Uses of Class
edu.cmu.tetrad.util.Parameters
Packages that use Parameters
Package
Description
Contains classes for searching for (mostly structural) causal models given data.
Contains some classes that aren't ready for prime time.
Contains an editable display graph for (small) lag graphs.
Contains classes for generating simulations of expression levels over a
collection
of genes.
-
Uses of Parameters in edu.cmu.tetrad.algcomparison
Methods in edu.cmu.tetrad.algcomparison with parameters of type ParametersModifier and TypeMethodDescriptionvoid
Comparison.compareFromFiles
(String filePath, Algorithms algorithms, Statistics statistics, Parameters parameters) void
Comparison.compareFromFiles
(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters) Compares algorithms.void
TimeoutComparison.compareFromFiles
(String filePath, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) void
TimeoutComparison.compareFromFiles
(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) Compares algorithms.void
Comparison.compareFromSimulations
(String resultsPath, Simulations simulations, Algorithms algorithms, Statistics statistics, Parameters parameters) void
Comparison.compareFromSimulations
(String resultsPath, Simulations simulations, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters) Compares algorithms.void
TimeoutComparison.compareFromSimulations
(String resultsPath, Simulations simulations, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) void
TimeoutComparison.compareFromSimulations
(String resultsPath, Simulations simulations, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) Compares algorithms.void
Comparison.generateReportFromExternalAlgorithms
(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters) void
Comparison.generateReportFromExternalAlgorithms
(String dataPath, String resultsPath, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters) void
TimeoutComparison.generateReportFromExternalAlgorithms
(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) void
TimeoutComparison.generateReportFromExternalAlgorithms
(String dataPath, String resultsPath, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters, long timeout, TimeUnit unit) void
Comparison.saveToFiles
(String dataPath, Simulation simulation, Parameters parameters) Saves simulationWrapper data.void
TimeoutComparison.saveToFiles
(String dataPath, Simulation simulation, Parameters parameters) Saves simulationWrapper data.void
Comparison.saveToFilesSingleSimulation
(String dataPath, Simulation simulation, Parameters parameters) Saves simulationWrapper data. -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm
Methods in edu.cmu.tetrad.algcomparison.algorithm with parameters of type ParametersModifier and TypeMethodDescriptionabstract long
ExternalAlgorithm.getElapsedTime
(DataModel dataSet, Parameters parameters) Algorithm.search
(DataModel dataSet, Parameters parameters) Runs the search.FirstInflection.search
(DataModel dataSet, Parameters parameters) MultiDataSetAlgorithm.search
(List<DataModel> dataSets, Parameters parameters) Runs the search.StabilitySelection.search
(DataModel dataSet, Parameters parameters) StARS.search
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.cluster
Methods in edu.cmu.tetrad.algcomparison.algorithm.cluster with parameters of type ParametersModifier and TypeMethodDescriptionBpc.search
(DataModel dataSet, Parameters parameters) Fofc.search
(DataModel dataSet, Parameters parameters) Ftfc.search
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
Methods in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag with parameters of type ParametersModifier and TypeMethodDescriptionDagma.search
(DataModel dataSet, Parameters parameters) DirectLingam.search
(DataModel dataSet, Parameters parameters) IcaLingam.search
(DataModel dataSet, Parameters parameters) IcaLingD.search
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.external
Methods in edu.cmu.tetrad.algcomparison.algorithm.external with parameters of type ParametersModifier and TypeMethodDescriptionlong
ExternalAlgorithmBnlearnMmhc.getElapsedTime
