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Use partition length instead of MSA length as sample size #74

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cda39ee
Use partition length instead of MSA length as sample size
stelzch Jan 16, 2025
c877e89
Output results in XML, increase floating point precision in output st…
stelzch Jan 22, 2025
eae0c0b
Print iteration count
stelzch Feb 5, 2025
59b1825
Use custom XML format
stelzch Feb 12, 2025
c9b0cff
Slightly modify XML output format
stelzch Sep 11, 2025
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2 changes: 1 addition & 1 deletion src/global_defs.h
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@
#define ERR_MSG_SIZE 240

#define UNUSED(expr) do { (void)(expr); } while (0)
#define MT_PRECISION_DIGITS 4
#define MT_PRECISION_DIGITS 17

#define DEFAULT_GAMMA_RATE_CATS 4
#define DEFAULT_GAMMA_RATE_MODE PLL_GAMMA_RATES_MEAN
Expand Down
28 changes: 28 additions & 0 deletions src/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,12 @@ int main(int argc, char *argv[])

ofstream * results_stream = 0;

ofstream xml_stream;
if (ROOT) {
xml_stream = ofstream(opts.output_results_file + ".xml", std::ios::out);
xml_stream << "<modeltestresults criterion=\"BIC\">" << std::setprecision(17) << endl;
}

if (ROOT)
results_stream = modeltest::Utils::open_file_for_writing(opts.output_results_file);

Expand Down Expand Up @@ -283,6 +289,19 @@ int main(int argc, char *argv[])
MT_INFO);
}

for (const auto model : ModelTestService::instance()->get_modeltest()->get_models(part_id)) {
xml_stream << "<model partition=\"" << i
<< "\" name=\"" << model->get_name()
<< "\" lnL=\"" << model->get_loglh()
<< "\" score=\"" << model->get_bic()
<< "\" score-bic=\"" << model->get_bic()
<< "\" score-aic=\"" << model->get_aic()
<< "\" score-aicc=\"" << model->get_aicc()
<< "\" free-params=\"" << model->get_n_free_variables()
<< "\" />" << endl;
}


delete bic_selection;
delete aic_selection;
delete aicc_selection;
Expand Down Expand Up @@ -368,6 +387,14 @@ int main(int argc, char *argv[])
<< opts.output_tree_file << endl;
//MT_INFO << "Log written to " << opts.output_log_file << endl;


if (ROOT) {
xml_stream << "</modeltestresults>" << endl;
xml_stream.close();

MT_INFO << "Model selections written to " << opts.output_results_file << ".xml." << endl;
}

/* clean */
if (opts.partitions_desc)
delete opts.partitions_desc;
Expand Down Expand Up @@ -400,5 +427,6 @@ BARRIER;

ModelTestService::finalize( false );


return return_val;
}
6 changes: 5 additions & 1 deletion src/optimize/model_optimizer_pll.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ ModelOptimizerPll::ModelOptimizerPll (MsaPll &_msa,
model.set_loglh(cur_loglh);
model.set_exec_time(end_time - start_time);

model.evaluate_criteria(n_branches, msa.get_n_sites());
model.evaluate_criteria(n_branches, partition.get_n_sites());

if (optimize_topology)
model.set_tree(pll_tree);
Expand Down Expand Up @@ -198,6 +198,7 @@ ModelOptimizerPll::ModelOptimizerPll (MsaPll &_msa,
if (opt_per_param)
{
bool all_params_done = false;
size_t i = 0;
while ((fabs (cur_loglh - save_loglh) > epsilon && cur_loglh > save_loglh))
{
save_loglh = cur_loglh;
Expand All @@ -222,7 +223,10 @@ ModelOptimizerPll::ModelOptimizerPll (MsaPll &_msa,
opt_delta = cur_loglh;
notify();
}
++i;
}

LOG_INFO << "\t\t" << model.get_name() << " part " << partition.get_unique_id() << " eps-iteration count: " << i << endl;
}
else
{
Expand Down