bool TestAutocorrelatedBranchHeterogeneousGtrModel::run( void ) {
// fix the rng seed
std::vector<unsigned int> seed;
seed.push_back(25);
seed.push_back(42);
GLOBAL_RNG->setSeed(seed);
/* 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));
// 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) );
//Root frequencies
StochasticNode<std::vector<double> > *rf = new StochasticNode<std::vector<double> >( "rf", new DirichletDistribution(bf) );
StochasticNode<std::vector<double> > * er = new StochasticNode<std::vector<double> >( "er", new DirichletDistribution(e) ) ;
std::cout << "bf:\t" << bf->getValue() << std::endl;
std::cout << "e:\t" << e->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;
std::vector<StochasticNode < std::vector<double> >* > pis;
// std::vector<StochasticNode < std::vector<double> >* > ers;
std::vector< const TypedDagNode < RateMatrix>* > qs;
ConstantNode<double> *alpha_prior_shape = new ConstantNode< double >("alpha_prior_shape", new double( 5.0 ) );
ConstantNode<double> *alpha_prior_rate = new ConstantNode< double >("alpha_prior_rtae", new double( 0.5 ) );
StochasticNode<double> *alpha = new StochasticNode<double>("alpha", new GammaDistribution( alpha_prior_shape, alpha_prior_rate ) );
ConstantNode<double> *beta_prior_shape1 = new ConstantNode< double >("beta_prior_shape1", new double( 2.0 ) );
ConstantNode<double> *beta_prior_shape2 = new ConstantNode< double >("beta_prior_shape2", new double( 5.0 ) );
StochasticNode<double> *beta = new StochasticNode<double>("beta", new BetaDistribution( beta_prior_shape1, beta_prior_shape2 ) );
StochasticNode< RbVector<RateMatrix> > *perBranchQ = new StochasticNode< RbVector< RateMatrix > >( "autocorrBranchRate", new AutocorrelatedBranchMatrixDistribution( tau, beta, rf, er, alpha ) );
// StochasticNode< std::vector<RateMatrix> > *perBranchQ = new StochasticNode< std::vector< RateMatrix > >( "autocorrBranchRate", new DPP< RateMatrix >( tau, ... ) );
//
// for (unsigned int i = 0 ; i < numBranches ; i++ ) {
// std::ostringstream pi_name;
// pi_name << "pi(" << i << ")";
// pis.push_back(new StochasticNode<std::vector<double> >( pi_name.str(), new DirichletDistribution(bf) ) );
// // ers.push_back(new StochasticNode<std::vector<double> >( "er", new DirichletDistribution(e) ) );
// std::ostringstream q_name;
// q_name << "q(" << i << ")";
// qs.push_back(new DeterministicNode<RateMatrix>( q_name.str(), new GtrRateMatrixFunction(er, pis[i]) ));
// std::cout << "Q:\t" << qs[i]->getValue() << std::endl;
// }
// and the character model
GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *phyloCTMC = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, 4, true, data[0]->getNumberOfCharacters());
phyloCTMC->setRootFrequencies( rf );
phyloCTMC->setRateMatrix( perBranchQ );
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 SimplexMove( er, 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( rf, 10.0, 1, 0, true, 2.0 ) );
moves.push_back( new SimplexMove( rf, 100.0, 4, 0, true, 2.0 ) );
// for (unsigned int i = 0 ; i < numBranches ; i ++ ) {
// // moves.push_back( new SimplexMove( ers[i], 10.0, 1, true, 2.0 ) );
// moves.push_back( new SimplexMove( pis[i], 10.0, 1, 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, "TestAutocorrelatedBranchHeterogeneousGtrModel.log", "\t" ) );
std::set<DagNode*> monitoredNodes1;
monitoredNodes1.insert( er );
/* for (unsigned int i = 0 ; i < numBranches ; i ++ ) {
monitoredNodes1.insert( pis[i] );
}*/
monitoredNodes1.insert( rf );
monitoredNodes1.insert( treeHeight );
monitors.push_back( new FileMonitor( monitoredNodes1, 10, "TestAutocorrelatedBranchHeterogeneousGtrModelSubstRates.log", "\t" ) );
monitors.push_back( new ScreenMonitor( monitoredNodes1, 10, "\t" ) );
std::set<DagNode*> monitoredNodes2;
monitoredNodes2.insert( tau );
monitors.push_back( new FileMonitor( monitoredNodes2, 10, "TestAutocorrelatedBranchHeterogeneousGtrModel.tree", "\t", false, false, false ) );
/* instantiate the model */
Model myModel = Model( tau );
std::vector<DagNode*> &nodes = myModel.getDagNodes();
for (std::vector<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it) {
std::cerr << (*it)->getName() << std::endl;
}
/* 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 Autocorrelated Branch Heterogeneous GTR model test." << std::endl;
return true;
}
bool TestBranchHeterogeneousHkyModel::run( void ) {
/* 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;
/* 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));
// hky model priors
ConstantNode<std::vector<double> > *bfPrior = new ConstantNode<std::vector<double> >( "bfPrior", new std::vector<double>(4,1.0) );
ConstantNode< double > *tstvPrior = new ConstantNode< double >( "tstvPrior", new double(1.0) );
// root frequencies
StochasticNode<std::vector<double> > *rf = new StochasticNode<std::vector<double> >( "rf", new DirichletDistribution(bfPrior) );
// // first the hyper-priors of the clock model
ConstantNode<double> *a = new ConstantNode<double>("a", new double(0.5) );
ConstantNode<double> *b = new ConstantNode<double>("b", new double(0.25) );
//
//
// then the parameters
ContinuousStochasticNode *expectLN = new ContinuousStochasticNode( "UCLN.expectation", new ExponentialDistribution(a) ); // the expectation of the LN dist so mu = log(expectLN) - (sigLN^2)/2