(DataModel dataSet, Parameters parameters) long
ExternalAlgorithmBNTPc.getElapsedTime
(DataModel dataSet, Parameters parameters) long
ExternalAlgorithmIntersection.getElapsedTime
(DataModel dataSet, Parameters parameters) long
ExternalAlgorithmPcalgGes.getElapsedTime
(DataModel dataSet, Parameters parameters) long
ExternalAlgorithmPcalgPc.getElapsedTime
(DataModel dataSet, Parameters parameters) long
ExternalAlgorithmTetrad.getElapsedTime
(DataModel dataSet, Parameters parameters) ExternalAlgorithmBnlearnMmhc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmBNTPc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmIntersection.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmPcalgGes.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmPcalgPc.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file (see above) and returns it.ExternalAlgorithmTetrad.search
(DataModel dataSet, Parameters parameters) Reads in the relevant graph from the file and returns it. -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.mixed
Methods in edu.cmu.tetrad.algcomparison.algorithm.mixed with parameters of type Parameters -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.multi
Methods in edu.cmu.tetrad.algcomparison.algorithm.multi with parameters of type ParametersModifier and TypeMethodDescriptionFask.search
(DataModel dataSet, Parameters parameters) FaskConcatenated.search
(DataModel dataSet, Parameters parameters) FaskConcatenated.search
(List<DataModel> dataSets, Parameters parameters) FaskLofsConcatenated.search
(DataModel dataSet, Parameters parameters) FaskLofsConcatenated.search
(List<DataModel> dataModels, Parameters parameters) FaskVote.search
(DataModel dataSet, Parameters parameters) FaskVote.search
(List<DataModel> dataSets, Parameters parameters) FasLofs.search
(DataModel dataSet, Parameters parameters) FciIod.search
(DataModel dataSet, Parameters parameters) FciIod.search
(List<DataModel> dataSets, Parameters parameters) FgesConcatenated.search
(DataModel dataSet, Parameters parameters) FgesConcatenated.search
(List<DataModel> dataModels, Parameters parameters) Images.search
(DataModel dataSet, Parameters parameters) Images.search
(List<DataModel> dataSets, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag with parameters of type ParametersModifier and TypeMethodDescriptionBoss.search
(DataModel dataModel, Parameters parameters) Cpc.search
(DataModel dataModel, Parameters parameters) Fas.search
(DataModel dataSet, Parameters parameters) Fges.search
(DataModel dataModel, Parameters parameters) FgesMb.search
(DataModel dataSet, Parameters parameters) FgesMeasurement.search
(DataModel dataModel, Parameters parameters) GesMe.search
(DataModel dataSet, Parameters parameters) Grasp.search
(DataModel dataModel, Parameters parameters) Pc.search
(DataModel dataModel, Parameters parameters) Pcd.search
(DataModel dataSet, Parameters parameters) PcLingam.search
(DataModel dataModel, Parameters parameters) PcMb.search
(DataModel dataSet, Parameters parameters) RestrictedBoss.search
(DataModel dataModel, Parameters parameters) SingleGraphAlg.search
(DataModel dataSet, Parameters parameters) Sp.search
(DataModel dataModel, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag with parameters of type ParametersModifier and TypeMethodDescriptionBfci.search
(DataModel dataModel, Parameters parameters) Ccd.search
(DataModel dataSet, Parameters parameters) Cfci.search
(DataModel dataModel, Parameters parameters) Fci.search
(DataModel dataModel, Parameters parameters) FciMax.search
(DataModel dataModel, Parameters parameters) Gfci.search
(DataModel dataModel, Parameters parameters) GraspFci.search
(DataModel dataModel, Parameters parameters) PagSampleRfci.search
(DataModel dataSet, Parameters parameters) Rfci.search
(DataModel dataModel, Parameters parameters) RfciBsc.search
(DataModel dataSet, Parameters parameters) SpFci.search
(DataModel dataModel, Parameters parameters) SvarFci.search
(DataModel dataModel, Parameters parameters) SvarGfci.search
(DataModel dataModel, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern
