/**
* Set the file extension.
*/
void AbstractFileMonitor::addFileExtension(const std::string &s, bool dir)
{
// compute the working filename
if ( dir == false )
{
RbFileManager fm = RbFileManager(filename);
working_file_name = fm.getFilePath() + fm.getPathSeparator() + fm.getFileNameWithoutExtension() + s + "." + fm.getFileExtension();
}
else
{
RbFileManager fm = RbFileManager(filename);
working_file_name = fm.getFilePath() + fm.getPathSeparator() + s + fm.getPathSeparator() + fm.getFileName();
}
}
/**
* Should we stop now?
* Yes, if the minimum ESS is larger than the provided threshold.
*/
bool GewekeStoppingRule::stop( size_t g )
{
bool passed = true;
for ( size_t i = 1; i <= numReplicates; ++i)
{
std::string fn = filename;
if ( numReplicates > 1 )
{
RbFileManager fm = RbFileManager(filename);
fn = fm.getFilePath() + fm.getPathSeparator() + fm.getFileNameWithoutExtension() + "_run_" + StringUtilities::to_string(i) + "." + fm.getFileExtension();
}
TraceContinuousReader reader = TraceContinuousReader( fn );
// get the vector of traces from the reader
std::vector<Trace> &data = reader.getTraces();
size_t maxBurnin = 0;
for ( size_t j = 0; j < data.size(); ++j)
{
Trace &t = data[j];
const std::vector<double> &v = t.getValues();
size_t b = burninEst->estimateBurnin( v );
if ( maxBurnin < b )
{
maxBurnin = b;
}
}
GewekeTest gTest = GewekeTest( alpha, frac1, frac2 );
for ( size_t j = 0; j < data.size(); ++j)
{
RevBayesCore::Trace &t = data[j];
const std::vector<double> &v = t.getValues();
t.setBurnin( maxBurnin );
t.computeStatistics();
passed &= gTest.assessConvergenceSingleChain( v, maxBurnin );
}
}
return passed;
}
void PowerPosteriorAnalysis::summarizeStones( void )
{
// create the directory if necessary
RbFileManager f = RbFileManager(filename);
f.createDirectoryForFile();
std::ofstream outStream;
outStream.open( filename.c_str(), std::fstream::out);
outStream << "state\t" << "power\t" << "likelihood" << std::endl;
/* Append each stone */
for (size_t idx = 0; idx < powers.size(); ++idx)
{
RbFileManager fm = RbFileManager(filename);
std::string stoneFileName = fm.getFileNameWithoutExtension() + "_stone_" + idx + "." + fm.getFileExtension();
RbFileManager f = RbFileManager(fm.getFilePath(), stoneFileName);
// read the i-th stone
std::ifstream inStream;
inStream.open( f.getFullFileName().c_str(), std::fstream::in);
if (inStream.is_open())
{
bool header = true;
std::string line = "";
while ( std::getline (inStream,line) )
{
// we need to skip the header line
if ( header == true )
{
header = false;
}
else
{
outStream << line << std::endl;
}
}
inStream.close();
}
else
{
std::cerr << "Problem reading stone " << idx+1 << " from file " << stoneFileName << "." << std::endl;
}
}
}
/**
* Combine output for the monitor.
* Overwrite this method for specialized behavior.
*/
void AbstractFileMonitor::combineReplicates( size_t n_reps )
{
if ( enabled == true )
{
std::fstream combined_output_stream;
int sample_number = 0;
// open the stream to the file
combined_output_stream.open( filename.c_str(), std::fstream::out);
combined_output_stream.close();
combined_output_stream.open( filename.c_str(), std::fstream::in | std::fstream::out);
for (size_t i=0; i<n_reps; ++i)
{
std::stringstream ss;
ss << "_run_" << (i+1);
std::string s = ss.str();
RbFileManager fm = RbFileManager(filename);
std::string current_file_name = fm.getFilePath() + fm.getPathSeparator() + fm.getFileNameWithoutExtension() + s + "." + fm.getFileExtension();
RbFileManager current_fm = RbFileManager(current_file_name);
std::ifstream current_input_stream;
if ( current_fm.openFile(current_input_stream) == false )
{
throw RbException( "Could not open file '" + current_file_name + "'." );
}
std::string read_line = "";
size_t lines_skipped = 0;
size_t lines_to_skip = 1;
while (std::getline(current_input_stream,read_line))
{
++lines_skipped;
if ( lines_skipped <= lines_to_skip)
{
if ( i == 0 )
{
// write output
combined_output_stream << read_line;
// add a new line
combined_output_stream << std::endl;
}
continue;
}
std::vector<std::string> fields;
StringUtilities::stringSplit(read_line, separator, fields);
// add the current sample number
combined_output_stream << sample_number;
++sample_number;
for (size_t j=1; j<fields.size(); ++j)
{
// add a separator before every new element
combined_output_stream << separator;
// write output
combined_output_stream << fields[j];
}
// add a new line
combined_output_stream << std::endl;
};
fm.closeFile( current_input_stream );
}
combined_output_stream.close();
}
}
void PowerPosteriorAnalysis::runStone(size_t idx, size_t gen)
{
// create the directory if necessary
RbFileManager fm = RbFileManager(filename);
std::string stoneFileName = fm.getFileNameWithoutExtension() + "_stone_" + idx + "." + fm.getFileExtension();
RbFileManager f = RbFileManager(fm.getFilePath(), stoneFileName);
f.createDirectoryForFile();
std::fstream outStream;
outStream.open( f.getFullFileName().c_str(), std::fstream::out);
outStream << "state\t" << "power\t" << "likelihood" << std::endl;
// reset the counters for the move schedules
sampler->reset();
// if ( sampler->getCurrentGeneration() == 0 )
// {
// }
/* Reset the monitors */
// for (size_t i=0; i<replicates; ++i)
// {
// for (size_t j=0; i<runs[i].getMonitors().size(); i++)
// {
// runs[i].getMonitors()[j].reset( kIterations);
// }
// }
// reset the stopping rules
// for (size_t i=0; i<rules.size(); ++i)
// {
// rules[i].runStarted();
// }
size_t burnin = size_t( ceil( 0.25*gen ) );
size_t printInterval = size_t( round( fmax(1,gen/20.0) ) );
size_t digits = size_t( ceil( log10( powers.size() ) ) );
/* Run the chain */
if ( processActive )
{
std::cout << "Step ";
for (size_t d = size_t( ceil( log10( idx+1.1 ) ) ); d < digits; d++ )
{
std::cout << " ";
}
std::cout << (idx+1) << " / " << powers.size();
std::cout << "\t\t";
}
// set the power of this sampler
sampler->setLikelihoodHeat( powers[idx] );
sampler->setStoneIndex( idx );
// Monitor
sampler->startMonitors(gen);
sampler->monitor(0);
double p = powers[idx];
for (size_t k=1; k<=gen; k++)
{
if ( processActive )
{
if ( k % printInterval == 0 )
{
std::cout << "**";
std::cout.flush();
}
}
sampler->nextCycle( true );
// Monitor
sampler->monitor(k);
// sample the likelihood
if ( k > burnin && k % sampleFreq == 0 )
{
// compute the joint likelihood
double likelihood = sampler->getModelLnProbability();
outStream << k << "\t" << p << "\t" << likelihood << std::endl;
}
}
if ( processActive )
{
std::cout << std::endl;
}
outStream.close();
}