Package edu.cmu.tetrad.algcomparison

Class Comparison

java.lang.Object

edu.cmu.tetrad.algcomparison.Comparison

All Implemented Interfaces:

TetradSerializable, Serializable

public class Comparison
extends Object
implements TetradSerializable

Script to do a comparison of a list of algorithms using a list of statistics and a list of parameters and their values.

Version:

$Id: $Id

Author:

josephramsey, danielmalinsky

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	Comparison.ComparisonGraph	An enum of comparison graphs types.

Constructor Summary

Constructors

Constructor	Description
Comparison()	Initializes a new instance of the Comparison class.

Method Summary

Modifier and Type	Method	Description
void	compareFromFiles(String filePath, Algorithms algorithms, Statistics statistics, Parameters parameters)	compareFromFiles.
void	compareFromFiles(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters)	Compares algorithms.
void	compareFromSimulations(String resultsPath, Simulations simulations, Algorithms algorithms, Statistics statistics, Parameters parameters)	Compare simulation results using the provided parameters and write the comparison results to a file.
void	compareFromSimulations(String resultsPath, Simulations simulations, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters)	Compares the results obtained from simulations.
void	compareFromSimulations(String resultsPath, Simulations simulations, String outputFileName, PrintStream localOut, Algorithms algorithms, Statistics statistics, Parameters parameters)	Compares the results of simulations and generates an output file.
void	compareFromSimulations(String resultsPath, Simulations simulations, String outputFileName, PrintStream localOut, PrintStream localOut2, Algorithms algorithms, Statistics statistics, Parameters parameters)	Compares the results of different simulations and algorithms.
void	configuration(String path)	Generates a configuration file containing information about available algorithms, statistics, independence tests, scores, and simulations.
void	generateReportFromExternalAlgorithms(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters)	Generates a report from external algorithms.
void	generateReportFromExternalAlgorithms(String dataPath, String resultsPath, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters)	Generates a report from external algorithms based on the given parameters.
Comparison.ComparisonGraph	getComparisonGraph()	Returns the ComparisonGraph instance.
Knowledge	getKnowledge()	Retrieves the knowledge.
boolean	isSaveCPDAGs()	Checks if the CPDAGs are saved.
boolean	isSaveData()	Returns the status of whether data is being saved or not.
boolean	isSavePags()	Checks if the "savePags" variable is true or false.
boolean	isShowUtilities()	Checks if the utilities are currently being shown.
boolean	isSortByUtility()	Returns whether utility does the sorting.
void	saveToFiles(String dataPath, Simulation simulation, Parameters parameters)	Saves the simulation data to file in the specified data path.
void	saveToFilesSingleSimulation(String dataPath, Simulation simulation, Parameters parameters)	Saves the results of a single simulation to files.
void	setComparisonGraph(Comparison.ComparisonGraph comparisonGraph)	Sets the comparison graph.
void	setKnowledge(Knowledge knowledge)	Sets the knowledge for the current instance.
void	setParallelism(int parallelism)	Sets the number of threads to be used for parallel processing.
void	setSaveCPDAGs(boolean saveCPDAGs)	Sets whether to save CPDAGs.
void	setSaveData(boolean saveData)	Sets the flag indicating whether to save data.
void	setSaveGraphs(boolean saveGraphs)	Sets whether to save graphs.
void	setSavePags(boolean savePags)	Sets the value of 'savePags' flag.
void	setSetAlgorithmKnowledge(boolean setAlgorithmKnowledge)	Sets the algorithm knowledge flag.
void	setShowUtilities(boolean showUtilities)	Sets the value of the showUtilities property.
void	setSortByUtility(boolean sortByUtility)	Set the flag to determine if utility should do the sorting.
void	setTabDelimitedTables(boolean tabDelimitedTables)	Sets the flag indicating whether tab-delimited tables should be used.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Comparison

public Comparison()

Initializes a new instance of the Comparison class.

