void slice_sample_branch_length(owned_ptr<Probability_Model>& P,MoveStats& Stats,int b)
{
Parameters& PP = *P.as<Parameters>();
PP.select_root(b);
const double L = PP.T->directed_branch(b).length();
const double mu = PP.branch_mean();
MCMC::Result result(3);
//------------- Find new length --------------//
double sigma = loadvalue(P->keys,"slice_branch_sigma",1.5);
// NOTE - it is OK to depend on L below -- IF AND ONLY IF the likelihood is unimodal.
double w = sigma*(PP.branch_mean()+L);
branch_length_slice_function logp(PP,b);
double L2 = slice_sample(L,logp,w,100);
//---------- Record Statistics - -------------//
result.totals[0] = std::abs(L2 - L);
result.totals[1] = std::abs(log(L2/L));
result.totals[2] = logp.count;
Stats.inc("branch-length (slice) *",result);
if (L < mu/2.0)
Stats.inc("branch-length (slice) 1",result);
else if (L < mu)
Stats.inc("branch-length (slice) 2",result);
else if (L < mu*2)
Stats.inc("branch-length (slice) 3",result);
else
Stats.inc("branch-length (slice) 4",result);
}
void slide_node(owned_ptr<Probability_Model>& P, MoveStats& Stats,int b0)
{
Parameters* PP = P.as<Parameters>();
vector<const_branchview> b;
b.push_back( PP->T->directed_branch(b0) );
// choose branches to alter
if (uniform() < 0.5)
b[0] = b[0].reverse();
if (b[0].target().is_leaf_node())
b[0] = b[0].reverse();
append(b[0].branches_after(),b);
b0 = b[0].name();
int b1 = b[1].undirected_name();
int b2 = b[2].undirected_name();
double L1a = PP->T->branch(b1).length();
double L2a = PP->T->branch(b2).length();
PP->set_root(b[0].target());
double p = loadvalue(P->keys,"branch_slice_fraction",0.9);
if (uniform() < p)
{
slide_node_slice_function logp(*PP,b0);
double w = logp.total * loadvalue(P->keys,"slide_branch_slice_window",0.3);
double L1b = slice_sample(logp,w,100);
MCMC::Result result(2);
result.totals[0] = 2.0*std::abs(L1b-L1a);
result.totals[1] = logp.count;
Stats.inc("slide_node_slice",result);
}
else {
bool success; string name;
if (uniform() < 0.5) {
success = slide_node(P, b, slide_node_no_expand_branch);
name = "slide_node";
}
else {
success = slide_node(P, b, slide_node_expand_branch);
name = "slide_node_expand_branch";
}
PP = P.as<Parameters>();
double L1b = PP->T->branch(b1).length();
double L2b = PP->T->branch(b2).length();
MCMC::Result result(2);
result.totals[0] = success?1:0;
result.totals[1] = std::abs(L1b-L1a) + std::abs(L2b-L2a);
Stats.inc(name,result);
}
}
void SPR_inc(MoveStats& Stats, MCMC::Result result,const string& name,double L)
{
Stats.inc(name, result);
if (L < 0.5)
Stats.inc(name+"-0.5", result);
else if (L < 1)
Stats.inc(name+"-1.0", result);
else if (L < 2.0)
Stats.inc(name+"-2.0", result);
else
Stats.inc(name+"-2.0+", result);
}
void sample_tri_branch_one(Parameters& P, MoveStats& Stats,int b)
{
if (not P.smodel_full_tree and b>=P.T->n_leaves())
return;
MCMC::Result result(2);
assert(P.n_imodels() > 0);
const SequenceTree& T = *P.T;
int node1 = T.branch(b).target();
int node2 = T.branch(b).source();
if (myrandomf() < 0.5)
