bool TestUCLNRelaxedClockBHT92Model::run( void ) { std::vector<unsigned int> seeds; seeds.push_back(7); seeds.push_back(4); GLOBAL_RNG->setSeed( seeds ); /* First, we read in the data */ // the matrix std::vector<AbstractCharacterData*> data = NclReader::getInstance().readMatrices(alignmentFilename); std::cout << "Read " << data.size() << " matrices." << std::endl; std::cout << data[0] << std::endl; std::vector<TimeTree*> trees = NclReader::getInstance().readTimeTrees( treeFilename ); std::cout << "Read " << trees.size() << " trees." << std::endl; std::cout << trees[0]->getNewickRepresentation() << std::endl; /* set up the model graph */ ////////////////////// // first the priors // ////////////////////// // birth-death process priors StochasticNode<double> *div = new StochasticNode<double>("diversification", new UniformDistribution(new ConstantNode<double>("div_lower", new double(0.0)), new ConstantNode<double>("div_upper", new double(100.0)) )); ConstantNode<double> *turn = new ConstantNode<double>("turnover", new double(0.0)); ConstantNode<double> *rho = new ConstantNode<double>("rho", new double(1.0)); // Setting up the substitution model // //ts/tv ratio: ConstantNode<double > *tstv_prior = new ConstantNode<double >( "tstv_prior", new double(0.25) ); ContinuousStochasticNode *tstv = new ContinuousStochasticNode("tstv", new ExponentialDistribution(tstv_prior) ); //GC content prior: ConstantNode<double > *eq_gc_prior = new ConstantNode<double >( "eq_gc_prior_ab", new double(1.0) ); //Root GC frequency StochasticNode< double > *omega = new StochasticNode< double >( "omega", new BetaDistribution(eq_gc_prior,eq_gc_prior) ); DeterministicNode<std::vector<double> > *rf = new DeterministicNode< std::vector<double> >( "rf", new NucleotideFrequenciesFromGcContentFunction( omega ) ); std::cout << "omega:\t" << omega->getValue() << std::endl; std::cout << "rf:\t" << rf->getValue() << std::endl; std::cout << "tstv:\t" << tstv->getValue() << std::endl; //Declaring a vector of matrices, one per branch size_t numBranches = 2*data[0]->getNumberOfTaxa() - 2; std::vector<ContinuousStochasticNode*> thetas; std::vector< const TypedDagNode < RateMatrix >* > qs; //Equilibrium GC frequency: one per branch, defined in the loop along with the T92 rate matrices. for (unsigned int i = 0 ; i < numBranches ; i++ ) { std::ostringstream eq_gc_name; eq_gc_name << "eq_gc(" << i << ")"; thetas.push_back(new ContinuousStochasticNode( eq_gc_name.str(), new BetaDistribution(eq_gc_prior,eq_gc_prior) ) ); std::ostringstream q_name; q_name << "q(" << i << ")"; qs.push_back(new DeterministicNode< RateMatrix >( q_name.str(), new Tamura92RateMatrixFunction( thetas[i], tstv) )); //std::cout << "Matrix Q:\t"<<i<<"\t" << qs[i]->getValue() << std::endl; } //Build a node out of the vector of nodes DeterministicNode< RbVector< RateMatrix > >* qs_node = new DeterministicNode< RbVector< RateMatrix > >( "q_vector", new RbVectorFunction<RateMatrix>(qs) ); // Setting up the relaxed clock model // ConstantNode<double> *a = new ConstantNode<double>("a", new double(0.5) ); ConstantNode<double> *b = new ConstantNode<double>("b", new double(0.25) ); std::vector<const TypedDagNode<double> *> branchRates; std::vector< ContinuousStochasticNode *> branchRates_nonConst; for( size_t i=0; i<numBranches; i++){ std::ostringstream br_name; br_name << "br(" << i << ")"; ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode( br_name.str(), new LognormalDistribution(a, b, new ConstantNode<double>("offset", new double(0.0) ))); branchRates.push_back( tmp_branch_rate ); branchRates_nonConst.push_back( tmp_branch_rate ); } //Build a node out of the vector of nodes DeterministicNode< std::vector< double > >* br_vector = new DeterministicNode< std::vector< double > >( "br_vector", new VectorFunction< double >( branchRates ) ); // Putting it all together // std::vector<std::string> names = data[0]->getTaxonNames(); ConstantNode<double>* origin = new