Examples with SubtreeSlideOperator dr.evomodel.operators.SubtreeSlideOperator used on opensource projects

Example 1 with SubtreeSlideOperator

use of dr.evomodel.operators.SubtreeSlideOperator in project beast-mcmc by beast-dev.

the class SubtreeSlideOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean swapRates = xo.getAttribute(SWAP_RATES, false);
    boolean swapTraits = xo.getAttribute(SWAP_TRAITS, false);
    boolean scaledDirichletBranches = xo.getAttribute(DIRICHLET_BRANCHES, false);
    AdaptationMode mode = AdaptationMode.DEFAULT;
    if (xo.hasAttribute(AdaptableMCMCOperator.AUTO_OPTIMIZE)) {
        if (xo.getBooleanAttribute(AdaptableMCMCOperator.AUTO_OPTIMIZE)) {
            mode = AdaptationMode.ADAPTATION_ON;
        } else {
            mode = AdaptationMode.ADAPTATION_OFF;
        }
    }
    DefaultTreeModel treeModel = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final double targetAcceptance = xo.getAttribute(TARGET_ACCEPTANCE, 0.234);
    final double size = xo.getAttribute("size", 1.0);
    if (Double.isInfinite(size) || size <= 0.0) {
        throw new XMLParseException("size attribute must be positive and not infinite. was " + size + " for tree " + treeModel.getId());
    }
    final boolean gaussian = xo.getBooleanAttribute("gaussian");
    SubtreeSlideOperator operator = new SubtreeSlideOperator(treeModel, weight, size, gaussian, swapRates, swapTraits, scaledDirichletBranches, mode, targetAcceptance);
    return operator;
}

Example 2 with SubtreeSlideOperator

use of dr.evomodel.operators.SubtreeSlideOperator in project beast-mcmc by beast-dev.

the class YuleModelTest method testYuleWithSubtreeSlide.

public void testYuleWithSubtreeSlide() {
    DefaultTreeModel treeModel = new DefaultTreeModel("treeModel", tree);
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    MCMCOperator operator = new SubtreeSlideOperator(treeModel, 1, 1, true, false, false, false, AdaptationMode.ADAPTATION_ON, AdaptableMCMCOperator.DEFAULT_ADAPTATION_TARGET);
    schedule.addOperator(operator);
    yuleTester(treeModel, schedule);
}

Example 3 with SubtreeSlideOperator

use of dr.evomodel.operators.SubtreeSlideOperator in project beast-mcmc by beast-dev.

the class StrictClockTest method testStrictClock.

public void testStrictClock() throws Exception {
    Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 380.0, 0, 38000.0);
    ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
    TreeIntervals intervalList = new TreeIntervals(treeModel, null, null);
    CoalescentLikelihood coalescent = new CoalescentLikelihood(intervalList, constantModel);
    coalescent.setId("coalescent");
    // clock model
    Parameter rateParameter = new Parameter.Default(StrictClockBranchRates.RATE, 2.3E-5, 0, 100.0);
    StrictClockBranchRates branchRateModel = new StrictClockBranchRates(rateParameter);
    // Sub model
    Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
    Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 0, 100.0);
    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(rateParameter, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter allInternalHeights = ((DefaultTreeModel) treeModel).createNodeHeightsParameter(true, true, false);
    operator = new UpDownOperator(new Scalable[] { new Scalable.Default(rateParameter) }, new Scalable[] { new Scalable.Default(allInternalHeights) }, 0.75, 3.0, AdaptationMode.ADAPTATION_ON);
    schedule.addOperator(operator);
    operator = new ScaleOperator(popSize, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter rootHeight = ((DefaultTreeModel) treeModel).getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter internalHeights = ((DefaultTreeModel) treeModel).createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 30.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(((DefaultTreeModel) treeModel), 15.0, 1.0, true, false, false, false, AdaptationMode.ADAPTATION_ON, AdaptableMCMCOperator.DEFAULT_ADAPTATION_TARGET);
    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
    List<Likelihood> likelihoods = new ArrayList<Likelihood>();
    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, 500, false);
    loggers[0].add(posterior);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(rateParameter);
    loggers[0].add(popSize);
    loggers[0].add(kappa);
    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(rateParameter);
    loggers[1].add(coalescent);
    // 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="-3928.71"/>
    // <expectation name="clock.rate" value="8.04835E-4"/>
    // <expectation name="constant.popSize" value="37.3762"/>
    // <expectation name="hky.kappa" value="18.2782"/>
    // <expectation name="treeModel.rootHeight" value="69.0580"/>
    // <expectation name="treeLikelihood" value="-3856.59"/>
    // <expectation name="coalescent" value="-72.1285"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
    assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -3928.71);
    likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -3856.59);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 69.0580);
    TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
    assertExpectation(HKYParser.KAPPA, kappaStats, 18.2782);
    TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(StrictClockBranchRates.RATE));
    assertExpectation(StrictClockBranchRates.RATE, rateStats, 8.04835E-4);
    TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
    assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 37.3762);
    TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
    assertExpectation("coalescent", coalescentStats, -72.1285);
}

