use of dr.evomodel.coalescent.demographicmodel.ConstantPopulationModel in project beast-mcmc by beast-dev.
the class PMDTestProblem method testPMD.
public void testPMD() throws Exception {
Parameter popSize = new Parameter.Default(ConstantPopulationModelParser.POPULATION_SIZE, 496432.69917113904, 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 rateParameter = new Parameter.Default(StrictClockBranchRates.RATE, 4.0E-7, 0, 100.0);
StrictClockBranchRates branchRateModel = new StrictClockBranchRates(rateParameter);
// Sub model
Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
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);
// SequenceErrorModel
Parameter ageRelatedRateParameter = new Parameter.Default(SequenceErrorModelParser.AGE_RELATED_RATE, 4.0E-7, 0, 100.0);
TipStatesModel aDNADamageModel = new SequenceErrorModel(null, null, SequenceErrorModel.ErrorType.TRANSITIONS_ONLY, null, ageRelatedRateParameter, null);
// treeLikelihood
SitePatterns patterns = new SitePatterns(alignment, null, 0, -1, 1, true);
TreeLikelihood treeLikelihood = new TreeLikelihood(patterns, treeModel, siteModel, branchRateModel, aDNADamageModel, 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);
operator = new ScaleOperator(ageRelatedRateParameter, 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, 49643.2699171139, 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);
// ??? correct?
operator = new DeltaExchangeOperator(freqs, new int[] { 1, 1, 1, 1 }, 0.01, 1.0, false, AdaptationMode.ADAPTATION_ON);
schedule.addOperator(operator);
// CompoundLikelihood
OneOnXPrior likelihood1 = new OneOnXPrior();
likelihood1.addData(popSize);
OneOnXPrior likelihood2 = new OneOnXPrior();
likelihood2.addData(kappa);
List<Likelihood> likelihoods = new ArrayList<Likelihood>();
likelihoods.add(likelihood1);
likelihoods.add(likelihood2);
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(treeLikelihood);
loggers[0].add(rootHeight);
loggers[0].add(rateParameter);
loggers[0].add(ageRelatedRateParameter);
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);
// 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("PMDTest", traces, 0);
for (int i = 1; i < traces.size(); i++) {
traceList.analyseTrace(i);
}
// <expectation name="clock.rate" value="1.5E-7"/>
// <expectation name="errorModel.ageRate" value="0.7E-7"/>
// <expectation name="hky.kappa" value="10"/>
TraceCorrelation kappaStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(HKYParser.KAPPA));
assertExpectation(HKYParser.KAPPA, kappaStats, 10);
TraceCorrelation rateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(StrictClockBranchRates.RATE));
assertExpectation(StrictClockBranchRates.RATE, rateStats, 1.5E-7);
TraceCorrelation ageRateStats = traceList.getCorrelationStatistics(traceList.getTraceIndex(SequenceErrorModelParser.AGE_RELATED_RATE));
assertExpectation(SequenceErrorModelParser.AGE_RELATED_RATE, ageRateStats, 0.7E-7);
}
use of dr.evomodel.coalescent.demographicmodel.ConstantPopulationModel in project beast-mcmc by beast-dev.
the class TraceCorrelationAssert method createRandomInitialTree.
protected ConstantPopulationModel createRandomInitialTree(Parameter popSize) {
ConstantPopulationModel startingTree = new ConstantPopulationModel(popSize, Units.Type.YEARS);
ConstantPopulation constant = (ConstantPopulation) startingTree.getDemographicFunction();
createTreeModel(constant);
return startingTree;
}
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