void DelimitedDataReader::readData(void)
{
std::vector<std::string> tmpChars;
// open file
std::ifstream readStream;
RbFileManager* f = new RbFileManager(filename);
if (!f->openFile(readStream))
std::cout << "ERROR: Could not open file " << filename << "\n";
chars.clear();
// read file
// bool firstLine = true;
std::string readLine = "";
while (std::getline(readStream,readLine))
{
std::string field = "";
std::stringstream ss(readLine);
int pos = 0;
while (std::getline(ss,field,delimiter))
{
tmpChars.push_back(field);
pos++;
};
chars.push_back(tmpChars);
tmpChars.clear();
};
}
RbHelpType* RbHelpParser::parseHelpType(const std::string &fn)
{
// first we need to load the file
std::ifstream readStream;
RbFileManager fm = RbFileManager(fn);
fm.openFile( readStream );
// try to load the xml file
pugi::xml_document doc;
pugi::xml_parse_result result = doc.load_file(fn.c_str(), pugi::parse_default);
if (result.status != pugi::status_ok)
{
std::cerr << "Problem while parsing file " << fn << std::endl;
throw RbException( result.description() );
}
RbHelpType* helpEntry = new RbHelpType();
pugi::xpath_node node = doc.select_single_node( "//type-help-entry" );
parseInternalHelpType( node, helpEntry );
// now return the help entry
return helpEntry;
}
RbHelpFunction RbHelpParser::parseHelpFunction(const std::string &fn)
{
// first we need to load the file
std::ifstream readStream;
RbFileManager fm = RbFileManager(fn);
fm.openFile( readStream );
// try to load the xml file
pugi::xml_document doc;
pugi::xml_parse_result result = doc.load_file(fn.c_str(), pugi::parse_default);
if (result.status != pugi::status_ok)
{
std::cerr << "Problem while parsing file " << fn << std::endl;
throw RbException( result.description() );
}
std::vector<RbHelpFunction> functions;
// pugi::xpath_node node = doc.select_single_node( "//function-help-entry" );
pugi::xpath_node_set nodeSet = doc.select_nodes( "//function-help-entry" );
for (pugi::xpath_node_set::const_iterator it = nodeSet.begin(); it != nodeSet.end(); ++it)
{
pugi::xpath_node node = *it;
RbHelpFunction helpEntryFunction = parseInternalHelpFunction( node );
functions.push_back( helpEntryFunction );
}
RbHelpFunction helpEntry = functions[0];
return helpEntry;
}
/**
* Open the file stream to a file with the name used in the constructor.
*/
void NexusWriter::openStream( void )
{
RbFileManager f = RbFileManager(fileName);
f.createDirectoryForFile();
// open the stream to the file
outStream.open( fileName.c_str(), std::fstream::out );
// write header line
outStream << "#NEXUS" << std::endl;
}
RbHelpParser::HelpEntryType RbHelpParser::testHelpEntry(const std::string &fn)
{
// first we need to load the file
std::ifstream readStream;
RbFileManager fm = RbFileManager(fn);
fm.openFile( readStream );
// try to load the xml file
pugi::xml_document doc;
pugi::xml_parse_result result = doc.load_file(fn.c_str(), pugi::parse_default);
if (result.status != pugi::status_ok)
{
std::cerr << "Problem while parsing file " << fn << std::endl;
throw RbException( result.description() );
}
pugi::xpath_node_set nodeSet = doc.select_nodes("//function-help-entry");
if ( nodeSet.size() > 0 )
{
return FUNCTION;
}
nodeSet = doc.select_nodes("//type-help-entry");
if ( nodeSet.size() > 0 )
{
return TYPE;
}
nodeSet = doc.select_nodes("//distribution-help-entry");
if ( nodeSet.size() > 0 )
{
return DISTRIBUTION;
}
nodeSet = doc.select_nodes("//move-help-entry");
if ( nodeSet.size() > 0 )
{
return MOVE;
}
nodeSet = doc.select_nodes("//monitor-help-entry");
if ( nodeSet.size() > 0 )
{
return MONITOR;
}
throw RbException("Unknown help entry type in file '" + fn + "'.");
}
/**
* 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;
}
/** open the file stream for printing */
void AbstractFileMonitor::openStream(void)
{
RbFileManager f = RbFileManager(working_file_name);
f.createDirectoryForFile();
// open the stream to the file
if ( append == true )
{
out_stream.open( working_file_name.c_str(), std::fstream::in | std::fstream::out | std::fstream::app);
}
else
{
out_stream.open( working_file_name.c_str(), std::fstream::out);
out_stream.close();
out_stream.open( working_file_name.c_str(), std::fstream::in | std::fstream::out);
}
// out_stream.close();
}
/**
* This method simply writes a character data object into a file in Fasta format.