Example 4 with SubtreeSlideOperator

use of dr.evomodel.operators.SubtreeSlideOperator in project beast-mcmc by beast-dev.

the class GeneralSubstitutionModelTest method testGeneralSubstitutionModel.

public void testGeneralSubstitutionModel() {
    // Sub model
    FrequencyModel freqModel = new FrequencyModel(dataType, alignment.getStateFrequencies());
    // dimension="5" value="1.0"
    Parameter ratesPara = new Parameter.Default(GeneralSubstitutionModelParser.RATES, 5, 1.0);
    // relativeTo="5"
    GeneralSubstitutionModel generalSubstitutionModel = new GeneralSubstitutionModel(dataType, freqModel, ratesPara, 4);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(generalSubstitutionModel);
    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, null, null, false, false, true, false, false);
    treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
    // Operators
    OperatorSchedule schedule = new SimpleOperatorSchedule();
    MCMCOperator operator = new ScaleOperator(ratesPara, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    Parameter rootHeight = ((DefaultTreeModel) treeModel).getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.5);
    operator.setWeight(1.0);
    schedule.addOperator(operator);
    Parameter internalHeights = ((DefaultTreeModel) treeModel).createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 10.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(((DefaultTreeModel) treeModel), 1, 1, true, false, false, false, AdaptationMode.ADAPTATION_ON, AdaptableMCMCOperator.DEFAULT_ADAPTATION_TARGET);
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    operator = new ExchangeOperator(ExchangeOperator.WIDE, treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    operator = new WilsonBalding(treeModel, 1.0);
    // operator.doOperation();
    schedule.addOperator(operator);
    // Log
    ArrayLogFormatter formatter = new ArrayLogFormatter(false);
    MCLogger[] loggers = new MCLogger[2];
    loggers[0] = new MCLogger(formatter, 1000, false);
    loggers[0].add(treeLikelihood);
    loggers[0].add(rootHeight);
    loggers[0].add(ratesPara);
    loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 100000, false);
    loggers[1].add(treeLikelihood);
    loggers[1].add(rootHeight);
    loggers[1].add(ratesPara);
    // MCMC
    MCMC mcmc = new MCMC("mcmc1");
    MCMCOptions options = new MCMCOptions(10000000);
    mcmc.setShowOperatorAnalysis(true);
    mcmc.init(options, treeLikelihood, schedule, loggers);
    mcmc.run();
    // time
    System.out.println(mcmc.getTimer().toString());
    // Tracer
    List<Trace> traces = formatter.getTraces();
    ArrayTraceList traceList = new ArrayTraceList("GeneralSubstitutionModelTest", traces, 0);
    for (int i = 1; i < traces.size(); i++) {
        traceList.analyseTrace(i);
    }
    // <expectation name="likelihood" value="-1815.75"/>
    // <expectation name="treeModel.rootHeight" value="6.42048E-2"/>
    // <expectation name="rateAC" value="6.08986E-2"/>
    TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
    assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -1815.75);
    TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
    assertExpectation(TREE_HEIGHT, treeHeightStats, 0.0640787258170083);
    TraceCorrelation rateACStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(GeneralSubstitutionModelParser.RATES + "1"));
    assertExpectation(GeneralSubstitutionModelParser.RATES + "1", rateACStats, 0.061071756742081366);
}

Example 5 with SubtreeSlideOperator

use of dr.evomodel.operators.SubtreeSlideOperator in project beast-mcmc by beast-dev.

the class RandomLocalClockTestProblem method testRandomLocalClock.

public void testRandomLocalClock() throws Exception {
    Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 0.077, 0, Double.POSITIVE_INFINITY);
    ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
    TreeIntervals intervalList = new TreeIntervals(treeModel, null, null);
    CoalescentLikelihood coalescent = new CoalescentLikelihood(intervalList, 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, null);
    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 = ((DefaultTreeModel) treeModel).getRootHeightParameter();
    rootHeight.setId(TREE_HEIGHT);
    operator = new ScaleOperator(rootHeight, 0.75);
    operator.setWeight(3.0);
    schedule.addOperator(operator);
    Parameter internalHeights = ((DefaultTreeModel) treeModel).createNodeHeightsParameter(false, true, false);
    operator = new UniformOperator(internalHeights, 30.0);
    schedule.addOperator(operator);
    operator = new SubtreeSlideOperator(((DefaultTreeModel) treeModel), 15.0, 0.0077, true, false, false, false, AdaptationMode.ADAPTATION_ON, AdaptableMCMCOperator.DEFAULT_ADAPTATION_TARGET);
    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);
}