bd2kccd/r-causal source listing

DESCRIPTION

INDEX

NAMESPACE

data/9var/sub001.cent-table.9.dat.txt

data/9var/sub004.cent-table.9.dat.txt

data/9var/sub005.cent-table.9.dat.txt

data/9var/sub009.cent-table.9.dat.txt

data/9var/sub010.cent-table.9.dat.txt

data/9var/sub013.cent-table.9.dat.txt

data/9var/sub014.cent-table.9.dat.txt

data/9var/sub016.cent-table.9.dat.txt

data/9var/sub017.cent-table.9.dat.txt

data/audiology.txt

data/charity.txt

data/sim_discrete_data_20vars_100cases.txt

inst/extdata/9var/sub001.cent-table.9.dat.txt

inst/extdata/9var/sub004.cent-table.9.dat.txt

inst/extdata/9var/sub005.cent-table.9.dat.txt

inst/extdata/9var/sub009.cent-table.9.dat.txt

inst/extdata/9var/sub010.cent-table.9.dat.txt

inst/extdata/9var/sub013.cent-table.9.dat.txt

inst/extdata/9var/sub014.cent-table.9.dat.txt

inst/extdata/9var/sub016.cent-table.9.dat.txt

inst/extdata/9var/sub017.cent-table.9.dat.txt

inst/extdata/audiology.txt

inst/extdata/charity.txt

inst/java/causal-cmd-1.2.0-SNAPSHOT-jar-with-dependencies.jar

java/edu/cmu/tetrad/algcomparison/Comparison.java

java/edu/cmu/tetrad/algcomparison/TimeoutComparison.java

java/edu/cmu/tetrad/algcomparison/algorithm/Algorithm.java

java/edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory.java

java/edu/cmu/tetrad/algcomparison/algorithm/Algorithms.java

java/edu/cmu/tetrad/algcomparison/algorithm/ExternalAlgorithm.java

java/edu/cmu/tetrad/algcomparison/algorithm/FirstInflection.java

java/edu/cmu/tetrad/algcomparison/algorithm/MultiDataSetAlgorithm.java

java/edu/cmu/tetrad/algcomparison/algorithm/StARS.java

java/edu/cmu/tetrad/algcomparison/algorithm/StARS2.java

java/edu/cmu/tetrad/algcomparison/algorithm/StabilitySelection.java

java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Bpc.java

java/edu/cmu/tetrad/algcomparison/algorithm/cluster/ClusterAlgorithm.java

java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Fofc.java

java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Ftfc.java

java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/Ling.java

java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/Lingam.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmBNTPc.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmBnlearnMmhc.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmIntersection.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmPcalgGes.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmPcalgPc.java

java/edu/cmu/tetrad/algcomparison/algorithm/external/ExternalAlgorithmTetrad.java

java/edu/cmu/tetrad/algcomparison/algorithm/mixed/Mgm.java

java/edu/cmu/tetrad/algcomparison/algorithm/mixed/pattern/MixedFgesDiscretingContinuousVariables.java

java/edu/cmu/tetrad/algcomparison/algorithm/mixed/pattern/MixedFgesTreatingDiscreteAsContinuous.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/CcdMaxConcatenated.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/FasLofs.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/FasLofsConcatenated.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/Fask.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/FaskConcatenated.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/ImagesBDeu.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/ImagesCcd.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/ImagesPcStableMax.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/ImagesSemBic.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/MultiFask.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/PcStableMaxConcatenated.java

java/edu/cmu/tetrad/algcomparison/algorithm/multi/TsImagesSemBic.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Ccd.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/CcdMax.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Cfci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Fci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/FciMax.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Gfci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Rfci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/RfciBsc.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/TsFci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/TsGfci.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/TsImages.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/Cpc.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/CpcStable.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FAS.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/Fges.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FgesD.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FgesMb.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FgesMeasurement.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/GesMe.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/Jcpc.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/MBFS.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/Pc.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/PcAll.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/PcFges.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/PcStable.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/PcStableMax.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/Pcd.java

java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/SingleGraphAlg.java

java/edu/cmu/tetrad/algcomparison/algorithm/other/FactorAnalysis.java

java/edu/cmu/tetrad/algcomparison/algorithm/other/Glasso.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/EB.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/R1.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/R2.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/R3.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/R4.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/RSkew.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/RSkewE.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/Skew.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/SkewE.java

java/edu/cmu/tetrad/algcomparison/algorithm/pairwise/Tanh.java

java/edu/cmu/tetrad/algcomparison/examples/CompareExternalAlgorithms.java

java/edu/cmu/tetrad/algcomparison/examples/CompareFromFiles.java

java/edu/cmu/tetrad/algcomparison/examples/ExampleCompareFromFiles.java

java/edu/cmu/tetrad/algcomparison/examples/ExampleCompareSimulation.java

java/edu/cmu/tetrad/algcomparison/examples/ExampleCompareSimulationTimeSeries.java

