/*
* 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.analysis;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.collections15.CollectionUtils;
import org.apache.commons.collections15.Predicate;
import org.drugis.addis.entities.Arm;
import org.drugis.addis.entities.Entity;
import org.drugis.addis.entities.Indication;
import org.drugis.addis.entities.Measurement;
import org.drugis.addis.entities.OutcomeMeasure;
import org.drugis.addis.entities.RateVariableType;
import org.drugis.addis.entities.Study;
import org.drugis.addis.entities.StudyArmsEntry;
import org.drugis.addis.entities.relativeeffect.BasicMeanDifference;
import org.drugis.addis.entities.relativeeffect.BasicOddsRatio;
import org.drugis.addis.entities.relativeeffect.BasicRelativeEffect;
import org.drugis.addis.entities.relativeeffect.GaussianBase;
import org.drugis.addis.entities.relativeeffect.RandomEffectMetaAnalysisRelativeEffect;
import org.drugis.addis.entities.relativeeffect.RandomEffectsRelativeEffect;
import org.drugis.addis.entities.relativeeffect.RelativeEffect;
import org.drugis.addis.entities.relativeeffect.RelativeEffectFactory;
import org.drugis.addis.entities.treatment.TreatmentDefinition;
import org.drugis.addis.util.EntityUtil;
import org.drugis.mtc.summary.MultivariateNormalSummary;
import org.drugis.mtc.summary.SimpleMultivariateNormalSummary;
public class RandomEffectsMetaAnalysis extends AbstractMetaAnalysis implements PairWiseMetaAnalysis {
private static final String ANALYSIS_TYPE = "DerSimonian-Laird Random Effects Meta-Analysis";
public static final String PROPERTY_INCLUDED_STUDIES_COUNT = "studiesIncluded";
public static final String PROPERTY_CORRECTED = "isCorrected";
private boolean d_isCorrected = false;
public RandomEffectsMetaAnalysis(String name, OutcomeMeasure om,
TreatmentDefinition baseline, TreatmentDefinition subject,
List<StudyArmsEntry> studyArms, boolean corr) {
super(ANALYSIS_TYPE, name, getIndication(studyArms), om,
getStudies(studyArms), Arrays.asList(baseline, subject),
getArmMap(baseline, subject, studyArms));
d_isCorrected = corr;
}
private static Map<Study, Map<TreatmentDefinition, Arm>> getArmMap(
TreatmentDefinition baseline, TreatmentDefinition subject,
List<StudyArmsEntry> studyArms) {
Map<Study, Map<TreatmentDefinition, Arm>> armMap = new HashMap<Study, Map<TreatmentDefinition, Arm>>();
for (StudyArmsEntry sae : studyArms) {
Map<TreatmentDefinition, Arm> alternativeMap = new HashMap<TreatmentDefinition, Arm>();
alternativeMap.put(baseline, sae.getBase());
alternativeMap.put(subject, sae.getSubject());
armMap.put(sae.getStudy(), alternativeMap);
}
return armMap;
}
private static List<Study> getStudies(List<StudyArmsEntry> studyArms) {
return StudyArmsEntry.getStudyList(studyArms);
}
private static Indication getIndication(List<StudyArmsEntry> studyArms) {
return getStudies(studyArms).get(0).getIndication();
}
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException{
in.defaultReadObject();
}
@Override
public TreatmentDefinition getFirstAlternative() {
return d_alternatives.get(0);
}
@Override
public TreatmentDefinition getSecondAlternative() {
return d_alternatives.get(1);
}
public List<StudyArmsEntry> getStudyArms() {
List<StudyArmsEntry> studyArms = new ArrayList<StudyArmsEntry>();
for (Study s : getIncludedStudies()) {
studyArms.add(new StudyArmsEntry(s, getArm(s, getFirstAlternative()), getArm(s, getSecondAlternative())));
}
return studyArms;
}
List<RelativeEffect<? extends Measurement>> getRelativeEffects(Class<? extends RelativeEffect<?>> type) {
List<RelativeEffect<? extends Measurement>> relEffects = new ArrayList<RelativeEffect<? extends Measurement>>();
for (StudyArmsEntry entry : getStudyArms()) {
relEffects.add((BasicRelativeEffect<? extends Measurement>) RelativeEffectFactory.buildRelativeEffect(entry, d_outcome, type, d_isCorrected));
}
return relEffects;
}
List<RelativeEffect<? extends Measurement>> getFilteredRelativeEffects(Class<? extends RelativeEffect<?>> type) {
final List<RelativeEffect<? extends Measurement>> relativeEffects = getRelativeEffects(type);
CollectionUtils.filter(relativeEffects, new Predicate<RelativeEffect<? extends Measurement>>() {
public boolean evaluate(RelativeEffect<? extends Measurement> re) {
return re.isDefined();
}
});
return relativeEffects;
}
public RandomEffectMetaAnalysisRelativeEffect<Measurement> getRelativeEffect(Class<? extends RelativeEffect<?>> type) {
final List<RelativeEffect<? extends Measurement>> relativeEffects = getFilteredRelativeEffects(type);
if (relativeEffects.isEmpty()) {
return null;
}
return new RandomEffectsRelativeEffect(relativeEffects);
}
public boolean getIsCorrected() {
return d_isCorrected;
}
public void setIsCorrected(boolean iscorrected) {
boolean oldVal = d_isCorrected;
d_isCorrected = iscorrected;
firePropertyChange(PROPERTY_CORRECTED, oldVal, d_isCorrected);
}
@Override
public boolean deepEquals(Entity other) {
if (!super.deepEquals(other)) {
return false;
}
RandomEffectsMetaAnalysis o = (RandomEffectsMetaAnalysis) other;
for (StudyArmsEntry s : o.getStudyArms()) {
if ( !EntityUtil.deepEqual(s.getBase(), getArm(s.getStudy(), o.getFirstAlternative())) ||
!EntityUtil.deepEqual(s.getSubject(), getArm(s.getStudy(), o.getSecondAlternative()))) {
return false;
}
}
return true;
}
@Override
public MultivariateNormalSummary getRelativeEffectsSummary() {
Class<? extends RelativeEffect<?>> type = (d_outcome.getVariableType() instanceof RateVariableType) ?
BasicOddsRatio.class : BasicMeanDifference.class;
RelativeEffect<Measurement> effect = getRelativeEffect(type);
GaussianBase distribution = (GaussianBase) effect.getDistribution();
return new SimpleMultivariateNormalSummary(
new double[]{ distribution.getMu() },
new double[][] { { distribution.getSigma() * distribution.getSigma() } });
}
}