Methods in edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern with parameters of type Parameters -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.other
Methods in edu.cmu.tetrad.algcomparison.algorithm.other with parameters of type ParametersModifier and TypeMethodDescriptionFactorAnalysis.search
(DataModel ds, Parameters parameters) Glasso.search
(DataModel ds, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.algorithm.pairwise
Methods in edu.cmu.tetrad.algcomparison.algorithm.pairwise with parameters of type ParametersModifier and TypeMethodDescriptionEb.search
(DataModel dataSet, Parameters parameters) FaskPw.search
(DataModel dataModel, Parameters parameters) R1.search
(DataModel dataSet, Parameters parameters) R2.search
(DataModel dataSet, Parameters parameters) R3.search
(DataModel dataSet, Parameters parameters) Rskew.search
(DataModel dataSet, Parameters parameters) RskewE.search
(DataModel dataSet, Parameters parameters) Skew.search
(DataModel dataSet, Parameters parameters) SkewE.search
(DataModel dataSet, Parameters parameters) Tanh.search
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.graph
Methods in edu.cmu.tetrad.algcomparison.graph with parameters of type ParametersModifier and TypeMethodDescriptionCyclic.createGraph
(Parameters parameters) ErdosRenyi.createGraph
(Parameters parameters) RandomForward.createGraph
(Parameters parameters) RandomGraph.createGraph
(Parameters parameters) RandomSingleFactorMim.createGraph
(Parameters parameters) RandomTwoFactorMim.createGraph
(Parameters parameters) ScaleFree.createGraph
(Parameters parameters) SingleGraph.createGraph
(Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.independence
Methods in edu.cmu.tetrad.algcomparison.independence with parameters of type ParametersModifier and TypeMethodDescriptionBdeuTest.getTest
(DataModel dataSet, Parameters parameters) Returns the test.CciTest.getTest
(DataModel dataSet, Parameters parameters) ChiSquare.getTest
(DataModel dataSet, Parameters parameters) ConditionalGaussianLRT.getTest
(DataModel dataSet, Parameters parameters) DegenerateGaussianLRT.getTest
(DataModel dataSet, Parameters parameters) DiscreteBicTest.getTest
(DataModel dataSet, Parameters parameters) FisherZ.getTest
(DataModel dataSet, Parameters parameters) GICScoreTests.getTest
(DataModel dataSet, Parameters parameters) Gsquare.getTest
(DataModel dataSet, Parameters parameters) IndependenceWrapper.getTest
(DataModel dataSet, Parameters parameters) Returns true iff x and y are independent conditional on z for the given data set.Kci.getTest
(DataModel dataSet, Parameters parameters) MagSemBicTest.getTest
(DataModel dataSet, Parameters parameters) Mnlrlrt.getTest
(DataModel dataSet, Parameters parameters) MSeparationTest.getTest
(DataModel dataSet, Parameters parameters) MultinomialLogisticRegressionWald.getTest
(DataModel dataSet, Parameters parameters) Mvplrt.getTest
(DataModel dataSet, Parameters parameters) PoissonScoreTest.getTest
(DataModel dataSet, Parameters parameters) PositiveCorr.getTest
(DataModel dataSet, Parameters parameters) ProbabilisticTest.getTest
(DataModel dataSet, Parameters parameters) SemBicDTest.getTest
(DataModel dataSet, Parameters parameters) SemBicTest.getTest
(DataModel dataSet, Parameters parameters) UniformScatterTest.getTest
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.score
Methods in edu.cmu.tetrad.algcomparison.score with parameters of type ParametersModifier and TypeMethodDescriptionBdeuScore.getScore
(DataModel dataSet, Parameters parameters) CciScore.getScore
(DataModel dataSet, Parameters parameters) ConditionalGaussianBicScore.getScore
(DataModel dataSet, Parameters parameters) DegenerateGaussianBicScore.getScore
(DataModel dataSet, Parameters parameters) DiscreteBicScore.getScore
(DataModel dataSet, Parameters parameters) EbicScore.getScore
(DataModel dataSet, Parameters parameters) FisherZScore.getScore
(DataModel dataSet, Parameters parameters) GicScores.getScore
(DataModel dataSet, Parameters parameters) MagSemBicScore.getScore
(DataModel dataSet, Parameters parameters) MSeparationScore.getScore