ContinuousStochasticNode *sigLN = new ContinuousStochasticNode("UCLN.variance", new ExponentialDistribution(b) );
DeterministicNode<double> *logExpLN = new DeterministicNode<double>("logUCLN.exp", new LnFunction(expectLN) );
DeterministicNode<double> *squareSigLN = new DeterministicNode<double>("squareSigLN", new BinaryMultiplication<double, double, double>(sigLN, sigLN) );
DeterministicNode<double> *divSqSigLN = new DeterministicNode<double>("divSqSigLN", new BinaryDivision<double, double, double>(squareSigLN, new ConstantNode<double>( "2", new double (2.0))) );
DeterministicNode<double> *muValLN = new DeterministicNode<double>("MuValLN", new BinarySubtraction<double, double, double>(logExpLN, divSqSigLN) );
//Declaring a vector of HKY matrices
size_t numBranches = 2*data[0]->getNumberOfTaxa() - 2;
std::vector<StochasticNode < std::vector<double> >* > pis;
std::vector< const TypedDagNode< RateMatrix >* > qs;
StochasticNode < double >* tstv = new ContinuousStochasticNode("tstv", new ExponentialDistribution( tstvPrior ) );
//
//
// declaring a vector of clock rates
std::vector<const TypedDagNode<double> *> branchRates;
std::vector< ContinuousStochasticNode *> branchRates_nonConst;
for (unsigned int i = 0 ; i < numBranches ; i++ ) {
// construct the per branch rate matrix
std::ostringstream pi_name;
pi_name << "pi(" << i << ")";
pis.push_back(new StochasticNode<std::vector<double> >( pi_name.str(), new DirichletDistribution(bfPrior) ) );
std::ostringstream q_name;
q_name << "q(" << i << ")";
qs.push_back(new DeterministicNode<RateMatrix>( q_name.str(), new HkyRateMatrixFunction( tstv, pis[i]) ));
std::cout << "Q:\t" << qs[i]->getValue() << std::endl;
// construct the per branch clock rate
std::ostringstream br_name;
br_name << "br(" << i << ")";
ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode( br_name.str(), new LognormalDistribution(muValLN, sigLN, new ConstantNode<double>("offset", new double(0.0) )));
branchRates.push_back( tmp_branch_rate );
branchRates_nonConst.push_back( tmp_branch_rate );
}
// build the vector containing all rates/rate-matrices
// instead of independent rates/rate-matrices we could have used anything that specifies a distribution on a set of values
// e.g. a mixture, DPP or an autocorrelated model
DeterministicNode< std::vector< double > >* br_vector = new DeterministicNode< std::vector< double > >( "br_vector", new VectorFunction< double >( branchRates ) );
DeterministicNode< RbVector< RateMatrix > >* qs_node = new DeterministicNode< RbVector< RateMatrix > >( "q_vector", new RbVectorFunction<RateMatrix>(qs) );
// create the variables for the rate variation across sites
// we use the standard 4 categorical gamma rate variation
// though, any other rates could be used too as long as they are normalized
ConstantNode<double> *alpha_prior = new ConstantNode<double>("alpha_prior", new double(0.5) );
ContinuousStochasticNode *alpha = new ContinuousStochasticNode("alpha", new ExponentialDistribution(alpha_prior) );
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) ) );
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) ) );
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) ) );
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) ) );
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) );
DeterministicNode<std::vector<double> > *site_rates_norm = new DeterministicNode<std::vector<double> >( "site_rates_norm", new NormalizeVectorFunction(site_rates) );
// we actually do not use different probabilities per rate (yet!)
// ConstantNode<std::vector<double> > *site_rate_probs = new ConstantNode<std::vector<double> >( "site_rate_probs", new std::vector<double>(4,1.0/4.0) );
// create the stochastic node for the tree
// we use a birth-death process prior and thus a time-tree
// we could use as well an unrooted tree
std::vector<std::string> names = data[0]->getTaxonNames();
ConstantNode<double>* origin = new ConstantNode<double>( "origin", new double( 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>()) );
// //rescale the tree so that its root age is 1
TimeTree *t = tau->getValue().clone();
const TopologyNode &root = t->getRoot();
TreeUtilities::rescaleTree(t, &t->getRoot(), 1.0 / root.getAge());
//
tau->setValue( t );
std::cout << "tau:\t" << tau->getValue() << std::endl;
// and the character model
//GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *charModel = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, true, data[0]->getNumberOfCharacters() );
GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *charModel = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, 4, true, data[0]->getNumberOfCharacters() );
// set the branch heterogeneous substitution matrices
// if you set instead of a vector a single matrix, then you get a homogeneous model
charModel->setRateMatrix( qs_node );
charModel->setRootFrequencies( rf );
// set the per branch clock rates
// if you instead specify a single rate, you get a strict clock model
charModel->setClockRate( br_vector );
// specify the rate variation across sites
// if you skip this then you get the model without rate variation across sites.