By default, the saveGraphs property is set to true. The showUtilities and sortByUtility properties are set to false.

Usage: Comparison comparison = new Comparison();

Method Details

compareFromFiles

public void compareFromFiles(String filePath,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

compareFromFiles.

Parameters:

filePath - a String object

algorithms - a Algorithms object

statistics - a Statistics object

parameters - a Parameters object

compareFromFiles

public void compareFromFiles(String dataPath,
 String resultsPath,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Compares algorithms.

Parameters:

dataPath - Path to the directory where data and graph files have been saved.

resultsPath - Path to the file where the results should be stored.

algorithms - The list of algorithms to be compared.

statistics - a Statistics object

parameters - a Parameters object

generateReportFromExternalAlgorithms

public void generateReportFromExternalAlgorithms(String dataPath,
 String resultsPath,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Generates a report from external algorithms.

Parameters:

dataPath - - The path to the data file.

resultsPath - - The path to where the report will be saved.

algorithms - - The algorithms to compare.

statistics - - The statistics to include in the report.

parameters - - The parameters to use for the algorithms.

generateReportFromExternalAlgorithms

public void generateReportFromExternalAlgorithms(String dataPath,
 String resultsPath,
 String outputFileName,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Generates a report from external algorithms based on the given parameters.

Parameters:

dataPath - The path to the data files.

resultsPath - The path to save the results.

outputFileName - The name of the output file.

algorithms - The collection of algorithms to compare.

statistics - The statistics to include in the report.

parameters - The additional parameters for the algorithms.

Throws:

IllegalArgumentException - if any algorithm in the collection is not an instance of ExternalAlgorithm.

NullPointerException - if there are no files in the specified data path.

compareFromSimulations

public void compareFromSimulations(String resultsPath,
 Simulations simulations,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Compare simulation results using the provided parameters and write the comparison results to a file.

Parameters:

resultsPath - The path to write the comparison results file.

simulations - The simulations to compare results from.

algorithms - The algorithms used in the simulations.

statistics - The statistics used in the simulations.

parameters - The parameters used in the simulations.

compareFromSimulations

public void compareFromSimulations(String resultsPath,
 Simulations simulations,
 String outputFileName,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Compares the results obtained from simulations.

Parameters:

resultsPath - The path to the directory containing the simulation results.

simulations - The simulations to compare the results from.

outputFileName - The name of the output file.

algorithms - The algorithms used in the simulations.

statistics - The statistics used in the simulations.

parameters - The parameters used in the simulations.

compareFromSimulations

public void compareFromSimulations(String resultsPath,
 Simulations simulations,
 String outputFileName,
 PrintStream localOut,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Compares the results of simulations and generates an output file.

Parameters:

resultsPath - The path to the directory containing the simulation results.

simulations - The simulations to compare.

outputFileName - The name of the file to generate.

localOut - The print stream to write the output to.

algorithms - The algorithms to use for comparison.

statistics - The statistics to calculate for comparison.

parameters - The parameters for comparison.

compareFromSimulations

public void compareFromSimulations(String resultsPath,
 Simulations simulations,
 String outputFileName,
 PrintStream localOut,
 PrintStream localOut2,
 Algorithms algorithms,
 Statistics statistics,
 Parameters parameters)

Compares the results of different simulations and algorithms.

Parameters:

resultsPath - the path to the results directory

simulations - the simulation object containing the simulation data

outputFileName - the name of the output file

localOut - the local output stream; may be null.

localOut2 - the second local output stream; may be null.

algorithms - the algorithms object containing the algorithm data

statistics - the statistics object containing the statistics data

parameters - the parameter object containing the parameter data

saveToFiles

public void saveToFiles(String dataPath,
 Simulation simulation,
 Parameters parameters)

Saves the simulation data to file in the specified data path.