(DataModel dataSet, Parameters parameters) MVPBicScore.getScore
(DataModel dataSet, Parameters parameters) PoissonPriorScore.getScore
(DataModel dataSet, Parameters parameters) PositiveCorrScore.getScore
(DataModel dataSet, Parameters parameters) ScoreWrapper.getScore
(DataModel dataSet, Parameters parameters) Returns true iff x and y are independent conditional on z for the given data set.SemBicScore.getScore
(DataModel dataSet, Parameters parameters) SemBicScoreDeterministic.getScore
(DataModel dataSet, Parameters parameters) ZhangShenBoundScore.getScore
(DataModel dataSet, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.simulation
Methods in edu.cmu.tetrad.algcomparison.simulation with parameters of type ParametersModifier and TypeMethodDescriptionvoid
BayesNetSimulation.createData
(Parameters parameters, boolean newModel) Creates the data.void
BooleanGlassSimulation.createData
(Parameters parameters, boolean newModel) void
ConditionalGaussianSimulation.createData
(Parameters parameters, boolean newModel) void
GeneralSemSimulation.createData
(Parameters parameters, boolean newModel) void
GeneralSemSimulationSpecial1.createData
(Parameters parameters, boolean newModel) void
LeeHastieSimulation.createData
(Parameters parameters, boolean newModel) void
LinearFisherModel.createData
(Parameters parameters, boolean newModel) void
LinearSineSimulation.createData
(Parameters parameters, boolean newModel) void
NLSemSimulation.createData
(Parameters parameters, boolean newModel) void
SemSimulation.createData
(Parameters parameters, boolean newModel) void
SemThenDiscretize.createData
(Parameters parameters, boolean newModel) void
Simulation.createData
(Parameters parameters, boolean newModel) Creates a data set and simulates data.void
StandardizedSemSimulation.createData
(Parameters parameters, boolean newModel) void
TimeSeriesSemSimulation.createData
(Parameters parameters, boolean newModel) -
Uses of Parameters in edu.cmu.tetrad.algcomparison.utils
Methods in edu.cmu.tetrad.algcomparison.utils that return Parameters -
Uses of Parameters in edu.cmu.tetrad.data.simulation
Methods in edu.cmu.tetrad.data.simulation that return ParametersModifier and TypeMethodDescriptionLoadContinuousDataAndSingleGraph.getParameterValues()
LoadContinuousDataSmithSim.getParameterValues()
Methods in edu.cmu.tetrad.data.simulation with parameters of type ParametersModifier and TypeMethodDescriptionvoid
LoadContinuousDataAndGraphs.createData
(Parameters parameters, boolean newModel) void
LoadContinuousDataAndSingleGraph.createData
(Parameters parameters, boolean newModel) void
LoadContinuousDataSmithSim.createData
(Parameters parameters, boolean newModel) void
LoadDataAndGraphs.createData
(Parameters parameters, boolean newModel) void
LoadDataFromFileWithoutGraph.createData
(Parameters parameters, boolean newModel) -
Uses of Parameters in edu.cmu.tetrad.graph
Methods in edu.cmu.tetrad.graph with parameters of type ParametersModifier and TypeMethodDescriptionstatic Graph
GraphUtils.getComparisonGraph
(Graph graph, Parameters params) -
Uses of Parameters in edu.cmu.tetrad.search
Constructors in edu.cmu.tetrad.search with parameters of type ParametersModifierConstructorDescriptionCstar
(IndependenceWrapper test, ScoreWrapper score, Parameters parameters) Constructor. -
Uses of Parameters in edu.cmu.tetrad.search.work_in_progress
Methods in edu.cmu.tetrad.search.work_in_progress with parameters of type Parameters -
Uses of Parameters in edu.cmu.tetrad.sem
Methods in edu.cmu.tetrad.sem that return ParametersMethods in edu.cmu.tetrad.sem with parameters of type ParametersConstructors in edu.cmu.tetrad.sem with parameters of type ParametersModifierConstructorDescriptionSemIm
(SemPm semPm, SemIm oldSemIm, Parameters parameters) Constructs a new SEM IM from the given SEM PM, using the old SEM IM and params object to guide the choice of parameter values.SemIm
(SemPm semPm, Parameters params) Constructs a new SEM IM from the given SEM PM, using the given params object to guide the choice of parameter values.StandardizedSemIm