charModel->setSiteRates( site_rates_norm );
StochasticNode< AbstractCharacterData > *charactermodel = new StochasticNode< AbstractCharacterData >("S", charModel );
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 ) );
//Fixintg the root age at 1:
// moves.push_back( new TreeScale( tau, 1.0, true, 2.0 ) );
// moves.push_back( new RootTimeSlide( tau, 1.0, true, 2.0 ) );
//test: only 20 instead of 30
moves.push_back( new NodeTimeSlideUniform( tau, 20.0 ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(tstv, 1.0), 2, true ) );
moves.push_back( new SimplexSingleElementScale( rf, 10.0, true, 2.0 ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(alpha, 1.0), 2, true ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(expectLN, 1.0), 2, true ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(sigLN, 1.0), 2, true ) );
std::vector<StochasticNode<double> * > rates;
for (unsigned int i = 0 ; i < numBranches ; i ++ ) {
rates.push_back( branchRates_nonConst[i] );
}
moves.push_back( new RateAgeBetaShift( tau, rates, 1.0, true, 10.0) ); //!< constructor
for (unsigned int i = 0 ; i < numBranches ; i ++ ) {
moves.push_back( new SimplexSingleElementScale( pis[i], 10.0, true, 2.0 ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(branchRates_nonConst[i], 1.0), 1, true ) );
}
// 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( tstv );
monitoredNodes.insert( treeHeight );
monitors.push_back( new ScreenMonitor( monitoredNodes, 1, "\t" ) );
std::set<DagNode*> monitoredNodes2;
monitoredNodes2.insert( tau );
monitors.push_back( new FileMonitor( monitoredNodes2, 10, "TestBranchHeterogeneousHkyModel.tree", "\t", false, false, false ) );
/* instantiate the model */
Model myModel = Model(qs[0]);
monitors.push_back( new ModelMonitor( 10, "TestBranchHeterogeneousHkyModel.log", "\t" ) );
/* instiate and run the MCMC */
Mcmc myMcmc = Mcmc( myModel, moves, monitors );
// myMcmc.burnin(1000, 100);
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 TestAdmixtureGraph::run(void) {
std::cout << "Running TestAdmixtureGraph\n";
std::cout << "argc: " << argc << "\n";
if (argc > 1)
{
for (int i = 0; i < argc; i++)
{
argTokens.push_back(argv[i]);
std::cout << i << " " << argTokens[i] << "\n";
}
std::cout << argc << " == " << argTokens.size() << " arguments\n";
snpFilename = argTokens[1];
}
// MODEL GRAPH
std::vector<unsigned int> seed;
seed = GLOBAL_RNG->getSeed();
std::cout << "seed " << seed[0] << " " << seed[1] << "\n";
//seed.clear(); seed.push_back(53866); seed.push_back(21201); GLOBAL_RNG->setSeed(seed);
// 53866 21201
// read in data
std::string fn = snpFilepath + snpFilename;
int snpThinBy = 100;
SnpData* snps = PopulationDataReader().readSnpData(fn,snpThinBy);
// read in tree
std::vector<AdmixtureTree*> trees;
bool startTree = false;
//treeFilename = "";
if (treeFilename != "")
{
// NclReader does not seem to work for Newick strings at this time
/*
trees = NclReader::getInstance().readAdmixtureTrees( snpFilepath + treeFilename, "newick" );
std::cout << "Read " << trees.size() << " trees." << std::endl;
std::cout << trees[0]->getNewickRepresentation() << std::endl;
*/
// hacky workaround for now...
//std::string newickStr = "(San:1,((Han:0.348958,Dai:0.348958):0.194964,(((Ket:0.351687,(Koryak:0.344761,(SiberianEskimo:0.325112,(((Huichol:0.269256,(Pima:0.233362,((Karitiana:0.104362,Aymara:0.104362):0.0120051,(Yukpa:0.100877,Mayan:0.100877):0.0154902):0.116995):0.0358943):0.0341607,Athabascan:0.303417):0.0128117,((EastGreenland:0.158699,WestGreenland:0.158699):0.0369703,Aleuts:0.195669):0.120559):0.00888335):0.0196487):0.0069259):0.0987521,((Nivhks:0.278599,Buryat:0.278599):0.0642882,Yakut:0.342887):0.107551):0.0756044,Altai:0.526043):0.0178791):0.456078)";
//std::string newickStr = "((A:.5,B:.5):.5,C:.5)";
std::string newickStr = "(San:1,((Koryak:0.926938,(SiberianEskimo:0.812519,((Aleuts:0.762302,(EastGreenland:0.4824,WestGreenland:0.4824):0.279902):0.0144746,((Huichol:0.353522,(Pima:0.324226,((Mayan:0.223067,Yukpa:0.223067):0.0856916,(Aymara:0.173581,Karitiana:0.173581):0.135178):0.015467):0.0292956):0.109212,Athabascan:0.462734):0.314043):0.0357419):0.114419):0.0600046,(Ket:0.772384,((Altai:0.640188,(Han:0.481097,Dai:0.481097):0.159091):0.0445788,((Buryat:0.596074,Nivhks:0.596074):0.015206,Yakut:0.61128):0.0734876):0.0876171):0.214558):0.0130575);";
NewickConverter nc;
BranchLengthTree* blt = nc.convertFromNewick(newickStr);
AdmixtureTree* at = TreeUtilities::convertToAdmixtureTree(*blt, snps->getPopulationNames());
at->setNames(snps->getPopulationNames());
at->updateTipOrderByNames(snps->getPopulationNames());
trees.push_back(at);
startTree = true;
}
size_t numTaxa = snps->getNumPopulations();
size_t numNodes = 2 * numTaxa - 1;
size_t numBranches = numNodes - 1;
//size_t numSites = snps->getNumSnps();
int blockSize = 5000;
double divGens = 1;//.01;
int delay = 1000;
int numTreeResults = 500;
int numAdmixtureResults = 500;
int maxNumberOfAdmixtureEvents = 1;
double residualWeight = 2.0;
bool useWishart = true; // if false, the composite likelihood function is used
bool useBias = true; // if false, no covariance bias correction for small sample size is used
bool useAdmixtureEdges = true; // if false, no admixture moves or edges are used
bool useBranchRates = true; // if false, all populations are of the same size
bool allowSisterAdmixture = true; // if false, admixture events cannot be between internal lineages who share a divergence parent
bool discardNonPosDefMtx = true; // if false, round negative eigenvalues to positive eps
