/**
* 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 RevBayesCore::PosteriorPredictiveSimulation::run( int thinning )
{
// some general constant variables
RbFileManager fm = RbFileManager( directory );
const std::string path_separator = fm.getPathSeparator();
// this is where we need to implement the posterior predictive simulation
size_t n_samples = traces[0].size();
size_t n_traces = traces.size();
std::vector<DagNode*> nodes = model.getDagNodes();
size_t sim_pid_start = size_t(floor( (double(pid) / num_processes * (n_samples/double(thinning) ) ) ) );
size_t sim_pid_end = std::max( int(sim_pid_start), int(floor( (double(pid+1) / num_processes * (n_samples/double(thinning) ) ) ) - 1) );
for (size_t i=sim_pid_start; i<=sim_pid_end; ++i)
{
// create a new directory name for this simulation
std::stringstream s;
s << directory << path_separator << "posterior_predictive_sim_" << (i+1);
std::string sim_directory_name = s.str();
// now for the numerical parameters
for ( size_t j=0; j<n_traces; ++j )
{
std::string parameter_name = traces[j].getParameterName();
// iterate over all DAG nodes (variables)
for ( std::vector<DagNode*>::iterator it = nodes.begin(); it!=nodes.end(); ++it )
{
DagNode *the_node = *it;
if ( the_node->getName() == parameter_name )
{
// set the value for the variable with the i-th sample
the_node->setValueFromString( traces[j].objectAt( i ) );
}
}
}
// next we need to simulate the data and store it
// iterate over all DAG nodes (variables)
for ( std::vector<DagNode*>::iterator it = nodes.begin(); it!=nodes.end(); ++it )
{
DagNode *the_node = *it;
if ( the_node->isClamped() == true )
{
// redraw new values
the_node->redraw();
// we need to store the new simulated data
the_node->writeToFile(sim_directory_name);
}
}
} // end for over all samples
}
/**
* 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();
}
}