*
* \param[in] fileName The name of the file into which the objects is to be written.
* \param[in] data The character data object which is written out.
*/
void FastaWriter::writeData(std::string const &fileName, const AbstractHomologousDiscreteCharacterData &data)
{
// the filestream object
std::fstream outStream;
RbFileManager f = RbFileManager(fileName);
f.createDirectoryForFile();
// open the stream to the file
outStream.open( fileName.c_str(), std::fstream::out );
const std::vector<Taxon> &taxa = data.getTaxa();
for (std::vector<Taxon>::const_iterator it = taxa.begin(); it != taxa.end(); ++it)
{
if ( !data.isTaxonExcluded( it->getName() ) )
{
const AbstractDiscreteTaxonData &taxon = data.getTaxonData( it->getName() );
outStream << ">" << it->getName() << std::endl;
size_t nChars = taxon.getNumberOfCharacters();
for (size_t i = 0; i < nChars; ++i)
{
if ( !data.isCharacterExcluded( i ) )
{
const CharacterState &c = taxon.getCharacter( i );
outStream << c.getStringValue();
}
}
outStream << std::endl;
}
}
// close the stream
outStream.close();
}
/**
* 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();
}
}
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;
}
}
}
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();
}
}
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();
}
void PosteriorPredictiveAnalysis::runAll(size_t gen)
{
// print some information to the screen but only if we are the active process
if ( process_active == true )
{
std::cout << std::endl;
std::cout << "Running posterior predictive analysis ..." << std::endl;
}
// create the directory if necessary
RbFileManager fm = RbFileManager( directory );
if ( fm.testFile() == false && fm.testDirectory() == false )
{
std::string errorStr = "";
fm.formatError(errorStr);
throw RbException("Could not find file or path with name \"" + directory + "\"");
}
// set up a vector of strings containing the name or names of the files to be read
std::vector<std::string> dir_names;
if ( fm.isDirectory() == true )
{
fm.setStringWithNamesOfFilesInDirectory( dir_names, false );
}
else
{
throw RbException( "\"" + directory + "\" is not a directory.");
}
size_t num_runs = dir_names.size();
processors_per_likelihood = ceil( double(num_processes) / num_runs );
size_t run_pid_start = floor( pid / double(num_processes) * num_runs );
size_t run_pid_end = floor( (pid+1) / double(num_processes) * num_runs );
if ( run_pid_start == run_pid_end )
{
++run_pid_end;
}
// int number_processes_per_run = int(run_pid_end) - int(run_pid_start) + 1;
// set the processors for this analysis
size_t active_proc = floor( pid / double(processors_per_likelihood) ) * processors_per_likelihood;
template_sampler.setActivePID( active_proc, processors_per_likelihood );
#ifdef RB_MPI
MPI_Comm analysis_comm;
MPI_Comm_split(MPI_COMM_WORLD, active_proc, pid, &analysis_comm);
#endif
for ( size_t i = run_pid_start; i < run_pid_end; ++i)
{
// size_t run_pid_start = size_t(floor( double(i) / num_processes * num_runs ) );
// size_t run_pid_end = std::max( int(run_pid_start), int(floor( double(i+1) / num_processes * num_runs ) ) - 1);
// create an independent copy of the analysis
MonteCarloAnalysis *current_analysis = template_sampler.clone();
current_analysis->disableScreenMonitors( true );
// get the model of the analysis
Model* current_model = current_analysis->getModel().clone();
// get the DAG nodes of the model
std::vector<DagNode*> ¤t_nodes = current_model->getDagNodes();
// initialize values from files
for (size_t j = 0; j < current_nodes.size(); ++j)
{
DagNode *the_node = current_nodes[j];
if ( the_node->isClamped() == true )
{
the_node->setValueFromFile( dir_names[i] );
}
}
RbFileManager tmp = RbFileManager( dir_names[i] );
// now set the model of the current analysis
current_analysis->setModel( current_model );
// set the monitor index
current_analysis->addFileMonitorExtension(tmp.getLastPathComponent(), true);
// print some info
if ( process_active == true )
{
size_t digits = size_t( ceil( log10( num_runs ) ) );
std::cout << "Sim ";
for (size_t d = size_t( ceil( log10( i+1.1 ) ) ); d < digits; ++d )
{
std::cout << " ";
}
std::cout << (i+1) << " / " << num_runs;
std::cout << std::endl;
}
// run the i-th analysis
#ifdef RB_MPI
runSim(current_analysis, gen, analysis_comm);
#else
runSim(current_analysis, gen);
#endif
// free memory
delete current_analysis;
}
#ifdef RB_MPI
MPI_Comm_free(&analysis_comm);
// wait until all chains complete
MPI::COMM_WORLD.Barrier();
#endif
}