std::swap(node1,node2);
if (node1 < T.n_leaves())
std::swap(node1,node2);
const double sigma = 0.3/2;
double length1 = T.branch(b).length();
double length2 = length1 + gaussian(0,sigma);
if (length2 < 0) length2 = -length2;
if (tri_sample_alignment_branch(P,node1,node2,b,1,length2)) {
result.totals[0] = 1;
result.totals[1] = std::abs(length2 - length1);
}
Stats.inc("sample_tri_branch",result);
}
void sample_tri_branch_type_one(Parameters& P, MoveStats& Stats,int b)
{
if (not P.smodel_full_tree and b>=P.T->n_leaves())
return;
MCMC::Result result(1);
assert(P.n_imodels() > 0);
const SequenceTree& T = *P.T;
int node1 = T.branch(b).target();
int node2 = T.branch(b).source();
if (myrandomf() < 0.5)
std::swap(node1,node2);
if (node1 < T.n_leaves())
std::swap(node1,node2);
if (tri_sample_alignment_branch_model(P,node1,node2)) {
result.totals[0] = 1;
}
Stats.inc("sample_tri_branch_type",result);
}
void change_branch_length_flat(owned_ptr<Probability_Model>& P,
MoveStats& Stats,int b,double sigma)
{
Parameters& PP = *P.as<Parameters>();
const double L = PP.T->directed_branch(b).length();
const double mu = PP.branch_mean();
MCMC::Result result = change_branch_length_(P, b, sigma*PP.branch_mean(), branch_twiddle_positive);
Stats.inc("branch-length *",result);
if (L < mu/2.0)
Stats.inc("branch-length 1",result);
else if (L < mu)
Stats.inc("branch-length 2",result);
else if (L < mu*2)
Stats.inc("branch-length 3",result);
else
Stats.inc("branch-length 4",result);
}
void change_branch_length_log_scale(owned_ptr<Probability_Model>& P,
MoveStats& Stats,
int b,
double sigma)
{
const double L = P.as<Parameters>()->T->directed_branch(b).length();
const double mu = P.as<Parameters>()->branch_mean();
MCMC::Result result = change_branch_length_(P, b, sigma, scale_gaussian );
Stats.inc("branch-length (log) *",result);
if (L < mu/2.0)
Stats.inc("branch-length (log) 1",result);
else if (L < mu)
Stats.inc("branch-length (log) 2",result);
else if (L < mu*2)
Stats.inc("branch-length (log) 3",result);
else
Stats.inc("branch-length (log) 4",result);
}
void sample_SPR_nodes(Parameters& P,MoveStats& Stats)
{
double f = loadvalue(P.keys,"SPR_amount",0.1);
int n = poisson(P.T->n_branches()*f);
double p = loadvalue(P.keys,"SPR_slice_fraction",-0.25);
for(int i=0; i<n; i++) {
int b1=-1, b2=-1;
choose_subtree_branch_nodes(*P.T, b1, b2);
if (P.n_imodels() == 0 and uniform()< p) {
MCMC::Result result = sample_SPR(P,b1,b2,true);
Stats.inc("SPR (path/slice)", result);
}
else {
MCMC::Result result = sample_SPR(P,b1,b2);
Stats.inc("SPR (path)", result);
}
}
}
void Parameter_Slice_Move::iterate(owned_ptr<Model>& P,MoveStats& Stats,int)
{
double v1 = P->get_parameter_value(index).as_double();
parameter_slice_function logp(*P,index,transform,inverse);
double v2 = sample(*P,logp,v1);
//---------- Record Statistics - -------------//
Result result(2);
result.totals[0] = std::abs(v2-v1);
result.totals[1] = logp.count;
Stats.inc(name,result);
}
/// Update statistics counters for an NNI move.
