use of dr.inference.trace.Trace in project beast-mcmc by beast-dev.
the class MCMCTest method testMCMC.
public void testMCMC() {
// Sub model
// new double[]{0.25, 0.25, 0.25, 0.25});
Parameter freqs = new Parameter.Default(alignment.getStateFrequencies());
Parameter kappa = new Parameter.Default(HKYParser.KAPPA, 1.0, 1.0E-8, 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, null, null, false, false, true, false, false);
treeLikelihood.setId(TreeLikelihoodParser.TREE_LIKELIHOOD);
// Operators
OperatorSchedule schedule = new SimpleOperatorSchedule();
MCMCOperator operator = new ScaleOperator(kappa, 0.5);
operator.setWeight(1.0);
schedule.addOperator(operator);
// Parameter rootParameter = treeModel.createNodeHeightsParameter(true, false, false);
// ScaleOperator scaleOperator = new ScaleOperator(rootParameter, 0.75, AdaptationMode.ADAPTATION_ON, 1.0);
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(kappa);
loggers[1] = new MCLogger(new TabDelimitedFormatter(System.out), 100000, false);
loggers[1].add(treeLikelihood);
loggers[1].add(rootHeight);
loggers[1].add(kappa);
// 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("MCMCTest", 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="hky.kappa" value="32.8941"/>
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, 6.42048E-2);
TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
assertExpectation(HKYParser.KAPPA, kappaStats, 32.8941);
}
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