ConstantNode<double>( "origin", new double( trees[0]->getRoot().getAge()*2.0 ) ); StochasticNode<TimeTree> *tau = new StochasticNode<TimeTree>( "tau", new ConstantRateBirthDeathProcess(origin, div, turn, rho, "uniform", "survival", int(names.size()), names, std::vector<Clade>()) ); //If we want to get a good starting tree // tau->setValue( trees[0] ); std::cout << "tau:\t" << tau->getValue() << std::endl; // and the character model // StochasticNode<CharacterData<DnaState> > *charactermodel = new StochasticNode<CharacterData <DnaState> >("S", new SimpleGTRBranchRateTimeCharEvoModel<DnaState, TimeTree>(tau, q, br_vector, true, data[0]->getNumberOfCharacters()) ); GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *phyloCTMC = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, 4, true, data[0]->getNumberOfCharacters()); phyloCTMC->setRootFrequencies( rf ); phyloCTMC->setRateMatrix( qs_node ); phyloCTMC->setClockRate( br_vector ); StochasticNode< AbstractCharacterData > *charactermodel = new StochasticNode< AbstractCharacterData >("S", phyloCTMC ); charactermodel->clamp( data[0] ); /* add the moves */ RbVector<Move> moves; moves.push_back( new MetropolisHastingsMove( new ScaleProposal(div, 1.0), 2, true ) ); moves.push_back( new NearestNeighborInterchange( tau, 5.0 ) ); moves.push_back( new NarrowExchange( tau, 10.0 ) ); moves.push_back( new FixedNodeheightPruneRegraft( tau, 2.0 ) ); moves.push_back( new SubtreeScale( tau, 5.0 ) ); moves.push_back( new TreeScale( tau, 1.0, true, 2.0 ) ); moves.push_back( new NodeTimeSlideUniform( tau, 30.0 ) ); moves.push_back( new RootTimeSlide( tau, 1.0, true, 2.0 ) ); moves.push_back( new BetaSimplexMove( omega, 10.0, true, 2.0 ) ); moves.push_back( new MetropolisHastingsMove( new ScaleProposal(tstv, 1.0), 2, true ) ); for (unsigned int i = 0 ; i < numBranches ; i ++ ) { moves.push_back( new BetaSimplexMove( dynamic_cast<StochasticNode<double>* >(thetas[i]), 10.0, true, 2.0 ) ); moves.push_back( new SlidingMove( thetas[i], 0.05, true, 2.0) ); // moves.push_back( new SimplexMove( ers[i], 100.0, 6, true, 2.0 ) ); // moves.push_back( new SimplexMove( pis[i], 100.0, 4, true, 2.0 ) ); } // add some tree stats to monitor DeterministicNode<double> *treeHeight = new DeterministicNode<double>("TreeHeight", new TreeHeightStatistic(tau) ); /* add the monitors */ RbVector<Monitor> monitors; std::set<DagNode*> monitoredNodes; // monitoredNodes.insert( er ); // monitoredNodes.insert( pi ); monitoredNodes.insert( div ); monitors.push_back( new FileMonitor( monitoredNodes, 10, "TestUCLNRelaxedClockBHT92Model.log", "\t" ) ); std::set<DagNode*> monitoredNodes1; // monitoredNodes1.insert( er ); for (unsigned int i = 0 ; i < numBranches ; i ++ ) { monitoredNodes1.insert( thetas[i] ); } monitoredNodes1.insert( rf ); monitoredNodes1.insert( treeHeight ); monitors.push_back( new FileMonitor( monitoredNodes1, 10, "TestUCLNRelaxedClockBHT92ModelSubstRates.log", "\t" ) ); monitors.push_back( new ScreenMonitor( monitoredNodes1, 10, "\t" ) ); std::set<DagNode*> monitoredNodes2; monitoredNodes2.insert( tau ); monitors.push_back( new FileMonitor( monitoredNodes2, 10, "TestUCLNRelaxedClockBHT92Model.tree", "\t", false, false, false ) ); /* instantiate the model */ Model myModel = Model(qs[0]); /* instiate and run the MCMC */ Mcmc myMcmc = Mcmc( myModel, moves, monitors ); myMcmc.run(mcmcGenerations); myMcmc.printOperatorSummary(); /* clean up */ // for (size_t i = 0; i < 10; ++i) { // delete x[i]; // } // delete [] x; delete div; // delete sigma; // delete a; // delete b; // delete c; std::cout << "Finished GTR model test." << std::endl; return true; }