void NNI_inc(MoveStats& Stats, const string& name, MCMC::Result result,double L)
{
Stats.inc(name, result);
if (L < 0.0325)
Stats.inc(name+"-0.0325", result);
else if (L < 0.065)
Stats.inc(name+"-0.065", result);
else if (L < 0.125)
Stats.inc(name+"-0.125", result);
else if (L < 0.25)
Stats.inc(name+"-0.25", result);
else if (L < 0.5)
Stats.inc(name+"-0.5", result);
else if (L < 1)
Stats.inc(name+"-1.0", result);
else if (L < 2.0)
Stats.inc(name+"-2.0", result);
else
Stats.inc(name+"-2.0+", result);
}
void Modifiable_Slice_Move::iterate(owned_ptr<Model>& P,MoveStats& Stats,int)
{
#ifndef NDEBUG
clog<<" [modifiable slice] move = "<<m_index<<endl;
#endif
double v1 = P->get_modifiable_value(m_index).as_double();
modifiable_slice_function logp(*P, m_index, bounds, transform, inverse);
double v2 = sample(*P,logp,v1);
//---------- Record Statistics --------------//
Result result(2);
result.totals[0] = std::abs(v2-v1);
result.totals[1] = logp.count;
Stats.inc(name,result);
}
void Dirichlet_Modifiable_Slice_Move::iterate(owned_ptr<Model>& P,MoveStats& Stats,int)
{
#ifndef NDEBUG
clog<<" [dirichlet modifiable slice] move"<<endl;
#endif
double v1 = P->get_modifiable_value(indices[n]).as_double();
constant_sum_modifiable_slice_function slice_levels_function(*P,indices,n);
double v2 = sample(*P,slice_levels_function,v1);
//---------- Record Statistics - -------------//
Result result(2);
vector<double> x = vec_to_double(P->get_modifiable_values(indices));
double total = sum(x);
double factor = (total - v2)/(total-v1);
result.totals[0] = std::abs(log(v2/v1)) + (indices.size()-1)*(std::abs(log(factor)));
result.totals[1] = slice_levels_function.count;
Stats.inc(name,result);
}
void Scale_Means_Only_Slice_Move::iterate(owned_ptr<Model>& P, MoveStats& Stats,int)
{
#ifndef NDEBUG
clog<<" [scale means only slice] move"<<endl;
#endif
Parameters& PP = *P.as<Parameters>();
// If any of the branch means are fixed, this won't work.
double v1 = 0;
try
{
scale_means_only_slice_function slice_levels_function(PP);
double v2 = sample(PP,slice_levels_function, v1);
//---------- Record Statistics --------------//
Result result(2);
result.totals[0] = std::abs(v2);
result.totals[1] = slice_levels_function.count;
Stats.inc(name,result);
}
catch (...) {}
}
/// Propose three neighboring branch lengths all anti-correlated
void change_3_branch_lengths(owned_ptr<Probability_Model>& P,MoveStats& Stats,int n)
{
Parameters* PP = P.as<Parameters>();
MCMC::Result result(2);
const Tree& T = *PP->T;
if (not T[n].is_internal_node()) return;
//-------------- Find branches ------------------//
vector<const_branchview> branches;
append(T[n].branches_out(),branches);
int b1 = branches[0].undirected_name();
int b2 = branches[1].undirected_name();
int b3 = branches[2].undirected_name();
//------------ Change coordinates ---------------//
double T1 = T.branch(b1).length();
double T2 = T.branch(b2).length();
double T3 = T.branch(b3).length();
double S12 = T1 + T2;
double S23 = T2 + T3;
double S31 = T3 + T1;
//----------- Propose new distances -------------//
double sigma = loadvalue(P->keys,"log_branch_sigma",0.6)/2.0;
double ratio = 1.0;
double T1_ = T1;
double T2_ = T2;
double T3_ = T3;
for(int i=0;i<20;i++)
{
double R12 = exp(gaussian(0,sigma));
double R23 = exp(gaussian(0,sigma));
double R31 = exp(gaussian(0,sigma));
double S12_ = S12 * R12;
double S23_ = S23 * R23;
double S31_ = S31 * R31;
//---------------- Change back ------------------//
T1_ = (S12_ + S31_ - S23_)/2.0;
T2_ = (S12_ + S23_ - S31_)/2.0;
T3_ = (S23_ + S31_ - S12_)/2.0;
ratio = R12 * R23 * R31;
if (T1_ > 0.0 and T2_ > 0.0 and T3_ > 0.0) break;
}
if (T1_ <= 0.0 or T2_ <= 0.0 or T3_ <= 0.0) return;
//----------- Construct proposed Tree -----------//
PP->set_root(n);
owned_ptr<Probability_Model> P2 = P;
P2.as<Parameters>()->setlength(b1,T1_);
P2.as<Parameters>()->setlength(b2,T2_);
P2.as<Parameters>()->setlength(b3,T3_);
//--------- Do the M-H step if OK--------------//
if (do_MH_move(P,P2,ratio)) {
result.totals[0] = 1;
result.totals[1] = abs(T1_-T1) + abs(T2_-T2) + abs(T3_-T3);
}
Stats.inc("3-branch-lengths",result);
}
void scale_means_only(owned_ptr<Probability_Model>& P,MoveStats& Stats)
{
Parameters* PP = P.as<Parameters>();
// If any of the partition rates are fixed, then we're out of luck
// FIXME - techincally, we could recompute likelihoods in just THOSE partitions :P
// - also, I suppose, if they are fixed, then there is no mixing problem.