(SemIm im, StandardizedSemIm.Initialization initialization, Parameters parameters) Constructs a new standardized SEM IM from the freeParameters in the given SEM IM.StandardizedSemIm
(SemIm im, Parameters parameters) Constructs a new standardized SEM IM, initializing from the freeParameters in the given SEM IM. -
Uses of Parameters in edu.cmu.tetrad.session
Methods in edu.cmu.tetrad.session that return ParametersModifier and TypeMethodDescriptionGets the parameter object for the givem model class.SessionNode.getParameters()
Methods in edu.cmu.tetrad.session with parameters of type ParametersModifier and TypeMethodDescriptionvoid
SessionNode.putParam
(Class modelClass, Parameters param) Sets the parameter object for the given model class to the given object.Constructors in edu.cmu.tetrad.session with parameters of type ParametersModifierConstructorDescriptionType1
(Type2 model1, Type3 model2, Parameters parameters) A sample constructor that takes Model 2 and Type3 as parent.Type10
(Type6 model1, Type6 model2, Parameters parameters) Type11
(Parameters parameters) Type12
(Type11 a, Parameters parameters) Type12
(Type12 a, Parameters parameters) Type2
(Parameters parameters) A sample constructor that takes Model 2 and Type3 as parent.Type3
(Type2 model1, Parameters parameters) It should be possible to construct a Type3-model with a Type1-node as parent.Type4
(Type1 model1, Parameters parameters) It should be possible to construct a Type4-model with a Type1-node as parent.Type5
(Type1 model1, Type1 model2, Parameters parameters) It should not be possible to constuct Type5, because it contains two arguments of the same type.Type6
(Type7 model1, Type8 model2, Parameters parameters) Type7
(Parameters parameters) Type8
(Type7 model1, Type9 model2, Parameters parameters) Type8
(Type7 model1, Parameters parameters) Type9
(Type6 model1, Parameters parameters) Type9
(Type7 model1, Type8 model2, Parameters parameters) -
Uses of Parameters in edu.cmu.tetrad.study.gene.tetrad.gene.graph
Constructors in edu.cmu.tetrad.study.gene.tetrad.gene.graph with parameters of type Parameters -
Uses of Parameters in edu.cmu.tetrad.study.gene.tetrad.gene.simulation
Constructors in edu.cmu.tetrad.study.gene.tetrad.gene.simulation with parameters of type ParametersModifierConstructorDescriptionMeasurementSimulator
(Parameters parameters) Constructs a measurement simulator using the given history. -
Uses of Parameters in edu.cmu.tetrad.study.gene.tetradapp.model
Constructors in edu.cmu.tetrad.study.gene.tetradapp.model with parameters of type ParametersModifierConstructorDescriptionBooleanGlassGeneIm
(BooleanGlassGenePm genePm, Parameters parameters) Obtains a boolean Glass function from the boolean Glass gene PM provided and uses it to create a Glass history and a measurement simulator.MeasurementSimulatorParams
(Parameters parameters) Constructs a measurement simulator using the given history. -
Uses of Parameters in edu.cmu.tetrad.util
Methods in edu.cmu.tetrad.util that return ParametersModifier and TypeMethodDescriptionstatic Parameters
Create parameters with their default values.static Parameters
Parameters.serializableInstance()
Methods in edu.cmu.tetrad.util with parameters of type ParametersConstructors in edu.cmu.tetrad.util with parameters of type Parameters -
Uses of Parameters in edu.pitt.dbmi.algo.resampling
Methods in edu.pitt.dbmi.algo.resampling with parameters of type ParametersModifier and TypeMethodDescriptionvoid
GeneralResamplingSearch.setParameters
(Parameters parameters) void
GeneralResamplingTest.setParameters
(Parameters parameters) -
Uses of Parameters in edu.pitt.dbmi.algo.resampling.task
Constructors in edu.pitt.dbmi.algo.resampling.task with parameters of type ParametersModifierConstructorDescriptionGeneralResamplingSearchRunnable
(DataModel dataModel, Algorithm algorithm, Parameters parameters, GeneralResamplingSearch resamplingAlgorithmSearch, boolean verbose) GeneralResamplingSearchRunnable
(List<DataModel> dataModel, MultiDataSetAlgorithm algorithm, Parameters parameters, GeneralResamplingSearch resamplingAlgorithmSearch, boolean verbose)