bool TestGtrGammaModel::run( void ) { /* First, we read in the data */ // the matrix NclReader& reader = NclReader::getInstance(); std::vector<AbstractCharacterData*> data = reader.readMatrices(alignmentFilename); std::cout << "Read " << data.size() << " matrices." << std::endl; std::vector<TimeTree*> trees = NclReader::getInstance().readTimeTrees( treeFilename ); std::cout << "Read " << trees.size() << " trees." << std::endl; std::cout << trees[0]->getNewickRepresentation() << std::endl; /* set up the model graph */ ////////////////////// // first the priors // ////////////////////// // birth-death process priors StochasticNode<double> *div = new StochasticNode<double>("diversification", new UniformDistribution(new ConstantNode<double>("", new double(0.0)), new ConstantNode<double>("", new double(100.0)) )); ConstantNode<double> *turn = new ConstantNode<double>("turnover", new double(0.0)); ConstantNode<double> *rho = new ConstantNode<double>("rho", new double(1.0)); // gtr model priors ConstantNode<std::vector<double> > *bf = new ConstantNode<std::vector<double> >( "bf", new std::vector<double>(4,1.0) ); ConstantNode<std::vector<double> > *e = new ConstantNode<std::vector<double> >( "e", new std::vector<double>(6,1.0) ); std::cout << "bf:\t" << bf->getValue() << std::endl; std::cout << "e:\t" << e->getValue() << std::endl; // then the parameters StochasticNode<std::vector<double> > *pi = new StochasticNode<std::vector<double> >( "pi", new DirichletDistribution(bf) ); StochasticNode<std::vector<double> > *er = new StochasticNode<std::vector<double> >( "er", new DirichletDistribution(e) ); //Rate heterogeneity ConstantNode<double> *alpha_prior = new ConstantNode<double>("alpha_prior", new double(0.5) ); ContinuousStochasticNode *alpha = new ContinuousStochasticNode("alpha", new ExponentialDistribution(alpha_prior) ); alpha->setValue( new double(0.5) ); std::cout << "alpha:\t" << alpha->getValue() << std::endl; ConstantNode<double> *q1 = new ConstantNode<double>("q1", new double(0.125) ); DeterministicNode<double> *q1_value = new DeterministicNode<double>("q1_value", new QuantileFunction(q1, new GammaDistribution(alpha, alpha) ) ); // StochasticNode<double> *q1_value = new StochasticNode<double>("q1_value", new GammaDistribution(alpha, alpha) ); ConstantNode<double> *q2 = new ConstantNode<double>("q2", new double(0.375) ); DeterministicNode<double> *q2_value = new DeterministicNode<double>("q2_value", new QuantileFunction(q2, new GammaDistribution(alpha, alpha) ) ); // StochasticNode<double> *q2_value = new StochasticNode<double>("q2_value", new GammaDistribution(alpha, alpha) ); ConstantNode<double> *q3 = new ConstantNode<double>("q3", new double(0.625) ); DeterministicNode<double> *q3_value = new DeterministicNode<double>("q3_value", new QuantileFunction(q3, new GammaDistribution(alpha, alpha) ) ); // StochasticNode<double> *q3_value = new StochasticNode<double>("q3_value", new GammaDistribution(alpha, alpha) ); ConstantNode<double> *q4 = new ConstantNode<double>("q4", new double(0.875) ); DeterministicNode<double> *q4_value = new DeterministicNode<double>("q4_value", new QuantileFunction(q4, new GammaDistribution(alpha, alpha) ) ); // StochasticNode<double> *q4_value = new StochasticNode<double>("q4_value", new GammaDistribution(alpha, alpha) ); std::vector<const TypedDagNode<double>* > gamma_rates = std::vector<const TypedDagNode<double>* >(); gamma_rates.push_back(q1_value); gamma_rates.push_back(q2_value); gamma_rates.push_back(q3_value); gamma_rates.push_back(q4_value); DeterministicNode<std::vector<double> > *site_rates = new DeterministicNode<std::vector<double> >( "site_rates", new VectorFunction<double>(gamma_rates) ); // currently unused // ConstantNode<std::vector<double> > *site_rate_probs = new ConstantNode<std::vector<double> >( "site_rate_probs", new std::vector<double>(4,1.0/4.0) ); DeterministicNode<std::vector<double> > *site_rates_norm = new DeterministicNode<std::vector<double> >( "site_rates_norm", new NormalizeVectorFunction(site_rates) ); pi->setValue( new std::vector<double>(4,1.0/4.0) ); er->setValue( new std::vector<double>(6,1.0/6.0) ); std::cout << "pi:\t" << pi->getValue() << std::endl; std::cout << "er:\t" << er->getValue() << std::endl; std::cout << "rates:\t" << site_rates->getValue() << std::endl; std::cout << "rates:\t" << site_rates_norm->getValue() << std::endl; DeterministicNode<RateMatrix> *q = new DeterministicNode<RateMatrix>( "Q", new GtrRateMatrixFunction(er, pi) ); std::cout << "Q:\t" << q->getValue() << std::endl; std::vector<std::string> names = data[0]->getTaxonNames(); ConstantNode<double>* origin = new ConstantNode<double>( "origin", new double( trees[0]->getRoot().getAge()*2.0 ) ); std::vector<RevBayesCore::Taxon> taxa; for (size_t i = 0; i < names.size(); ++i) { taxa.push_back( Taxon( names[i] ) ); } StochasticNode<TimeTree> *tau = new StochasticNode<TimeTree>( "tau", new ConstantRateBirthDeathProcess(origin, NULL, div, turn, rho, "uniform", "survival", taxa, std::vector<Clade>()) ); tau->setValue( trees[0] ); std::cout << "tau:\t" << tau->getValue() << std::endl; // and the character model // (unused) size_t numChar = data[0]->getNumberOfCharacters(); GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *phyloCTMC = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, 4, true, data[0]->getNumberOfCharacters()); phyloCTMC->setSiteRates( site_rates_norm ); phyloCTMC->setRateMatrix( q ); StochasticNode< AbstractCharacterData > *charactermodel = new StochasticNode< AbstractCharacterData >("S", phyloCTMC ); charactermodel->clamp( static_cast<DiscreteCharacterData<DnaState> *>( data[0] ) ); std::cout << "LnL:\t\t" << charactermodel->getLnProbability() << std::endl; /* add the moves */ RbVector<Move> moves; // moves.push_back( new ScaleMove(div, 1.0, true, 2.0) ); // moves.push_back( new NearestNeighborInterchange( tau, 5.0 ) ); // moves.push_back( new NarrowExchange( tau, 10.0 ) ); // moves.push_back( new FixedNodeheightPruneRegraft( tau, 2.0 ) ); // moves.push_back( new SubtreeScale( tau, 5.0 ) ); // moves.push_back( new TreeScale( tau, 1.0, true, 2.0 ) ); // moves.push_back( new NodeTimeSlideUniform( tau, 30.0 ) ); // moves.push_back( new RootTimeSlide( tau, 1.0, true, 2.0 ) ); // moves.push_back( new SimplexMove( er, 10.0, 1, 0, true, 2.0 ) ); // moves.push_back( new SimplexMove( pi, 10.0, 1, 0, true, 2.0 ) ); // moves.push_back( new SimplexMove( er, 100.0, 6, 0, true, 2.0 ) ); // moves.push_back( new SimplexMove( pi, 100.0, 4, 0, true, 2.0 ) ); moves.push_back( new MetropolisHastingsMove( new ScaleProposal(alpha, 1.0), 1, true) ); // moves.push_back( new ScaleMove(q1_value, 1.0, true, 2.0) ); // moves.push_back( new ScaleMove(q2_value, 1.0, true, 2.0) ); // moves.push_back( new ScaleMove(q3_value, 1.0, true, 2.0) ); // moves.push_back( new ScaleMove(q4_value, 1.0, true, 2.0) ); // add some tree stats to monitor DeterministicNode<double> *treeHeight = new DeterministicNode<double>("TreeHeight", new TreeHeightStatistic(tau) ); /* add the monitors */ RbVector<Monitor> monitors; std::set<DagNode*> monitoredNodes; // monitoredNodes.insert( er ); // monitoredNodes.insert( pi ); // monitoredNodes.insert( q ); // monitoredNodes.insert( q1_value ); // monitoredNodes.insert( q2_value ); // monitoredNodes.insert( q3_value ); // monitoredNodes.insert( q4_value ); monitoredNodes.insert( site_rates_norm ); monitoredNodes.insert( alpha ); monitoredNodes.insert( treeHeight ); monitors.push_back( new FileMonitor( monitoredNodes, 1000, "TestGtrGammaModelSubstRates.log", "\t" ) ); monitors.push_back( new ScreenMonitor( monitoredNodes, 1000, "\t" ) ); std::set<DagNode*> monitoredNodes2; monitoredNodes2.insert( tau ); monitors.push_back( new FileMonitor( monitoredNodes2, 1000, "TestGtrGammaModel.tree", "\t", false, false, false ) ); /* instantiate the model */ Model myModel = Model(q); /* instiate and run the MCMC */ Mcmc myMcmc = Mcmc( myModel, moves, monitors ); myMcmc.run(mcmcGenerations); myMcmc.printOperatorSummary(); /* clean up */ // for (size_t i = 0; i < 10; ++i) { // delete x[i]; // } // delete [] x; delete div; // delete sigma; // delete a; // delete b; // delete c; std::cout << "Finished GTR+Gamma model test." << std::endl; return true; }