package test.dr.evomodel.branchratemodel;
import dr.inference.model.Parameter;
import test.dr.inference.trace.TraceCorrelationAssert;
/**
* @author Walter Xie
* convert testUncorrelatedRelaxedClock.xml in the folder /example
*/
public class UncorrelatedRelaxedClockTest extends TraceCorrelationAssert {
private Parameter meanParam;
private Parameter stdevParam;
public UncorrelatedRelaxedClockTest(String name) {
super(name);
}
// public void setUp() throws Exception {
// super.setUp();
//
// MathUtils.setSeed(666);
//
// createAlignment(DENGUE4_TAXON_SEQUENCE, Nucleotides.INSTANCE);
// }
//
// public void testLogNormal() throws Exception {
// meanParam = new Parameter.Default(LogNormalDistributionModelParser.MEAN, 2.3E-5, 0, 100.0);
// stdevParam = new Parameter.Default(LogNormalDistributionModelParser.STDEV, 0.1, 0, 10.0);
// ParametricDistributionModel distributionModel = new LogNormalDistributionModel(meanParam, stdevParam, 0.0, true, false); // meanInRealSpace="true"
//
// ArrayTraceList traceList = UncorrelatedRelaxedClock(distributionModel);
//
//// <expectation name="posterior" value="-3927.81"/>
//// <expectation name="ucld.mean" value="8.28472E-4"/>
//// <expectation name="ucld.stdev" value="0.17435"/>
//// <expectation name="meanRate" value="8.09909E-4"/>
//// <expectation name="coefficientOfVariation" value="0.15982"/>
//// <expectation name="covariance" value="-3.81803E-2"/>
//// <expectation name="constant.popSize" value="37.3524"/>
//// <expectation name="hky.kappa" value="18.3053"/>
//// <expectation name="treeModel.rootHeight" value="69.2953"/>
//// <expectation name="treeLikelihood" value="-3855.78"/>
//// <expectation name="skyline" value="-72.0313"/> ???
//
// TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
// assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -3927.81);
//
// likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
// assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -3855.78);
//
// TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
// assertExpectation(TREE_HEIGHT, treeHeightStats, 69.2953);
//
// TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
// assertExpectation(HKYParser.KAPPA, kappaStats, 18.06518);
//
// TraceCorrelation ucldStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(LogNormalDistributionModelParser.MEAN));
// assertExpectation(LogNormalDistributionModelParser.MEAN, ucldStats, 8.0591451486E-4);
//
// ucldStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(LogNormalDistributionModelParser.STDEV));
// assertExpectation(LogNormalDistributionModelParser.STDEV, ucldStats, 0.16846023066431434);
//
// TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("meanRate"));
// assertExpectation("meanRate", rateStats, 8.010906E-4);
//
// TraceCorrelation coefficientOfVariationStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(RateStatisticParser.COEFFICIENT_OF_VARIATION));
// assertExpectation(RateStatisticParser.COEFFICIENT_OF_VARIATION, coefficientOfVariationStats, 0.15982);
//
// TraceCorrelation covarianceStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("covariance"));
// assertExpectation("covariance", covarianceStats, -0.0260333026);
//
// TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
// assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 37.3524);
//
// TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
// assertExpectation("coalescent", coalescentStats, -72.0313);
// }
//
// public void testExponential() throws Exception {
// meanParam = new Parameter.Default(1.0);
// meanParam.setId(DistributionModelParser.MEAN);
// stdevParam = null;
// ParametricDistributionModel distributionModel = new ExponentialDistributionModel(meanParam); // offset = 0
//
// ArrayTraceList traceList = UncorrelatedRelaxedClock(distributionModel);
//
// TraceCorrelation likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(CompoundLikelihoodParser.POSTERIOR));
// assertExpectation(CompoundLikelihoodParser.POSTERIOR, likelihoodStats, -3958.7409);
//// System.out.println("likelihoodStats = " + likelihoodStats.getMean());
//
// likelihoodStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TreeLikelihoodParser.TREE_LIKELIHOOD));
// assertExpectation(TreeLikelihoodParser.TREE_LIKELIHOOD, likelihoodStats, -3885.26939);
//// System.out.println("treelikelihoodStats = " + likelihoodStats.getMean());
//
// TraceCorrelation treeHeightStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(TREE_HEIGHT));
// assertExpectation(TREE_HEIGHT, treeHeightStats, 84.3529526);
//
// TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