for(int i=0;i<PP->n_branch_means();i++)
if (PP->is_fixed(PP->branch_mean_index(i)))
return;
MCMC::Result result(2);
//------------ Propose scaling ratio ------------//
const double sigma = loadvalue(P->keys,"log_branch_mean_sigma",0.6);
Bounds<double> b;
for(int i=0; i<PP->n_branch_means(); i++)
{
Bounds<double> b2 = PP->get_bounds(PP->branch_mean_index(i));
double mu = PP->get_parameter_value_as<Double>(PP->branch_mean_index(i));
if (b2.has_lower_bound and b2.lower_bound > 0)
{
b2.has_lower_bound = true;
b2.lower_bound = log(b2.lower_bound) - log(mu);
}
else
b2.has_lower_bound = false;
if (b2.has_upper_bound)
b2.upper_bound = log(b2.upper_bound) - log(mu);
b = b and b2;
}
double scale = gaussian(0,sigma);
scale = wrap(scale, b);
scale = exp(scale);
//-------- Change branch lengths and mean -------//
owned_ptr<Parameters> P2 = PP;
#ifndef NDEBUG
{
owned_ptr<Parameters> P3 = P2;
check_caching(*PP,*P3);
}
#endif
SequenceTree& T2 = *P2->T;
for(int b=0;b<T2.n_branches();b++) {
const double length = T2.branch(b).length();
T2.branch(b).set_length(length/scale);
}
P2->tree_propagate();
for(int i=0;i<PP->n_branch_means();i++)
P2->branch_mean_tricky(i, P2->get_parameter_value_as<Double>(P2->branch_mean_index(i)) * scale);
#ifndef NDEBUG
owned_ptr<Parameters> P3 = P2;
P3->recalc_imodels();
P3->recalc_smodels();
efloat_t L1 = PP->likelihood();
efloat_t L2 = P3->likelihood();
double diff = std::abs(log(L1)-log(L2));
if (diff > 1.0e-9) {
std::cerr<<"scale_mean_only: likelihood diff = "<<diff<<std::endl;
std::abort();
}
#endif
//--------- Compute proposal ratio ---------//
efloat_t p_ratio = pow(efloat_t(scale),P2->n_data_partitions()-T2.n_branches());
efloat_t a_ratio = P2->prior_no_alignment()/PP->prior_no_alignment()*p_ratio;
#ifndef NDEBUG
efloat_t a_ratio2 = P2->probability()/PP->probability()*p_ratio;
double diff2 = std::abs(log(a_ratio2)-log(a_ratio));
if (diff2 > 1.0e-9) {
std::cerr<<"scale_mean_only: a_ratio diff = "<<diff2<<std::endl;
std::cerr<<"probability ratio = "<<log(P2->probability()/PP->probability())<<std::endl;
std::cerr<<"likelihood ratio = "<<log(P2->likelihood()/PP->likelihood())<<std::endl;
std::cerr<<"prior ratio = "<<log(P2->prior()/PP->prior())<<std::endl;
std::cerr<<"prior ratio (no A)= "<<log(P2->prior_no_alignment()/PP->prior_no_alignment())<<std::endl;
std::cerr<<"prior ratio ( A)= "<<log(P2->prior_alignment()/PP->prior_alignment())<<std::endl;
std::cerr<<" a ratio = "<<log(a_ratio)<<std::endl;
std::abort();
}
#endif
if (uniform() < double(a_ratio))
{
P=P2;
result.totals[0] = 1;
result.totals[1] = std::abs(log(scale));
}
Stats.inc("branch-means-only",result);
}
void change_branch_length_and_T(owned_ptr<Probability_Model>& P,MoveStats& Stats,int b)
{
Parameters& PP = *P.as<Parameters>();
MCMC::Result result(5,0);
result.counts[0] = 1;
//------------- Propose new length --------------//
const double length = PP.T->directed_branch(b).length();
double newlength = length;
double ratio = branch_twiddle(newlength,PP.branch_mean()*0.6);
//----- positive => propose length change -----//
if (newlength >= 0)
{
result.counts[1] = 1;
result.counts[3] = 1;
//---------- Construct proposed Tree ----------//
PP.select_root(b);
owned_ptr<Probability_Model> P2 = P;
