int main() {
TreeTemplate<Node>* tree = TreeTemplateTools::parenthesisToTree("(((A:0.1, B:0.2):0.3,C:0.1):0.2,(D:0.3,(E:0.2,F:0.05):0.1):0.1);");
vector<string> seqNames= tree->getLeavesNames();
vector<int> ids = tree->getNodesId();
//-------------
const NucleicAlphabet* alphabet = &AlphabetTools::DNA_ALPHABET;
FrequenciesSet* rootFreqs = new GCFrequenciesSet(alphabet);
SubstitutionModel* model = new T92(alphabet, 3.);
std::vector<std::string> globalParameterNames;
globalParameterNames.push_back("T92.kappa");
map<string, string> alias;
SubstitutionModelSet* modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, alias, globalParameterNames);
//DiscreteDistribution* rdist = new ConstantDistribution(1.0, true);
//Very difficult to optimize on small datasets:
DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
size_t nsites = 1000;
unsigned int nrep = 20;
size_t nmodels = modelSet->getNumberOfModels();
vector<double> thetas(nmodels);
vector<double> thetasEst1(nmodels);
vector<double> thetasEst2(nmodels);
for (size_t i = 0; i < nmodels; ++i) {
double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
cout << "Theta" << i << " set to " << theta << endl;
modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
thetas[i] = theta;
}
NonHomogeneousSequenceSimulator simulator(modelSet, rdist, tree);
for (unsigned int j = 0; j < nrep; j++) {
OutputStream* profiler = new StlOutputStream(new ofstream("profile.txt", ios::out));
OutputStream* messenger = new StlOutputStream(new ofstream("messages.txt", ios::out));
//Simulate data:
auto_ptr<SiteContainer> sites(simulator.simulate(nsites));
//Now fit model:
auto_ptr<SubstitutionModelSet> modelSet2(modelSet->clone());
auto_ptr<SubstitutionModelSet> modelSet3(modelSet->clone());
RNonHomogeneousTreeLikelihood tl(*tree, *sites.get(), modelSet2.get(), rdist, true, true, false);
tl.initialize();
RNonHomogeneousTreeLikelihood tl2(*tree, *sites.get(), modelSet3.get(), rdist, true, true, true);
tl2.initialize();
unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
&tl, tl.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
&tl2, tl2.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;
for (size_t i = 0; i < nmodels; ++i) {
cout << modelSet2->getModel(i)->getParameter("theta").getValue() << "\t" << modelSet3->getModel(i)->getParameter("theta").getValue() << endl;
//if (abs(modelSet2->getModel(i)->getParameter("theta").getValue() - modelSet3->getModel(i)->getParameter("theta").getValue()) > 0.1)
// return 1;
thetasEst1[i] += modelSet2->getModel(i)->getParameter("theta").getValue();
thetasEst2[i] += modelSet3->getModel(i)->getParameter("theta").getValue();
}
}
thetasEst1 /= static_cast<double>(nrep);
thetasEst2 /= static_cast<double>(nrep);
//Now compare estimated values to real ones:
for (size_t i = 0; i < thetas.size(); ++i) {
cout << thetas[i] << "\t" << thetasEst1[i] << "\t" << thetasEst2[i] << endl;
double diff1 = abs(thetas[i] - thetasEst1[i]);
double diff2 = abs(thetas[i] - thetasEst2[i]);
if (diff1 > 0.2 || diff2 > 0.2)
return 1;
}
//-------------
delete tree;
delete modelSet;
delete rdist;
return 0;
}
int main() {
TreeTemplate<Node>* tree = TreeTemplateTools::parenthesisToTree("((A:0.01, B:0.02):0.03,C:0.01,D:0.1);");
vector<string> seqNames= tree->getLeavesNames();
vector<int> ids = tree->getNodesId();
//-------------
NucleicAlphabet* alphabet = new DNA();
SubstitutionModel* model = new T92(alphabet, 3.);
FrequenciesSet* rootFreqs = new GCFrequenciesSet(alphabet);
std::vector<std::string> globalParameterNames;
globalParameterNames.push_back("T92.kappa");
map<string, string> alias;
SubstitutionModelSet* modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, alias, globalParameterNames);
DiscreteDistribution* rdist = new ConstantRateDistribution();
vector<double> thetas;
for (unsigned int i = 0; i < modelSet->getNumberOfModels(); ++i) {
double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
cout << "Theta" << i << " set to " << theta << endl;
modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
thetas.push_back(theta);
}
NonHomogeneousSequenceSimulator simulator(modelSet, rdist, tree);
unsigned int n = 100000;
OutputStream* profiler = new StlOutputStream(new ofstream("profile.txt", ios::out));
OutputStream* messenger = new StlOutputStream(new ofstream("messages.txt", ios::out));
//Check fast simulation first:
cout << "Fast check:" << endl;
//Generate data set:
VectorSiteContainer sites(seqNames, alphabet);
for (unsigned int i = 0; i < n; ++i) {
auto_ptr<Site> site(simulator.simulateSite());
site->setPosition(static_cast<int>(i));
sites.addSite(*site, false);
}
//Now fit model:
SubstitutionModelSet* modelSet2 = modelSet->clone();
RNonHomogeneousTreeLikelihood tl(*tree, sites, modelSet2, rdist);
tl.initialize();
OptimizationTools::optimizeNumericalParameters2(
&tl, tl.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
//Now compare estimated values to real ones:
for (size_t i = 0; i < thetas.size(); ++i) {
cout << thetas[i] << "\t" << modelSet2->getModel(i)->getParameter("theta").getValue() << endl;
double diff = abs(thetas[i] - modelSet2->getModel(i)->getParameter("theta").getValue());
if (diff > 0.1)
return 1;
}
delete modelSet2;
//Now try detailed simulations:
cout << "Detailed check:" << endl;
//Generate data set:
VectorSiteContainer sites2(seqNames, alphabet);
for (unsigned int i = 0; i < n; ++i) {
RASiteSimulationResult* result = simulator.dSimulateSite();
auto_ptr<Site> site(result->getSite(*simulator.getSubstitutionModelSet()->getModel(0)));
site->setPosition(static_cast<int>(i));
sites2.addSite(*site, false);
delete result;
}
//Now fit model:
SubstitutionModelSet* modelSet3 = modelSet->clone();
RNonHomogeneousTreeLikelihood tl2(*tree, sites2, modelSet3, rdist);
tl2.initialize();
OptimizationTools::optimizeNumericalParameters2(
&tl2, tl2.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
//Now compare estimated values to real ones:
for (size_t i = 0; i < thetas.size(); ++i) {
cout << thetas[i] << "\t" << modelSet3->getModel(i)->getParameter("theta").getValue() << endl;
double diff = abs(thetas[i] - modelSet3->getModel(i)->getParameter("theta").getValue());
if (diff > 0.1)
return 1;
}
delete modelSet3;
//-------------
delete tree;
delete alphabet;
delete modelSet;
delete rdist;
return 0;
}
int main() {
TreeTemplate<Node>* tree = TreeTemplateTools::parenthesisToTree("(((A:0.1, B:0.2):0.3,C:0.1):0.2,(D:0.3,(E:0.2,F:0.05):0.1):0.1);");
vector<string> seqNames= tree->getLeavesNames();
vector<int> ids = tree->getNodesId();
//-------------
const NucleicAlphabet* alphabet = &AlphabetTools::DNA_ALPHABET;
FrequenciesSet* rootFreqs = new GCFrequenciesSet(alphabet);
SubstitutionModel* model = new T92(alphabet, 3.);
std::vector<std::string> globalParameterNames;
globalParameterNames.push_back("T92.kappa");
//Very difficult to optimize on small datasets:
DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
ParametrizableTree* parTree = new ParametrizableTree(*tree);
FrequenciesSet* rootFreqs2 = rootFreqs->clone();
DiscreteDistribution* rdist2 = rdist->clone();
SubstitutionModel* model2=model->clone();
map<string, string> alias;
SubstitutionModelSet* modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, alias, globalParameterNames);
unique_ptr<SubstitutionModelSet> modelSetSim(modelSet->clone());
NonHomogeneousSubstitutionProcess* subPro= NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(model2, rdist2, rootFreqs2, parTree, globalParameterNames);
// Simulation
size_t nsites = 1000;
unsigned int nrep = 20;
size_t nmodels = modelSet->getNumberOfModels();
vector<double> thetas(nmodels);
vector<double> thetasEst1(nmodels);
vector<double> thetasEst2(nmodels);
vector<double> thetasEst1n(nmodels);
vector<double> thetasEst2n(nmodels);
for (size_t i = 0; i < nmodels; ++i) {
double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
cout << "Theta" << i << " set to " << theta << endl;
modelSetSim->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