bool useContrasts = false; // nothing really, need to remove
bool updateParameters = true;
bool updateTopology = true;
bool updateNodeAges = true;
bool useParallelMcmcmc = true;
int numChains = 4;
int numProcesses = numChains;
// numProcesses=80;
int swapInterval = 1;
double deltaTemp = .1;
double sigmaTemp = 1.0;
double hottestTemp = 0.001;
if (!true)
{
deltaTemp = exp(-log(hottestTemp)/pow(numChains-1,sigmaTemp)) - 1;
std::cout << deltaTemp << "\n";
}
double startingHeat = 1.0;
double likelihoodScaler = 1.0;
std::stringstream rndStr;
rndStr << std::setw(9) << std::fixed << std::setprecision(0) << std::setfill('0') << std::floor(GLOBAL_RNG->uniform01()*1e9);
// std::string outName = "papa." + rndStr.str();
std::string simName = "hgdp";
std::string outName = simName + "." + rndStr.str();
// std::string outName = simName + "." + rndStr.str() + "." + snpFilename;
// BM diffusion rate
ConstantNode<double>* a_bm = new ConstantNode<double>( "bm_a", new double(3));
ConstantNode<double>* b_bm = new ConstantNode<double>( "bm_b", new double(100));
//ConstantNode<double>* c_bm = new ConstantNode<double>( "bm_c", new double(0));
//ConstantNode<double>* d_bm = new ConstantNode<double>( "bm_d", new double(100));
StochasticNode<double>* diffusionRate = new StochasticNode<double> ("rate_BM", new ExponentialDistribution(b_bm));
//StochasticNode<double>* diffusionRate = new StochasticNode<double> ("rate_BM", new UniformDistribution(c_bm, d_bm));
// CPP rate
// MJL 071713: Flat Poisson prior cannot overpower model overfitting when lnL is large.
// Consider implementing Conway-Maxewell-Poisson distn instead.
// This prior requires admixture events to improve lnL by N units
// Negative values -> admixture rare
// Positive values -> admixture common (set admixture cap)
double adm_th_lnL = 10;
double rate_cpp_prior = exp(adm_th_lnL);
ConstantNode<double>* c = new ConstantNode<double>( "c", new double(1.0/rate_cpp_prior)); // admixture rate prior
StochasticNode<double>* admixtureRate = new StochasticNode<double> ("rate_CPP", new ExponentialDistribution(c));
StochasticNode<int>* admixtureCount = new StochasticNode<int> ("count_CPP", new PoissonDistribution(admixtureRate));
admixtureCount->clamp(new int(0));
admixtureRate->clamp(new double(rate_cpp_prior));
if (!useAdmixtureEdges)
{
admixtureRate->clamp(new double(rate_cpp_prior));
admixtureCount->clamp(new int(0));
}
// birth-death process for ultrametric tree
StochasticNode<double>* diversificationRate = new StochasticNode<double>("div", new UniformDistribution(new ConstantNode<double>("div_lower", new double(0.0)), new ConstantNode<double>("div_upper", new double(50.0)) ));
StochasticNode<double>* turnover = new StochasticNode<double>("turnover", new UniformDistribution(new ConstantNode<double>("do_lower", new double(0.0)), new ConstantNode<double>("do_upper", new double(1.0)) ));
// tree node
StochasticNode<AdmixtureTree>* tau = new StochasticNode<AdmixtureTree>( "tau", new AdmixtureConstantBirthDeathProcess(diversificationRate, turnover, (int)numTaxa, snps->getPopulationNames(), snps->getOutgroup()) );
if (startTree)
{
tau->setValue(new AdmixtureTree(*trees[0]));
tau->setIgnoreRedraw(true);
}
// branch multipliers (mutation rate is clocklike, but population sizes are not)
std::vector<const TypedDagNode<double> *> branchRates;
std::vector< ContinuousStochasticNode *> branchRates_nonConst;
ConstantNode<double>* branchRateA = new ConstantNode<double>( "branchRateA", new double(1));
ConstantNode<double>* branchRateB = new ConstantNode<double>( "branchRateB", new double(2));
ConstantNode<double>* branchRateC = new ConstantNode<double>( "branchRateC", new double(0));
ConstantNode<double>* branchRateD = new ConstantNode<double>( "branchRateD", new double(.01));
//ConstantNode<double>* branchRateE = new ConstantNode<double>( "branchRateE", new double(10));
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 ExponentialDistribution(branchRateD) );
//ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode( br_name.str(), new InverseGammaDistribution(branchRateA, branchRateB));
//ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode(br_name.str(), new LognormalDistribution(branchRateC, branchRateA));
//ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode(br_name.str(), new UniformDistribution(branchRateC, branchRateE));
// ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode( br_name.str(), new GammaDistribution(branchRateB, branchRateD));
ContinuousStochasticNode* tmp_branch_rate = new ContinuousStochasticNode( br_name.str(), new GammaDistribution(branchRateB, branchRateB));
if (!useBranchRates)
{
tmp_branch_rate->clamp(new double(1.0));
}
branchRates.push_back( tmp_branch_rate );
branchRates_nonConst.push_back( tmp_branch_rate );
}
DeterministicNode< std::vector< double > >* br_vector = new DeterministicNode< std::vector< double > >( "br_vector", new VectorFunction< double >( branchRates ) );
// model node
BrownianMotionAdmixtureGraph* bmag = new BrownianMotionAdmixtureGraph( tau, diffusionRate, admixtureRate, br_vector, snps, useWishart, useContrasts, useBias, discardNonPosDefMtx, blockSize, likelihoodScaler );
StochasticNode<ContinuousCharacterData >* admixtureModel;
admixtureModel = new StochasticNode<ContinuousCharacterData >("AdmixtureGraph", bmag);
// have to clamp to distinguish likelihood from prior (incidentally calls setValue(), but this is handled otherwise)
admixtureModel->clamp( new ContinuousCharacterData() ); // does it event matter how it's clamped?
