomSeed(); final SMAA2Simulation simulation = new SMAA2Simulation(d_model, random, 10000); TaskUtil.run(simulation.getTask()); checkResults(d_model, simulation, 2.0); } private static void verifyRelativeEffects(final MetaBenefitRiskPresentation brpm, final SMAAModel model, final String name, final CriterionMeasurement expected) { final PerCriterionMeasurements measurements = (PerCriterionMeasurements) model.getMeasurements(); final CriterionMeasurement actual = measurements.getCriterionMeasurement(brpm.getSMAAPresentation() .getSMAAFactory().getCriterion(EntityUtil.findByName(brpm.getBean().getCriteria(), name))); actual.reorderAlternatives(movePlacebo(actual.getAlternatives(), findPlacebo(actual.getAlternatives()), 2)); // Reorder alternatives expected.reorderAlternatives( movePlacebo(expected.getAlternatives(), findPlacebo(expected.getAlternatives()), 2)); // Reorder alternatives assertRelativeLogitEquals((RelativeLogitGaussianCriterionMeasurement) expected, (RelativeLogitGaussianCriterionMeasurement) actual, 0.05); } private static void assertRelativeLogitEquals(final RelativeLogitGaussianCriterionMeasurement expected, final RelativeLogitGaussianCriterionMeasurement actual, final double d) { assertRelativeGaussian(expected.getGaussianMeasurement(), actual.getGaussianMeasurement(), d); } private static void assertRelativeGaussian(final RelativeGaussianCriterionMeasurement expected, final RelativeGaussianCriterionMeasurement actual, final double d) { final GaussianMeasurement expectedBaseline = expected.getBaselineMeasurement(); final GaussianMeasurement actualBaseline = actual.getBaselineMeasurement(); assertEquals(expectedBaseline.getMean(), actualBaseline.getMean(), d); assertEquals(expectedBaseline.getStDev(), actualBaseline.getStDev(), d); final double[] expectedCovariance = flatten( expected.getRelativeMeasurement().getCovarianceMatrix().getData()); final double[] actualCovariance = flatten(actual.getRelativeMeasurement().getCovarianceMatrix().getData()); assertArrayEquals(expectedCovariance, actualCovariance, d); final RealVector expectedMeanVector = expected.getRelativeMeasurement().getMeanVector(); final RealVector actualMeanVector = actual.getRelativeMeasurement().getMeanVector(); assertArrayEquals(expectedMeanVector.toArray(), actualMeanVector.toArray(), d); } private static void verifyBaselineMeasurement(final MetaBenefitRiskAnalysis br, final String name, final double mu, final double sigma) { final OutcomeMeasure om = EntityUtil.findByName(br.getCriteria(), name); assertEquals(sigma, br.getBaselineDistribution(om).getSigma(), 0.05); assertEquals(mu, br.getBaselineDistribution(om).getMu(), 0.05); } private static int findPlacebo(final List<Alternative> alternatives) { int expPlaceboIdx = 0; for (int idx = 0; idx < alternatives.size(); idx++) { if (alternatives.get(idx).getName().equals("Placebo")) { expPlaceboIdx = idx; } } return expPlaceboIdx; } private static double[] flatten(final double[][] matrix2d) { final double[] newArray = new double[2 * matrix2d[0].length]; int index = 0; for (int n = 0; n < matrix2d[0].length; n++) { newArray[index++] = matrix2d[0][n]; newArray[index++] = matrix2d[1][n]; } return newArray; } }