//subPro->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
thetas[i] = theta;
}
NonHomogeneousSequenceSimulator simulator(modelSetSim.get(), rdist, tree);
NonHomogeneousSubstitutionProcess* subPro2 = subPro->clone();
for (unsigned int j = 0; j < nrep; j++) {
OutputStream* profiler = new StlOutputStream(new ofstream("profile.txt", ios::out));
OutputStream* messenger = new StlOutputStream(new ofstream("messages.txt", ios::out));
//Simulate data:
unique_ptr<SiteContainer> sites(simulator.simulate(nsites));
//Now fit model:
unique_ptr<SubstitutionModelSet> modelSet2(modelSet->clone());
RNonHomogeneousTreeLikelihood tl(*tree, *sites.get(), modelSet, rdist, true, true, false);
tl.initialize();
RNonHomogeneousTreeLikelihood tl2(*tree, *sites.get(), modelSet2.get(), rdist, true, true, true);
tl2.initialize();
SubstitutionProcess* nsubPro=subPro->clone();
SubstitutionProcess* nsubPro2=subPro2->clone();
RecursiveLikelihoodTreeCalculation* tlComp = new RecursiveLikelihoodTreeCalculation(*sites->clone(), nsubPro, true, false);
SingleProcessPhyloLikelihood ntl(nsubPro, tlComp, true);
RecursiveLikelihoodTreeCalculation* tlComp2 = new RecursiveLikelihoodTreeCalculation(*sites->clone(), nsubPro2, true);
SingleProcessPhyloLikelihood ntl2(nsubPro2, tlComp2, true);
for (size_t i = 0; i < nmodels; ++i) {
ntl.setParameterValue("T92.theta_" + TextTools::toString(i + 1), thetas[i]);
ntl2.setParameterValue("T92.theta_" + TextTools::toString(i + 1), thetas[i]);
}
cout << setprecision(10) << "OldTL init: " << tl.getValue() << "\t" << tl2.getValue() << endl;
cout << setprecision(10) << "NewTL init: " << ntl.getValue() << "\t" << ntl2.getValue() << endl;
unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
&tl, tl.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
&tl2, tl2.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
unsigned int nc1 = OptimizationTools::optimizeNumericalParameters2(
&ntl, ntl.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
unsigned int nc2 = OptimizationTools::optimizeNumericalParameters2(
&ntl2, ntl2.getParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
cout << "OldTL: " << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;
cout << "NewTL: " << nc1 << ": " << ntl.getValue() << "\t" << nc2 << ": " << ntl2.getValue() << endl;
cout << "Thetas : " << endl;
for (size_t i = 0; i < nmodels; ++i) {
// cerr << modelSet->getModel(i)->getParameter("theta").getValue() << "\t" << modelSet2->getModel(i)->getParameter("theta").getValue();
// cerr << "\t" << subPro->getModel(i)->getParameter("theta").getValue() << "\t" << subPro2->getModel(i)->getParameter("theta").getValue() << endl;
// if (abs(modelSet2->getModel(i)->getParameter("theta").getValue() - modelSet3->getModel(i)->getParameter("theta").getValue()) > 0.1)
// return 1;
thetasEst1[i] += modelSet->getModel(i)->getParameter("theta").getValue();
thetasEst2[i] += modelSet2->getModel(i)->getParameter("theta").getValue();
thetasEst1n[i] += dynamic_cast< NonHomogeneousSubstitutionProcess*>(nsubPro)->getModel(i)->getParameter("theta").getValue();
thetasEst2n[i] += dynamic_cast< NonHomogeneousSubstitutionProcess*>(nsubPro2)->getModel(i)->getParameter("theta").getValue();
}
}
thetasEst1 /= static_cast<double>(nrep);
thetasEst2 /= static_cast<double>(nrep);
thetasEst1n /= static_cast<double>(nrep);
thetasEst2n /= static_cast<double>(nrep);
//Now compare estimated values to real ones:
cout << "Real" << "\t" << "Est_Old1" << "\t" << "Est_Old2" << "\t";
cout << "Est_New1" << "\t" << "Est_New2" << endl;
for (size_t i = 0; i < thetas.size(); ++i) {
cout << thetas[i] << "\t" << thetasEst1[i] << "\t" << thetasEst2[i] << "\t";
cout << thetasEst1n[i] << "\t" << thetasEst2n[i] << endl;
double diff1 = abs(thetas[i] - thetasEst1[i]);
double diff2 = abs(thetas[i] - thetasEst2[i]);
double diffn1 = abs(thetas[i] - thetasEst1n[i]);
double diffn2 = abs(thetas[i] - thetasEst2n[i]);
if (diff1 > 0.2 || diff2 > 0.2 || diffn1 > 0.2 || diffn2 > 0.2)
return 1;
}
return 0;
}