// residuals
DeterministicNode<std::vector<double> >* residuals = new DeterministicNode<std::vector<double> >("residuals", new BrownianMotionAdmixtureGraphResiduals(admixtureModel));
// MOVES
std::cout << "Adding moves\n";
// moves vector
RbVector<Move> moves;
// model parameters
if (updateParameters)
{
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(diffusionRate, 0.1), 5, false ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(diversificationRate, 0.5), 5, false ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(turnover, 0.5), 5, false ) );
}
// non-admixture tree updates
if (updateTopology)
{
moves.push_back( new AdmixtureNarrowExchange( tau, 0.1, numTaxa/2) );
moves.push_back( new AdmixtureSubtreePruneRegraft( tau, 0.1, numTaxa/4) );
moves.push_back( new AdmixtureFixedNodeheightPruneRegraft(tau, numTaxa/4));
moves.push_back( new AdmixtureEdgeReplaceNNI( tau, residuals, residualWeight, delay, 0, allowSisterAdmixture, numTaxa));
moves.push_back( new AdmixtureEdgeReplaceFNPR( tau, residuals, residualWeight, delay, 0, allowSisterAdmixture, numTaxa));
moves.push_back( new AdmixtureEdgeReplaceSubtreeRegraft( tau, residuals, residualWeight, delay, 0, allowSisterAdmixture, numTaxa));
}
if (updateNodeAges)
{
for (size_t i = numTaxa; i < numNodes - 1; i++)
{
moves.push_back( new AdmixtureNodeTimeSlideBeta( tau, (int)i, 15.0, false, 1.0 ) );
moves.push_back( new AdmixtureNodeTimeSlideBeta( tau, (int)i, 1.0, false, 0.5 ) );
}
}
// branch rate updates
if (useBranchRates)
{
// branch rate multipliers
for( size_t i=0; i < numBranches; i++)
{
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(branchRates_nonConst[i], 0.1), 1, false ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(branchRates_nonConst[i], 1.0), .5, false ) );
}
// tree rate shift
moves.push_back( new AdmixtureShiftTreeRates(diffusionRate, branchRates_nonConst, 0.5, false, 2.0));
// shift node age for branch rate
for (size_t i = numTaxa; i < numNodes - 1; i++)
{
if (updateNodeAges)
moves.push_back( new AdmixtureShiftNodeAgeAndRate(tau, branchRates_nonConst, (int)i, 0.7, false, 1.0) );
// MJL 081513: not working, I think...
if (updateTopology)
{
std::vector<DagNode*> pvec;
pvec.push_back(tau);
pvec.push_back(branchRates_nonConst[i]);
//moves.push_back( new AdmixtureSubtreePruneRegraftAndRateShift(pvec, i, 0.5, 1.0) );
// ... something wrong with how the lnProb is computed using the lnProb ratios...
