package test.dr.evomodel.branchratemodel;
import dr.evolution.alignment.SitePatterns;
import dr.evolution.datatype.Nucleotides;
import dr.evolution.util.TaxonList;
import dr.evomodel.branchratemodel.RandomLocalClockModel;
import dr.evomodel.coalescent.CoalescentLikelihood;
import dr.evomodel.coalescent.ConstantPopulationModel;
import dr.evomodel.operators.ExchangeOperator;
import dr.evomodel.operators.SubtreeSlideOperator;
import dr.evomodel.operators.WilsonBalding;
import dr.oldevomodel.sitemodel.GammaSiteModel;
import dr.oldevomodel.substmodel.FrequencyModel;
import dr.oldevomodel.substmodel.HKY;
import dr.evomodel.tree.RateCovarianceStatistic;
import dr.evomodel.tree.RateStatistic;
import dr.oldevomodel.treelikelihood.TreeLikelihood;
import dr.evomodelxml.branchratemodel.RandomLocalClockModelParser;
import dr.evomodelxml.coalescent.ConstantPopulationModelParser;
import dr.oldevomodelxml.sitemodel.GammaSiteModelParser;
import dr.oldevomodelxml.substmodel.HKYParser;
import dr.evomodelxml.tree.RateStatisticParser;
import dr.oldevomodelxml.treelikelihood.TreeLikelihoodParser;
import dr.inference.distribution.DistributionLikelihood;
import dr.inference.loggers.ArrayLogFormatter;
import dr.inference.loggers.MCLogger;
import dr.inference.loggers.TabDelimitedFormatter;
import dr.inference.mcmc.MCMC;
import dr.inference.mcmc.MCMCOptions;
import dr.inference.model.*;
import dr.inference.operators.*;
import dr.inference.trace.ArrayTraceList;
import dr.inference.trace.Trace;
import dr.inference.trace.TraceCorrelation;
import dr.inferencexml.model.CompoundLikelihoodParser;
import dr.math.MathUtils;
import dr.math.distributions.GammaDistribution;
import dr.math.distributions.PoissonDistribution;
import junit.framework.Test;
import junit.framework.TestSuite;
import test.dr.inference.trace.TraceCorrelationAssert;
import java.util.ArrayList;
import java.util.List;
/**
* @author Walter Xie
* convert testRandomLocalClock.xml in the folder /example
* the Random Local Clock model has problem
*/
public class RandomLocalClockTestProblem extends TraceCorrelationAssert {
public RandomLocalClockTestProblem(String name) {
super(name);
}
public void setUp() throws Exception {
super.setUp();
MathUtils.setSeed(666);
createAlignment(PRIMATES_TAXON_SEQUENCE, Nucleotides.INSTANCE);
}
public void testRandomLocalClock() throws Exception {
Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 0.077, 0, Double.POSITIVE_INFINITY);
ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
CoalescentLikelihood coalescent = new CoalescentLikelihood(treeModel, null, new ArrayList<TaxonList>(), constantModel);
coalescent.setId("coalescent");
// clock model
Parameter ratesParameter = new Parameter.Default(RandomLocalClockModelParser.RATES, 10, 1);
Parameter rateIndicatorParameter = new Parameter.Default(RandomLocalClockModelParser.RATE_INDICATORS, 10, 1);
Parameter meanRateParameter = new Parameter.Default(RandomLocalClockModelParser.CLOCK_RATE, 1, 1.0);
RandomLocalClockModel branchRateModel = new RandomLocalClockModel(treeModel, meanRateParameter,
rateIndicatorParameter, ratesParameter, false, 0.5);
SumStatistic rateChanges = new SumStatistic("rateChangeCount", true);
rateChanges.addStatistic(rateIndicatorParameter);
RateStatistic meanRate = new RateStatistic("meanRate", treeModel, branchRateModel, true, true, RateStatisticParser.MEAN);
RateStatistic coefficientOfVariation = new RateStatistic(RateStatisticParser.COEFFICIENT_OF_VARIATION, treeModel, branchRateModel,
true, true, RateStatisticParser.COEFFICIENT_OF_VARIATION);
RateCovarianceStatistic covariance = new RateCovarianceStatistic("covariance", treeModel, branchRateModel);
// Sub model
Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, Double.POSITIVE_INFINITY);
FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
HKY hky = new HKY(kappa, f);
//siteModel
GammaSiteModel siteModel = new GammaSiteModel(hky);
Parameter mu = new Parameter.Default(GammaSiteModelParser.MUTATION_RATE, 1.0, 0, Double.POSITIVE_INFINITY);
siteModel.setMutationRateParameter(mu);
//treeLikelihood
SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, branchRateModel, null,
false, false, true, false, false);
treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
// Operators
OperatorSchedule schedule = new SimpleOperatorSchedule();
MCMCOperator operator = new ScaleOperator(kappa, 0.75);
operator.setWeight(1.0);
schedule.addOperator(operator);
operator = new ScaleOperator(ratesParameter, 0.75);
operator.setWeight(10.0);
schedule.addOperator(operator);
operator = new BitFlipOperator(rateIndicatorParameter, 15.0, true);
schedule.addOperator(operator);
operator = new ScaleOperator(popSize, 0.75);
operator.setWeight(3.0);
schedule.addOperator(operator);
Parameter rootHeight = treeModel.getRootHeightParameter();
rootHeight.setId(TREE_HEIGHT);