// assertExpectation(HKYParser.KAPPA, kappaStats, 18.38065);
//
// TraceCorrelation ucedStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(DistributionModelParser.MEAN));
// assertExpectation(DistributionModelParser.MEAN, ucedStats, 0.0019344134887784579);
//// System.out.println("ucedStats = " + ucedStats.getMean());
//
// TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("meanRate"));
// assertExpectation("meanRate", rateStats, 0.0020538802366337084);
//// System.out.println("rateStats = " + rateStats.getMean());
//
// TraceCorrelation coefficientOfVariationStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(RateStatisticParser.COEFFICIENT_OF_VARIATION));
// assertExpectation(RateStatisticParser.COEFFICIENT_OF_VARIATION, coefficientOfVariationStats, 0.773609960455);
//// System.out.println("coefficientOfVariationStats = " + coefficientOfVariationStats.getMean());
//
// TraceCorrelation covarianceStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("covariance"));
// assertExpectation("covariance", covarianceStats, -0.07042030641301375);
//// System.out.println("covarianceStats = " + covarianceStats.getMean());
//
// TraceCorrelation popStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(ConstantPopulationModelParser.POPULATION_SIZE));
// assertExpectation(ConstantPopulationModelParser.POPULATION_SIZE, popStats, 43.4478);
//// System.out.println("popStats = " + popStats.getMean());
//
// TraceCorrelation coalescentStats = traceList.getCorrelationStatistics(traceList.getTraceIndex("coalescent"));
// assertExpectation("coalescent", coalescentStats, -73.4715);
//// System.out.println("coalescentStats = " + coalescentStats.getMean());
// }
//
// private ArrayTraceList UncorrelatedRelaxedClock(ParametricDistributionModel distributionModel) throws Exception {
// Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 380.0, 0, 38000.0);
// ConstantPopulationModel constantModel = createRandomInitialTree(popSize);
//
// CoalescentLikelihood coalescent = new CoalescentLikelihood(treeModel, null, new ArrayList<TaxonList>(), constantModel);
// coalescent.setId("coalescent");
//
// // clock model
// Parameter rateCategoryParameter = new Parameter.Default(32);
// rateCategoryParameter.setId(DiscretizedBranchRates.BRANCH_RATES);
//
// DiscretizedBranchRates branchRateModel = new DiscretizedBranchRates(treeModel, rateCategoryParameter,
// distributionModel, 1, false, Double.NaN, false, false);
//
// 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, 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(meanParam, 0.75);
// operator.setWeight(3.0);
// schedule.addOperator(operator);
//
// if (stdevParam != null) {
// operator = new ScaleOperator(stdevParam, 0.75);
// operator.setWeight(3.0);
// schedule.addOperator(operator);
// }
//
// Parameter allInternalHeights = treeModel.createNodeHeightsParameter(true, true, false);
// operator = new UpDownOperator(new Scalable[]{new Scalable.Default(meanParam)},
// new Scalable[] {new Scalable.Default(allInternalHeights)}, 0.75, 3.0, CoercionMode.COERCION_ON);
// schedule.addOperator(operator);
//
// operator = new SwapOperator(rateCategoryParameter, 10);
// operator.setWeight(1.0);
// schedule.addOperator(operator);
//
// operator = new RandomWalkIntegerOperator(rateCategoryParameter, 1, 10.0);
// schedule.addOperator(operator);
//
// operator = new UniformIntegerOperator(rateCategoryParameter, (int) (double)rateCategoryParameter.getBounds().getLowerLimit(0),
// (int) (double)rateCategoryParameter.getBounds().getUpperLimit(0), 10.0);
// 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, 38.0, 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
// 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, 10000, false);
// loggers[0].add(posterior);
// loggers[0].add(treeLikelihood);
// loggers[0].add(rootHeight);
// loggers[0].add(meanParam);
// if (stdevParam != null) loggers[0].add(stdevParam);
// loggers[0].add(meanRate);
// loggers[0].add(coefficientOfVariation);
// loggers[0].add(covariance);
// loggers[0].add(popSize);
// loggers[0].add(kappa);
// loggers[0].add(coalescent);
//
// loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 100000, false);
// loggers[1].add(posterior);
// loggers[1].add(treeLikelihood);
// loggers[1].add(rootHeight);
// loggers[1].add(meanRate);
// loggers[1].add(coalescent);
//
// // MCMC
// MCMC mcmc = new MCMC("mcmc1");
// MCMCOptions options = new MCMCOptions(10000000);
//
// 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);
// }
//
// return traceList;
// }
//
// public static Test suite() {
// return new TestSuite(UncorrelatedRelaxedClockTest.class);
// }
}