}
}
// NNI with branch rate modifier (not working quite right, disabled)
if (updateTopology)
moves.push_back( new AdmixtureNearestNeighborInterchangeAndRateShift( tau, branchRates_nonConst, 0.1, false, numTaxa));
}
// admixture tree updates
if (useAdmixtureEdges)
{
moves.push_back( new AdmixtureEdgeAddResidualWeights( tau, admixtureRate, admixtureCount, residuals, residualWeight, delay, maxNumberOfAdmixtureEvents, allowSisterAdmixture, 10.0) );
moves.push_back( new AdmixtureEdgeRemoveResidualWeights( tau, admixtureRate, admixtureCount, residuals, residualWeight, delay, 10.0) );
moves.push_back( new AdmixtureEdgeReplaceResidualWeights( tau, admixtureRate, branchRates_nonConst, residuals, residualWeight, delay, allowSisterAdmixture, 20.0) );
//moves.push_back( new AdmixtureEdgeMultiRemove( tau, admixtureRate, admixtureCount, residuals, residualWeight, delay, 2.0 ) );
//moves.push_back( new AdmixtureReplaceAndNNI( tau, 0.5, 10.0) );
//moves.push_back( new AdmixtureEdgeAddCladeResiduals( tau, admixtureRate, admixtureCount, residuals, delay, maxNumberOfAdmixtureEvents, allowSisterAdmixture, 2.0) );
//moves.push_back( new AdmixtureEdgeReplaceCladeResiduals( tau, admixtureRate, branchRates_nonConst, residuals, delay, allowSisterAdmixture, 15.0) );
if (updateTopology)
{
moves.push_back( new AdmixtureEdgeDivergenceMerge( tau, admixtureRate, branchRates_nonConst, admixtureCount, residuals, delay, allowSisterAdmixture, 5.0 ));
moves.push_back( new AdmixtureEdgeRegraftReplace( tau, residuals, 1.0, delay, maxNumberOfAdmixtureEvents, allowSisterAdmixture, 5.0));
;
}
moves.push_back( new AdmixtureEdgeReweight( tau, delay, 10.0, 10.0) );
moves.push_back( new AdmixtureEdgeReversePolarity( tau, delay, 2.0, 10.0) );
moves.push_back( new AdmixtureEdgeSlide( tau, branchRates_nonConst, delay, allowSisterAdmixture, 10.0, 10.0) );
moves.push_back( new AdmixtureEdgeFNPR( tau, branchRates_nonConst, delay, allowSisterAdmixture, 10.0, 10.0) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(admixtureRate, 0.1), 5, false ) );
}
// MONITORS
std::cout << "Adding monitors\n";
RbVector<Monitor> monitors;
// parameter monitor
std::vector<DagNode*> monitoredNodes;
monitoredNodes.push_back( diffusionRate );
monitoredNodes.push_back( admixtureRate );
monitoredNodes.push_back( diversificationRate );
monitoredNodes.push_back( turnover );
monitoredNodes.push_back( admixtureCount );
if (useBranchRates)
{
for( size_t i=0; i<numBranches; i++){
monitoredNodes.push_back( branchRates_nonConst[i] );
}
}
monitors.push_back( new FileMonitor( monitoredNodes, 1, "/Users/mlandis/data/admix/output/" + outName + ".parameters.txt", "\t", true, true, true, useParallelMcmcmc, useParallelMcmcmc, useParallelMcmcmc ) );
monitors.push_back( new ScreenMonitor( monitoredNodes, 1, "\t" ) );
monitors.push_back( new AdmixtureBipartitionMonitor(tau, diffusionRate, br_vector, numTreeResults, numAdmixtureResults, 1, "/Users/mlandis/data/admix/output/" + outName + ".bipartitions.txt", "\t", true, true, true, true, true, true ) );
monitors.push_back( new AdmixtureResidualsMonitor(residuals, snps->getPopulationNames(), 10, "/Users/mlandis/data/admix/output/" + outName + ".residuals.txt", "\t", true, true, true, true ) );
//monitors.push_back( new ExtendedNewickAdmixtureTreeMonitor( tau, br_vector, true, true, 10, "/Users/mlandis/data/admix/output/" + outName + ".admixture_trees.txt", "\t", true, true, true, true ) );
//monitors.push_back( new ExtendedNewickAdmixtureTreeMonitor( tau, br_vector, false, true, 10, "/Users/mlandis/data/admix/output/" + outName + ".topology_trees.trees", "\t", true, true, true, true ) );
monitors.push_back( new ExtendedNewickAdmixtureTreeMonitor( tau, br_vector, false, false, 10, "/Users/mlandis/data/admix/output/" + outName + ".time_trees.trees", "\t", true, true, true, true ) );
// MODEL
std::cout << "Calling model\n";
std::set<const DagNode*> mset;
mset.insert(admixtureRate);
Model myModel = Model(mset);
// MCMC
std::cout << "Calling mcmc\n";
if (!useParallelMcmcmc)
{
Mcmc myMcmc = Mcmc(myModel, moves, monitors);
myMcmc.run(mcmcGenerations);
myMcmc.printOperatorSummary();
}
else
{
ParallelMcmcmc myPmc3(myModel, moves, monitors, "random", numChains, numProcesses, swapInterval, deltaTemp, sigmaTemp, startingHeat);
myPmc3.run(mcmcGenerations/divGens);
myPmc3.printOperatorSummary();
}
std::cout << "All done!\n";
// OBJECT CLEANUP
delete snps;
delete a_bm;
delete b_bm;
delete c;
delete tau;
delete diversificationRate;
delete turnover;
delete diffusionRate;
delete admixtureRate;
delete admixtureCount;
delete branchRateA;
delete branchRateB;
delete branchRateC;
delete branchRateD;
branchRates_nonConst.clear();
branchRates.clear();
delete br_vector;
//delete bmag; // malloc deallocation error
delete admixtureModel;
delete residuals;
moves.clear();
monitors.clear();
return true;
}
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 TestACLNRatesGen::run( void ) {
// alignmentFilename = "/Users/tracyh/Code/RevBayes_proj/tests/time_trees/tt_CLK_GTRG.nex";
// treeFilename = "/Users/tracyh/Code/RevBayes_proj/tests/time_trees/tt_CLK_true_relx.tre";
std::vector<AbstractCharacterData*> data = NclReader::getInstance().readMatrices(alignmentFilename);