P2.as<Parameters>()->setlength(b,newlength);
//--------- Do the M-H step if OK--------------//
if (do_MH_move(P,P2,ratio)) {
result.totals[0] = 1;
result.totals[1] = 1;
result.totals[3] = std::abs(newlength - length);
}
}
//----- negative => propose topology ---------//
else
{
result.counts[2] = 1;
result.counts[4] = 1;
//----- Generate the Different Topologies ------//
vector<Parameters> p(2,PP);
SequenceTree& T2 = *p[1].T;
vector<int> nodes = A5::get_nodes_random(T2,b);
int b1 = T2.directed_branch(nodes[4],nodes[1]);
int b2 = T2.directed_branch(nodes[5],nodes[2]);
exchange_subtrees(T2,b1,b2);
p[1].invalidate_subA_index_branch(b);
vector<efloat_t> rho(2,1);
rho[1] = ratio;
//------ Sample the Different Topologies ------//
int C = two_way_topology_sample(p,rho,b);
if (C != -1) {
PP = p[C];
}
if (C > 0) {
result.totals[0] = 1;
result.totals[2] = 1;
result.totals[4] = std::abs(length - newlength);
}
}
Stats.inc("change_branch_length_and_T",result);
}
void MH_Move::iterate(owned_ptr<Model>& P,MoveStats& Stats,int)
{
#ifndef NDEBUG
clog<<" [MH] move = "<<name<<endl;
#endif
iterations++;
owned_ptr<Model> P2 = P;
double ratio = 1;
try {
ratio = (*proposal)(*P2);
}
catch (myexception& e)
{
std::ostringstream o;
o<<" [MH] move = "<<name<<" (during proposal)\n";
e.prepend(o.str());
throw e;
}
int n = 1;
Proposal2* p2 = dynamic_cast<Proposal2*>(&(*proposal));
int n_indices = -1;
if (p2) {
n_indices = p2->get_indices().size();
n = 2;
}
Result result(n);
#ifndef NDEBUG
show_parameters(std::cerr,*P);
std::cerr<<P->probability()<<" = "<<P->likelihood()<<" + "<<P->prior()<<endl;
std::cerr<<endl;
show_parameters(std::cerr,*P2);
std::cerr<<P2->probability()<<" = "<<P2->likelihood()<<" + "<<P2->prior();
std::cerr<<endl<<endl;
#endif
#ifndef NDEBUG
// Check that we have not strayed outside the bounds.
for(int i=0;i<P->n_parameters();i++)
{
if (not P->parameter_is_modifiable(i)) continue;
if (not P->get_parameter_value(i).is_double()) continue;
if (not P->has_bounds(i)) continue;
Bounds<double> range = P->get_bounds(i);
if (not range.in_range(P->get_parameter_value(i).as_double()))
throw myexception()<<"Parameter "<<P->parameter_name(i)<<" = "<<P->get_parameter_value(i).as_double()<<" is NOT in range "<<range;
if (not range.in_range(P2->get_parameter_value(i).as_double()))
throw myexception()<<"Parameter "<<P->parameter_name(i)<<" = "<<P->get_parameter_value(i).as_double()<<" is NOT in range "<<range;
}
#endif
// Accept or Reject
if (accept_MH(*P,*P2,ratio)) {
result.totals[0] = 1;
if (n == 2) {
int first_index = p2->get_indices()[0];
if (n_indices == 1 and P->get_parameter_value(first_index).is_double())
{
double v1 = P->get_parameter_value(first_index).as_double();
double v2 = P2->get_parameter_value(first_index).as_double();
// cerr<<"v1 = "<<v1<<" v2 = "<<v2<<"\n";
result.totals[1] = std::abs(v2-v1);
}
else if (n_indices > 1 and P->get_parameter_value(first_index).is_double()) //currently this can only be a dirichlet proposal
{
double total = 0;
for(int i=0;i<n_indices;i++)
{
int j = p2->get_indices()[i];
double v1 = P->get_parameter_value(j).as_double();
double v2 = P2->get_parameter_value(j).as_double();
total += std::abs(log(v1/v2));
}
result.totals[1] = total;
}
}
P = P2;
}
Stats.inc(name,result);
}