Parameters:

dataPath - the path where the data files will be saved

simulation - the simulation object containing the data to be saved

parameters - the parameters used in the simulation

saveToFilesSingleSimulation

public void saveToFilesSingleSimulation(String dataPath,
 Simulation simulation,
 Parameters parameters)

Saves the results of a single simulation to files.

Parameters:

dataPath - The path to the directory where the files will be saved.

simulation - The simulation object containing the data and graphs.

parameters - The parameters used for the simulation.

configuration

public void configuration(String path)

Generates a configuration file containing information about available algorithms, statistics, independence tests, scores, and simulations.

Parameters:

path - The path to save the configuration file.

isShowUtilities

public boolean isShowUtilities()

Checks if the utilities are currently being shown.

Returns:

true if the utilities are being shown, false otherwise.

setShowUtilities

public void setShowUtilities(boolean showUtilities)

Sets the value of the showUtilities property.

Parameters:

showUtilities - the new value for the showUtilities property

isSortByUtility

public boolean isSortByUtility()

Returns whether utility does the sorting.

Returns:

true if utility does the sorting, false otherwise.

setSortByUtility

public void setSortByUtility(boolean sortByUtility)

Set the flag to determine if utility should do the sorting.

Parameters:

sortByUtility - a flag indicating whether to sort by utility or not

isSaveCPDAGs

public boolean isSaveCPDAGs()

Checks if the CPDAGs are saved.

Returns:

true if the CPDAGs are saved, false otherwise.

setSaveCPDAGs

public void setSaveCPDAGs(boolean saveCPDAGs)

Sets whether to save CPDAGs.

Parameters:

saveCPDAGs - indicates whether to save CPDAGs or not

isSavePags

public boolean isSavePags()

Checks if the "savePags" variable is true or false.

Returns:

true if the "savePags" variable is true, false otherwise.

setSavePags

public void setSavePags(boolean savePags)

Sets the value of 'savePags' flag. This method is used to set the value of the 'savePags' flag, which indicates whether the pags should be saved or not.

Parameters:

savePags - a boolean value indicating whether to save the pags or not.

isSaveData

public boolean isSaveData()

Returns the status of whether data is being saved or not.

Returns:

true if data is being saved, false otherwise.

setSaveData

public void setSaveData(boolean saveData)

Sets the flag indicating whether to save data.

Parameters:

saveData - true if data should be saved, false otherwise

setSaveGraphs

public void setSaveGraphs(boolean saveGraphs)

Sets whether to save graphs.

Parameters:

saveGraphs - true to save graphs, false otherwise

getComparisonGraph

public Comparison.ComparisonGraph getComparisonGraph()

Returns the ComparisonGraph instance.

Returns:

the ComparisonGraph instance

setComparisonGraph

public void setComparisonGraph(Comparison.ComparisonGraph comparisonGraph)

Sets the comparison graph.

Parameters:

comparisonGraph - the comparison graph to be set

Throws:

NullPointerException - if the comparison graph is null

setTabDelimitedTables

public void setTabDelimitedTables(boolean tabDelimitedTables)

Sets the flag indicating whether tab-delimited tables should be used.

Parameters:

tabDelimitedTables - true if tab-delimited tables should be used; false otherwise

setParallelism

public void setParallelism(int parallelism)

Sets the number of threads to be used for parallel processing. Note that this method does not enforce the actual parallel execution of the code.

Parameters:

parallelism - the number of threads to be used for parallel processing

getKnowledge

public Knowledge getKnowledge()

Retrieves the knowledge.

Returns:

The knowledge object.

setKnowledge

public void setKnowledge(Knowledge knowledge)

Sets the knowledge for the current instance.

Parameters:

knowledge - the knowledge to be set

setSetAlgorithmKnowledge

public void setSetAlgorithmKnowledge(boolean setAlgorithmKnowledge)

Sets the algorithm knowledge flag.

Parameters:

setAlgorithmKnowledge - the flag value to set