std::cout << "Read " << data.size() << " matrices." << std::endl;
std::cout << data[0] << std::endl;
// First, we read in the data
std::vector<TimeTree*> trees = NclReader::getInstance().readTimeTrees( treeFilename );
std::cout << "Read " << trees.size() << " trees." << std::endl;
std::cout << trees[0]->getNewickRepresentation() << std::endl;
// #######################################
// ###### birth-death process priors #####
// #######################################
// Constant nodes
ConstantNode<double> *dLambda = new ConstantNode<double>("div_rate", new double(1.0 / 5.0)); // Exponential rate for prior on div
ConstantNode<double> *turnA = new ConstantNode<double>("turn_alpha", new double(2.0)); // Beta distribution alpha
ConstantNode<double> *turnB = new ConstantNode<double>("turn_beta", new double(2.0)); // Beta distribution beta
ConstantNode<double> *rho = new ConstantNode<double>("rho", new double(1.0)); // assume 100% sampling for now
ConstantNode<double> *meanOT = new ConstantNode<double>("meanOT", new double(trees[0]->getRoot().getAge()*1.5));
ConstantNode<double> *stdOT = new ConstantNode<double>("stdOT", new double(10.0));
// Stochastic nodes
StochasticNode<double> *origin = new StochasticNode<double>( "origin", new NormalDistribution(meanOT, stdOT) );
StochasticNode<double> *div = new StochasticNode<double>("diversification", new ExponentialDistribution(dLambda));
StochasticNode<double> *turn = new StochasticNode<double>("turnover", new BetaDistribution(turnA, turnB));
// Deterministic nodes
// birthRate = div / (1 - turn)
DeterministicNode<double> *birthRate = new DeterministicNode<double>("birth_rate", new BirthRateConstBDStatistic(div, turn));
// deathRate = (div * turn) / ( 1 - turn)
DeterministicNode<double> *deathRate = new DeterministicNode<double>("death_rate", new DeathRateConstBDStatistic(div, turn));
// For some datasets with large root ages, if div>1.0 (or so), the probability is NaN
RandomNumberGenerator* rng = GLOBAL_RNG;
div->setValue(rng->uniform01() / 1.5);
// Birth-death tree
std::vector<std::string> names = data[0]->getTaxonNames();
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, birthRate, deathRate, rho, "uniform", "nTaxa", taxa, std::vector<Clade>()) );
DeterministicNode<double> *treeHeight = new DeterministicNode<double>("TreeHeight", new TreeHeightStatistic(tau) );
// ##############################################
// #### ACLN Model on Branch Rates #####
// ##############################################
size_t numBranches = 2 * data[0]->getNumberOfTaxa() - 2;
size_t numNodes = numBranches + 1; // model rates at nodes
ConstantNode<double> *a = new ConstantNode<double>("a", new double(4.0) );
ConstantNode<double> *b = new ConstantNode<double>("b", new double(4.0) );
ConstantNode<double> *anu = new ConstantNode<double>("a_nu", new double(1.0) );
ConstantNode<double> *bnu = new ConstantNode<double>("b_nu", new double(8.0) );
StochasticNode<double> *rootRate = new StochasticNode<double>("root.rate", new GammaDistribution(a, b));
StochasticNode<double> *bmNu = new StochasticNode<double>("BM_var", new GammaDistribution(anu, bnu));
size_t rootID = trees[0]->getRoot().getIndex();
ConstantNode<double> *crInv = new ConstantNode<double>("invCr", new double(1.0) );
DeterministicNode<double> *scaleRate = new DeterministicNode<double>("scaleRate", new BinaryDivision<double, double, double>(crInv, treeHeight));
StochasticNode< std::vector< double > > *nodeRates = new StochasticNode< std::vector< double > >( "NodeRates", new AutocorrelatedLognormalRateDistribution(tau, bmNu, rootRate, scaleRate) );
std::cout << nodeRates->getValue().size() << std::endl;
std::vector<const TypedDagNode<double> *> branchRates;
for( size_t i=0; i<numBranches; i++){
std::ostringstream brName;
brName << "br(" << i << ")";
DeterministicNode<double> *tmpBrRt = new DeterministicNode<double>(brName.str(), new RateOnBranchAve(nodeRates, tau, scaleRate, i));
branchRates.push_back( tmpBrRt );
}
DeterministicNode< std::vector< double > >* brVector = new DeterministicNode< std::vector< double > >( "branchRates", new VectorFunction< double >( branchRates ) );
// making a combined DagNode for a compound move
std::vector<DagNode*> treeAndRates;
treeAndRates.push_back( tau );
treeAndRates.push_back(nodeRates);
treeAndRates.push_back(rootRate);
// ####################################
// ###### GTR model priors ######
// Constant nodes
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) );
// Stochastic nodes
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) );
DeterministicNode<RateMatrix> *q = new DeterministicNode<RateMatrix>( "Q", new GtrRateMatrixFunction(er, pi) );
std::cout << "Q:\t" << q->getValue() << std::endl;
// ####### Gamma Rate Het. ######
ConstantNode<double> *shapePr = new ConstantNode<double>("gammaShPr", new double(0.5));
StochasticNode<double> *srAlpha = new StochasticNode<double>("siteRates.alpha", new ExponentialDistribution(shapePr));
ConstantNode<double> *q1 = new ConstantNode<double>("q1", new double(0.125) );
DeterministicNode<double> *q1Value = new DeterministicNode<double>("q1_value", new QuantileFunction(q1, new GammaDistribution(srAlpha, srAlpha) ) );
