Beispiel #1
0
double E_rate(const vector<vector<double> >& P, int c,const substitution::MultiModel& smodel)
{
  double R=0;
  for(int m=0;m<smodel.n_base_models();m++)
    R += P[c][m]*smodel.base_model(m).rate();
  return R;
}
Beispiel #2
0
void estimate_tree(const alignment& A,
		   SequenceTree& T,
		   substitution::MultiModel& smodel,
		   const vector<int>& parameters)
{
  //------- Estimate branch lengths -------------//
  log_branch_likelihood score2(A,smodel,T,parameters);
  
  // Initialize starting point
  optimize::Vector start(0.1, T.n_branches() + parameters.size());
  for(int b=0;b<T.n_branches();b++)
    start[b] = log(T.branch(b).length());
  for(int i=0;i<parameters.size();i++)
    start[i+T.n_branches()] = smodel.get_parameter_value_as<Double>( parameters[i] );

  //    optimize::Vector end = search_gradient(start,score);
  //    optimize::Vector end = search_basis(start,score);
  optimize::Vector end = search_gradient(start,score2,1e-3);

  for(int b=0;b<T.n_branches();b++)
    T.branch(b).set_length(exp(end[b]));

  for(int i=0;i<parameters.size();i++)
    smodel.set_parameter_value(parameters[i], end[i+T.n_branches()]);

  smodel.set_rate(1);
}
Beispiel #3
0
double getSimilarity(double t,substitution::MultiModel& SM) 
{
  double S = 0;

  for(int m=0;m<SM.n_base_models();m++) {
    // We can't use models with more than one part
    Matrix Q = SM.transition_p(t,0,m);
    double Sm = 0;
    for(int i=0;i<Q.size1();i++)
      Sm += SM.base_model(m).frequencies()[i]*Q(i,i);
    S += Sm * SM.distribution()[m];
  }
  
  return S;
}
Beispiel #4
0
void analyze_rates(const alignment& A,const SequenceTree& T,
		   const substitution::MultiModel& smodel)
{
  if (smodel.n_base_models() == 1) return;

  data_partition DP("DP",A,T,smodel);

  vector< vector<double> > rate_probs = substitution::get_model_probabilities_by_alignment_column(DP);

  vector<double> prior_bin_f = smodel.distribution();
  
  vector<double> post_bin_f = get_post_rate_probs(rate_probs);

  show_rate_probs(cout,rate_probs,smodel);
    
  double prior_rate=0;
  double post_rate=0;
  for(int i=0;i<prior_bin_f.size();i++) {
    prior_rate += prior_bin_f[i]*smodel.base_model(i).rate();
    post_rate += post_bin_f[i]*smodel.base_model(i).rate();
  }

  for(int i=0;i<smodel.n_base_models();i++)
    cout<<"    rate"<<i<<" = "<<smodel.base_model(i).rate();
  cout<<endl<<endl;
  
  cout<<" Prior rate = "<<prior_rate<<endl;;
  for(int i=0;i<smodel.n_base_models();i++)
    cout<<"    prior_bin_f"<<i<<" = "<<prior_bin_f[i];
  cout<<endl<<endl;
  
  cout<<" Posterior rate = "<<post_rate<<endl;;
  for(int i=0;i<smodel.n_base_models();i++)
    cout<<"    post_bin_f"<<i<<" = "<<post_bin_f[i];
  cout<<endl<<endl;
  
  for(int i=0;i<smodel.n_base_models();i++)
    cout<<"    odds_ratio"<<i<<" = "<<post_bin_f[i]/prior_bin_f[i];
  cout<<endl<<endl;
}
Beispiel #5
0
void show_frequencies(std::ostream& o,const substitution::MultiModel& MModel) {
  const alphabet& a = MModel.Alphabet();

  if (MModel.n_base_models() == 1) {
    const valarray<double>& f = MModel.base_model(0).frequencies();
    for(int i=0;i<a.size();i++)
      o<<"f"<<a.lookup(i)<<" = "<<f[i]<<"\n";
  }
  else {

    for(int i=0;i<a.size();i++) {
      double total = 0;
      for(int m=0;m<MModel.n_base_models();m++) {
	const valarray<double>& f = MModel.base_model(m).frequencies();
	o<<"f"<<a.lookup(i)<<m+1<<" = "<<f[i]<<"     ";
	total += MModel.distribution()[m] * f[i];
      }
      o<<"f"<<a.lookup(i)<<" = "<<total<<"\n";
    }
  }
}
Beispiel #6
0
Multi_Likelihood_Cache::Multi_Likelihood_Cache(const substitution::MultiModel& MM)
    :C(0),
     M(MM.n_base_models()),
     S(MM.n_states())
{ }