operator = new ScaleOperator(rootHeight, 0.75);
operator.setWeight(3.0);
schedule.addOperator(operator);
Parameter internalHeights = treeModel.createNodeHeightsParameter(false, true, false);
operator = new UniformOperator(internalHeights, 30.0);
schedule.addOperator(operator);
operator = new SubtreeSlideOperator(treeModel, 15.0, 0.0077, true, false, false, false, CoercionMode.COERCION_ON);
schedule.addOperator(operator);
operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 15.0);
// operator.doOperation();
schedule.addOperator(operator);
operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 3.0);
// operator.doOperation();
schedule.addOperator(operator);
operator = new WilsonBalding(treeModel, 3.0);
// operator.doOperation();
schedule.addOperator(operator);
//CompoundLikelihood
OneOnXPrior likelihood1 = new OneOnXPrior();
likelihood1.addData(popSize);
OneOnXPrior likelihood2 = new OneOnXPrior();
likelihood2.addData(kappa);
DistributionLikelihood likelihood3 = new DistributionLikelihood(new GammaDistribution(0.5, 2.0), 0.0);
likelihood3.addData(ratesParameter);
DistributionLikelihood likelihood4 = new DistributionLikelihood(new PoissonDistribution(1.0), 0.0);
likelihood4.addData(rateChanges);
List<Likelihood> likelihoods = new ArrayList<Likelihood>();
likelihoods.add(likelihood1);
likelihoods.add(likelihood2);
likelihoods.add(likelihood3);
likelihoods.add(likelihood4);
likelihoods.add(coalescent);
Likelihood prior = new CompoundLikelihood(0, likelihoods);
prior.setId(CompoundLikelihoodParser.PRIOR);
likelihoods.clear();
likelihoods.add(treeLikelihood);
Likelihood likelihood = new CompoundLikelihood(-1, likelihoods);
likelihoods.clear();
likelihoods.add(prior);
likelihoods.add(likelihood);
Likelihood posterior = new CompoundLikelihood(0, likelihoods);
posterior.setId(CompoundLikelihoodParser.POSTERIOR);
// Log
ArrayLogFormatter formatter = new ArrayLogFormatter(false);
MCLogger[] loggers = new MCLogger[2];
loggers[0] = new MCLogger(formatter, 1000, false);
loggers[0].add(posterior);
loggers[0].add(prior);
loggers[0].add(treeLikelihood);
loggers[0].add(rootHeight);
loggers[0].add(kappa);
// loggers[0].add(meanRate);
loggers[0].add(rateChanges);
loggers[0].add(coefficientOfVariation);
loggers[0].add(covariance);
loggers[0].add(popSize);
loggers[0].add(coalescent);
loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 10000, false);
loggers[1].add(posterior);
loggers[1].add(treeLikelihood);
loggers[1].add(rootHeight);
loggers[1].add(meanRate);
loggers[1].add(rateChanges);
// MCMC
MCMC mcmc = new MCMC("mcmc1");
MCMCOptions options = new MCMCOptions(1000000);
mcmc.setShowOperatorAnalysis(true);
mcmc.init(options, posterior, schedule, loggers);
mcmc.run();
// time
System.out.println(mcmc.getTimer().toString());
// Tracer
List<Trace> traces = formatter.getTraces();
ArrayTraceList traceList = new ArrayTraceList("RandomLocalClockTest", traces, 0);
for (int i = 1; i < traces.size(); i++) {
traceList.analyseTrace(i);
}
// <expectation name="posterior" value="-1818.26"/>
// <expectation name="prior" value="-2.70143"/>
// <expectation name="likelihood" value="-1815.56"/>
// <expectation name="treeModel.rootHeight" value="6.363E-2"/>
// <expectation name="constant.popSize" value="9.67405E-2"/>
// <expectation name="hky.kappa" value="30.0394"/>
// <expectation name="coefficientOfVariation" value="7.02408E-2"/>
// covariance 0.47952
// <expectation name="rateChangeCount" value="0.40786"/>
// <expectation name="coalescent" value="7.29521"/>
TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -1818.26);
likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.PRIOR));
assertExpectation(CompoundLikelihoodParser.PRIOR, likelihoodStats, -2.70143);
likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -1815.56);
TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
assertExpectation(TREE_HEIGHT, treeHeightStats, 6.363E-2);
TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
assertExpectation(HKYParser.KAPPA, kappaStats, 30.0394);
TraceCorrelation rateChangeStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("rateChangeCount"));
assertExpectation("rateChangeCount", rateChangeStats, 0.40786);
TraceCorrelation coefficientOfVariationStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(RateStatisticParser.COEFFICIENT_OF_VARIATION));
assertExpectation(RateStatisticParser.COEFFICIENT_OF_VARIATION, coefficientOfVariationStats, 7.02408E-2);
TraceCorrelation covarianceStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("covariance"));
assertExpectation("covariance", covarianceStats, 0.47952);
TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 9.67405E-2);
TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
assertExpectation("coalescent", coalescentStats, 7.29521);
}
public static Test suite() {
return new TestSuite(RandomLocalClockTestProblem.class);
}
}