CorrectedRiskRatioTest.java

/*
 * 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, Joël Kuiper, Wouter
 * Reckman.
 * Copyright © 2013 Gert van Valkenhoef, Joël 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.entities.relativeeffect;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;

import org.drugis.addis.ExampleData;
import org.drugis.addis.entities.BasicRateMeasurement;
import org.drugis.addis.entities.RateMeasurement;
import org.drugis.addis.entities.Study;
import org.drugis.addis.entities.treatment.TreatmentDefinition;
import org.junit.Before;
import org.junit.Test;

public class CorrectedRiskRatioTest extends RelativeEffectTestBase {
	private BasicRiskRatio d_riskRatio;
	
	@Before
	public void setUp() {
		Study study = ExampleData.buildRateStudy("A", 0, 144, 73, 142);
		d_riskRatio = (BasicRiskRatio) RelativeEffectFactory.buildRelativeEffect(study, d_rateEndpoint, TreatmentDefinition.createTrivial(d_fluox), TreatmentDefinition.createTrivial(d_sertr), BasicRiskRatio.class, true);
	}

	@Test
	public void testMu() {
		// c=0.5, n2 = 145, a = 73.5, n1 = 143 -> b = 69.5, d = 144.5
		Double expected = Math.log((73.5 / 143) / (0.5 / 145));
		assertEquals(expected, d_riskRatio.getMu(), 0.000001);
	}
	
	@Test
	public void testError() {
		// c=0.5, n2 = 145, a = 73.5, n1 = 143 -> b = 69.5, d = 144.5
		Double expected = Math.sqrt(1.0 / 73.5 + 1.0 / 0.5 - 1.0 / 143.0 - 1.0 / 145.0);
		assertEquals(expected, d_riskRatio.getError(), 0.00001);
		
	}

	@Test
	public void testZeroBaselineRateShouldBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(0, 100);
		RateMeasurement subj = new BasicRateMeasurement(50, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertTrue(or.isDefined());
	}
	
	@Test
	public void testZeroRateBaselineAndSubjectShouldNotBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(0, 100);
		RateMeasurement subj = new BasicRateMeasurement(0, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertFalse(or.isDefined());
	}
	
	@Test
	public void testZeroSubjectRateShouldBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(50, 100);
		RateMeasurement subj = new BasicRateMeasurement(0, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertTrue(or.isDefined());
	}

	@Test
	public void testFullBaselineRateShouldBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(100, 100);
		RateMeasurement subj = new BasicRateMeasurement(50, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertTrue(or.isDefined());
	}
	
	@Test
	public void testFullRateBaselineAndSubjectShouldNotBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(100, 100);
		RateMeasurement subj = new BasicRateMeasurement(100, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertFalse(or.isDefined());
	}
	
	@Test
	public void testFullSubjectRateShouldBeDefined() {
		RateMeasurement base = new BasicRateMeasurement(50, 100);
		RateMeasurement subj = new BasicRateMeasurement(100, 100);
		CorrectedBasicRiskRatio or = new CorrectedBasicRiskRatio(base, subj);
		assertTrue(or.isDefined());
	}
	
	@Test
	public void testUndefinedShouldResultInNaN() {
		RateMeasurement rmA1 = new BasicRateMeasurement(0, 100);
		RateMeasurement rmC1 = new BasicRateMeasurement(0, 100);
		BasicRiskRatio or = new CorrectedBasicRiskRatio(rmA1, rmC1);
		assertEquals(Double.NaN, or.getError(), 0.001);
		assertEquals(Double.NaN, or.getMu(), 0.001);
		assertEquals(Double.NaN, or.getConfidenceInterval().getPointEstimate(), 0.001);
	}

	@Test
	public void testDefinedShouldNotResultInNaN() {
		RateMeasurement rmA1 = new BasicRateMeasurement(0, 100);
		RateMeasurement rmC1 = new BasicRateMeasurement(50, 100);
		BasicRiskRatio or = new CorrectedBasicRiskRatio(rmA1, rmC1);
		assertFalse(or.getError() == Double.NaN);
		assertFalse(or.getMu() == Double.NaN);
		assertFalse(Double.NaN == or.getConfidenceInterval().getPointEstimate()); 
	}
}