double PartitionModel::optimizeLinkedAlpha(bool write_info, double gradient_epsilon) {
if (write_info)
cout << "Optimizing linked gamma shape..." << endl;
double negative_lh;
double current_shape = linked_alpha;
double ferror, optx;
optx = minimizeOneDimen(MIN_GAMMA_SHAPE, current_shape, MAX_GAMMA_SHAPE, max(gradient_epsilon, TOL_GAMMA_SHAPE), &negative_lh, &ferror);
if (write_info)
cout << "Linked alpha across partitions: " << linked_alpha << endl;
return site_rate->getTree()->computeLikelihood();
}
double RateGamma::optimizeParameters(double gradient_epsilon) {
if (fix_gamma_shape)
return phylo_tree->computeLikelihood();
if (verbose_mode >= VB_MAX)
cout << "Optimizing gamma shape..." << endl;
double negative_lh;
double current_shape = gamma_shape;
double ferror, optx;
optx = minimizeOneDimen(phylo_tree->params->min_gamma_shape, current_shape, MAX_GAMMA_SHAPE, max(gradient_epsilon, TOL_GAMMA_SHAPE), &negative_lh, &ferror);
// gamma_shape = optx;
// computeRates();
// phylo_tree->clearAllPartialLH();
// return -negative_lh;
return -computeFunction(optx);
}
double RateInvar::optimizeParameters(double gradient_epsilon) {
if (phylo_tree->aln->frac_const_sites == 0.0)
return -computeFunction(0.0);
if (fix_p_invar || !optimize_p_invar)
return -computeFunction(p_invar);
if (verbose_mode >= VB_MAX)
cout << "Optimizing proportion of invariable sites..." << endl;
double negative_lh;
double ferror;
p_invar = minimizeOneDimen(MIN_PINVAR, p_invar, min(phylo_tree->aln->frac_const_sites, 1.0-MIN_PINVAR), max(gradient_epsilon, TOL_PINVAR), &negative_lh, &ferror);
//p_invar = minimizeOneDimen(MIN_PINVAR, p_invar, 1.0 - MIN_PINVAR, TOL_PINVAR, &negative_lh, &ferror);
// phylo_tree->clearAllPartialLH();
// phylo_tree->computePtnInvar();
// return -negative_lh;
return -computeFunction(p_invar);
}
double RateMeyerDiscrete::optimizeCatRate(int cat) {
optimizing_cat = cat;
double negative_lh;
double current_rate = rates[cat];
double ferror, optx;
if (!rate_mh) {
IntVector ptn_id;
for (int i = 0; i < size(); i++)
if (ptn_cat[i] == optimizing_cat)
ptn_id.push_back(i);
prepareRateML(ptn_id);
}
if (phylo_tree->optimize_by_newton && rate_mh) // Newton-Raphson method
{
optx = minimizeNewtonSafeMode(MIN_SITE_RATE, current_rate, MAX_SITE_RATE, TOL_SITE_RATE, negative_lh);
}
else {
optx = minimizeOneDimen(MIN_SITE_RATE, current_rate, MAX_SITE_RATE, TOL_SITE_RATE, &negative_lh, &ferror);
double fnew;
if ((optx < MAX_SITE_RATE) && (fnew = computeFunction(MAX_SITE_RATE)) <= negative_lh+TOL_SITE_RATE) {
optx = MAX_SITE_RATE;
negative_lh = fnew;
}
if ((optx > MIN_SITE_RATE) && (fnew = computeFunction(MIN_SITE_RATE)) <= negative_lh+TOL_SITE_RATE) {
optx = MIN_SITE_RATE;
negative_lh = fnew;
}
}
//negative_lh = brent(MIN_SITE_RATE, current_rate, max_rate, 1e-3, &optx);
if (optx > MAX_SITE_RATE*0.99) optx = MAX_SITE_RATE;
if (optx < MIN_SITE_RATE*2) optx = MIN_SITE_RATE;
