/*
* #%L
* gitools-core
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* 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/gpl-3.0.html>.
* #L%
*/
package org.gitools.analysis.stats.test;
import com.google.common.collect.Lists;
import com.google.common.primitives.Doubles;
import org.apache.commons.math3.stat.inference.OneWayAnova;
import org.apache.commons.math3.stat.ranking.NaNStrategy;
import org.apache.commons.math3.stat.ranking.NaturalRanking;
import org.apache.commons.math3.stat.ranking.TiesStrategy;
import org.gitools.analysis.stats.test.results.OneWayAnovaResult;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
public class OneWayAnovaTest extends AbstractEnrichmentTest {
private NaturalRanking naturalRanking;
public OneWayAnovaTest() {
super("oneWayAnova", OneWayAnovaResult.class);
naturalRanking = new NaturalRanking(NaNStrategy.FIXED, TiesStrategy.AVERAGE);
}
public OneWayAnovaResult processTest(List<Iterable<Double>> groups) {
Collection<double[]> groupsCollection = new ArrayList<>();
//int[] groupNs = new int[groups.size()];
ArrayList<Integer> groupNs = new ArrayList<>();
int counter = 0;
int totalN = 0;
int minN = 0;
for (Iterable<Double> g : groups) {
double[] doubles = Doubles.toArray(Lists.newArrayList(g));
if (doubles.length > 1) {
groupsCollection.add(doubles);
totalN += doubles.length;
minN = minN == 0 ? doubles.length : Math.min(doubles.length, minN);
groupNs.add(doubles.length);
}
}
OneWayAnova anova = new OneWayAnova();
if (groupNs.size() > 1) {
double pvalue = anova.anovaPValue(groupsCollection);
double fvalue = anova.anovaFValue(groupsCollection);
return new OneWayAnovaResult(totalN, minN, groupNs.size(), pvalue, fvalue);
} else {
return new OneWayAnovaResult(totalN, minN, groupNs.size(), Double.NaN, Double.NaN);
}
}
}