ConstantNode<double> *q2 = new ConstantNode<double>("q2", new double(0.375) );
DeterministicNode<double> *q2Value = new DeterministicNode<double>("q2_value", new QuantileFunction(q2, new GammaDistribution(srAlpha, srAlpha) ) );
ConstantNode<double> *q3 = new ConstantNode<double>("q3", new double(0.625) );
DeterministicNode<double> *q3Value = new DeterministicNode<double>("q3_value", new QuantileFunction(q3, new GammaDistribution(srAlpha, srAlpha) ) );
ConstantNode<double> *q4 = new ConstantNode<double>("q4", new double(0.875) );
DeterministicNode<double> *q4Value = new DeterministicNode<double>("q4_value", new QuantileFunction(q4, new GammaDistribution(srAlpha, srAlpha) ) );
std::vector<const TypedDagNode<double>* > gammaRates = std::vector<const TypedDagNode<double>* >();
gammaRates.push_back(q1Value);
gammaRates.push_back(q2Value);
gammaRates.push_back(q3Value);
gammaRates.push_back(q4Value);
DeterministicNode<std::vector<double> > *siteRates = new DeterministicNode<std::vector<double> >( "site_rates", new VectorFunction<double>(gammaRates) );
DeterministicNode<std::vector<double> > *siteRatesNormed = new DeterministicNode<std::vector<double> >( "site_rates_norm", new NormalizeVectorFunction(siteRates) );
tau->setValue( trees[0] );
std::cout << "tau:\t" << tau->getValue() << std::endl;
std::cout << " ** origin " << origin->getValue() << std::endl;
std::cout << " ** root age " << trees[0]->getRoot().getAge() << std::endl;
GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree> *phyloCTMC = new GeneralBranchHeterogeneousCharEvoModel<DnaState, TimeTree>(tau, 4, true, data[0]->getNumberOfCharacters());
phyloCTMC->setClockRate( brVector );
phyloCTMC->setRateMatrix( q );
phyloCTMC->setSiteRates( siteRatesNormed );
StochasticNode< AbstractCharacterData > *charactermodel = new StochasticNode< AbstractCharacterData >("S", phyloCTMC );
charactermodel->clamp( data[0] );
std::cout << " diversification: " << div->getValue() << std::endl;
std::cout << " turnover: " << turn->getValue() << std::endl;
std::cout << " birth rate: " << birthRate->getValue() << std::endl;
std::cout << " death rate: " << deathRate->getValue() << std::endl;
/* add the moves */
RbVector<Move> moves;
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(div, 1.0), 1.0, true ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(turn, 1.0), 1.0, 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 RootTimeSlide( tau, 50.0, true, 10.0 ) );
moves.push_back( new OriginTimeSlide( origin, tau, 50.0, true, 10.0 ) );
moves.push_back( new NodeTimeSlideUniform( tau, 30.0 ) );
moves.push_back( new SimplexMove( er, 450.0, 6, 0, true, 2.0, 0.5 ) );
moves.push_back( new SimplexMove( pi, 250.0, 4, 0, true, 2.0, 0.5 ) );
moves.push_back( new SimplexMove( er, 200.0, 1, 0, false, 0.5 ) );
moves.push_back( new SimplexMove( pi, 100.0, 1, 0, false, 0.5 ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(srAlpha, log(2.0)), 1, true ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(bmNu, 0.75), 4, true ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(rootRate, 0.5), 2, false ) );
moves.push_back( new MetropolisHastingsMove( new ScaleProposal(rootRate, 1.0), 2, false ) );
moves.push_back( new ScaleSingleACLNRatesMove( nodeRates, 1.0, false, 8.0 * (double)numNodes) );
moves.push_back( new ScaleSingleACLNRatesMove( nodeRates, 2.0, false, 8.0 * (double)numNodes) );
moves.push_back( new RateAgeACLNMixingMove( treeAndRates, 0.02, false, 2.0 ) );
// add some tree stats to monitor
DeterministicNode<double> *meanNdRate = new DeterministicNode<double>("MeanNodeRate", new MeanVecContinuousValStatistic(nodeRates) );
/* add the monitors */
RbVector<Monitor> monitors;
std::vector<DagNode*> monitoredNodes;
monitoredNodes.push_back( meanNdRate );
monitoredNodes.push_back( treeHeight );
monitoredNodes.push_back( origin );
monitoredNodes.push_back( nodeRates );
monitoredNodes.push_back( rootRate );
monitoredNodes.push_back( bmNu );
monitoredNodes.push_back( scaleRate );
monitors.push_back( new ScreenMonitor( monitoredNodes, 10, "\t" ) );
monitoredNodes.push_back( div );
monitoredNodes.push_back( turn );
monitoredNodes.push_back( birthRate );
monitoredNodes.push_back( deathRate );
monitoredNodes.push_back( pi );
monitoredNodes.push_back( er );
monitoredNodes.push_back( srAlpha );
monitoredNodes.push_back( brVector );
std::string logFN = "clock_test/test_rb_ACLN_6June_rn_3.log";
monitors.push_back( new FileMonitor( monitoredNodes, 10, logFN, "\t" ) );
std::set<DagNode*> monitoredNodes2;
monitoredNodes2.insert( tau );
// std::string treFN = "clock_test/test_rb_ACLN_6June_pr.tre";
// monitors.push_back( new FileMonitor( monitoredNodes2, 10, treFN, "\t", false, false, false ) );
/* instantiate the model */
Model myModel = Model(q);
mcmcGenerations = 200000;
/* instiate and run the MCMC */
Mcmc myMcmc = Mcmc( myModel, moves, monitors );
myMcmc.run(mcmcGenerations);
myMcmc.printOperatorSummary();
/* clean up */
// delete div;
// delete turn;
// delete rho;
// delete cp;
// delete branchRates;
// delete q;
// delete tau;
delete charactermodel;
// delete a;
// delete birthRate;
// delete phyloCTMC;
// delete dLambda;
monitors.clear();
moves.clear();
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;
}