rates[cat] = optx;
//#ifndef NDEBUG
//#endif
if (!rate_mh) completeRateML();
return optx;
}
double RateMeyerHaeseler::optimizeRate(int pattern) {
optimizing_pattern = pattern;
double max_rate = MAX_SITE_RATE;
double minf = INFINITY, minx = 0;
double negative_lh;
double current_rate = at(pattern);
double ferror, optx;
/* constant site alway have ZERO rates */
if (phylo_tree->aln->at(pattern).is_const) {
return (at(pattern) = MIN_SITE_RATE);
}
if (!rate_mh) {
IntVector ptn_id;
ptn_id.push_back(optimizing_pattern);
prepareRateML(ptn_id);
}
if (phylo_tree->optimize_by_newton && rate_mh) // Newton-Raphson method
{
optx = minimizeNewtonSafeMode(MIN_SITE_RATE, current_rate, max_rate, TOL_SITE_RATE, negative_lh);
if (optx > MAX_SITE_RATE*0.99 || (optx < MIN_SITE_RATE*2 && !phylo_tree->aln->at(pattern).is_const))
{
double optx2, negative_lh2;
optx2 = minimizeOneDimen(MIN_SITE_RATE, current_rate, max_rate, TOL_SITE_RATE, &negative_lh2, &ferror);
if (negative_lh2 < negative_lh - 1e-4) {
cout << "+++NEWTON IS WRONG for pattern " << pattern << ": " << optx2 << " " <<
negative_lh2 << " (Newton: " << optx << " " << negative_lh <<")" << endl;
}
if (negative_lh < negative_lh2 - 1e-4 && verbose_mode >= VB_MED) {
cout << "Brent is wrong for pattern " << pattern << ": " << optx2 << " " <<
negative_lh2 << " (Newton: " << optx << " " << negative_lh <<")" << endl;
}
}
}
else {
optx = minimizeOneDimen(MIN_SITE_RATE, current_rate, max_rate, TOL_SITE_RATE, &negative_lh, &ferror);
double fnew;
if ((optx < max_rate) && (fnew = computeFunction(max_rate)) <= negative_lh+TOL_SITE_RATE) {
optx = max_rate;
negative_lh = fnew;
}
if ((optx > MIN_SITE_RATE) && (fnew = computeFunction(MIN_SITE_RATE)) <= negative_lh+TOL_SITE_RATE) {
optx = MIN_SITE_RATE;
negative_lh = fnew;
}
}
//negative_lh = brent(MIN_SITE_RATE, current_rate, max_rate, 1e-3, &optx);
if (optx > max_rate*0.99) optx = MAX_SITE_RATE;
if (optx < MIN_SITE_RATE*2) optx = MIN_SITE_RATE;
at(pattern) = optx;
if (!rate_mh) {
completeRateML();
return optx;
}
//#ifndef NDEBUG
if (optx == MAX_SITE_RATE || (optx == MIN_SITE_RATE && !phylo_tree->aln->at(pattern).is_const)) {
ofstream out;
if (verbose_mode >= VB_MED) {
cout << "Checking pattern " << pattern << " (" << current_rate << ", " << optx << ")" << endl;
out.open("x", ios::app);
out << pattern;
}
for (double val=0.1; val <= 100; val += 0.1) {
double f = computeFunction(val);
if (verbose_mode >= VB_MED) out << " " << f;
if (f < minf) { minf = f; minx = val; }
if (verbose_mode < VB_MED && minf < negative_lh) break;
}
if (verbose_mode >= VB_MED) {
out << endl;
out.close();
}
//cout << "minx: " << minx << " " << minf << endl;
if (negative_lh > minf+1e-3) {
optx = minimizeOneDimen(MIN_SITE_RATE, minx, max_rate, 1e-3, &negative_lh, &ferror);
at(pattern) = optx;
if (verbose_mode >= VB_MED)
cout << "FIX rate: " << minx << " , " << optx << endl;
}
}
//#endif
return optx;
}