java/edu/cmu/tetrad/algcomparison/examples/ExampleNonlinearSave.java

java/edu/cmu/tetrad/algcomparison/examples/ExampleSave.java

java/edu/cmu/tetrad/algcomparison/examples/RunConfig.java

java/edu/cmu/tetrad/algcomparison/examples/RunKemmeren.java

java/edu/cmu/tetrad/algcomparison/examples/Save.java

java/edu/cmu/tetrad/algcomparison/examples/SaveDGSimulations.java

java/edu/cmu/tetrad/algcomparison/examples/TestDegenerateGaussian.java

java/edu/cmu/tetrad/algcomparison/graph/Cyclic.java

java/edu/cmu/tetrad/algcomparison/graph/GraphTypes.java

java/edu/cmu/tetrad/algcomparison/graph/RandomForward.java

java/edu/cmu/tetrad/algcomparison/graph/RandomGraph.java

java/edu/cmu/tetrad/algcomparison/graph/RandomSingleFactorMim.java

java/edu/cmu/tetrad/algcomparison/graph/RandomTwoFactorMim.java

java/edu/cmu/tetrad/algcomparison/graph/ScaleFree.java

java/edu/cmu/tetrad/algcomparison/graph/SingleGraph.java

java/edu/cmu/tetrad/algcomparison/independence/BDeuTest.java

java/edu/cmu/tetrad/algcomparison/independence/CciTest.java

java/edu/cmu/tetrad/algcomparison/independence/ChiSquare.java

java/edu/cmu/tetrad/algcomparison/independence/ConditionalGaussianLRT.java

java/edu/cmu/tetrad/algcomparison/independence/CorrelationT.java

java/edu/cmu/tetrad/algcomparison/independence/DSeparationTest.java

java/edu/cmu/tetrad/algcomparison/independence/DegenerateGaussianLRT.java

java/edu/cmu/tetrad/algcomparison/independence/DiscreteBicTest.java

java/edu/cmu/tetrad/algcomparison/independence/FisherZ.java

java/edu/cmu/tetrad/algcomparison/independence/GSquare.java

java/edu/cmu/tetrad/algcomparison/independence/IndependenceWrapper.java

java/edu/cmu/tetrad/algcomparison/independence/Kci.java

java/edu/cmu/tetrad/algcomparison/independence/MNLRLRT.java

java/edu/cmu/tetrad/algcomparison/independence/MVPLRT.java

java/edu/cmu/tetrad/algcomparison/independence/MultinomialLogisticRegressionWald.java

java/edu/cmu/tetrad/algcomparison/independence/PositiveCorr.java

java/edu/cmu/tetrad/algcomparison/independence/ProbabilisticTest.java

java/edu/cmu/tetrad/algcomparison/independence/SemBicDTest.java

java/edu/cmu/tetrad/algcomparison/independence/SemBicTest.java

java/edu/cmu/tetrad/algcomparison/score/BdeuScore.java

java/edu/cmu/tetrad/algcomparison/score/CciScore.java

java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianBicScore.java

java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianOtherBicScore.java

java/edu/cmu/tetrad/algcomparison/score/DegenerateGaussianBicScore.java

java/edu/cmu/tetrad/algcomparison/score/DiscreteBicScore.java

java/edu/cmu/tetrad/algcomparison/score/DiscreteMixedBicScore.java

java/edu/cmu/tetrad/algcomparison/score/DseparationScore.java

java/edu/cmu/tetrad/algcomparison/score/FisherZScore.java

java/edu/cmu/tetrad/algcomparison/score/MNLRBicScore.java

java/edu/cmu/tetrad/algcomparison/score/MVPBicScore.java

java/edu/cmu/tetrad/algcomparison/score/PeterScore.java

java/edu/cmu/tetrad/algcomparison/score/PositiveCorrScore.java

java/edu/cmu/tetrad/algcomparison/score/ScoreWrapper.java

java/edu/cmu/tetrad/algcomparison/score/SemBicScore.java

java/edu/cmu/tetrad/algcomparison/score/SemBicScoreDeterministic.java

java/edu/cmu/tetrad/algcomparison/simulation/BayesNetSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/BooleanGlassSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/ConditionalGaussianSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/GeneralSemSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/GeneralSemSimulationSpecial1.java

java/edu/cmu/tetrad/algcomparison/simulation/LeeHastieSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/LinearFisherModel.java

java/edu/cmu/tetrad/algcomparison/simulation/LinearSineSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/SemSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/SemThenDiscretize.java

java/edu/cmu/tetrad/algcomparison/simulation/Simulation.java

java/edu/cmu/tetrad/algcomparison/simulation/SimulationTypes.java

java/edu/cmu/tetrad/algcomparison/simulation/SimulationUtils.java

java/edu/cmu/tetrad/algcomparison/simulation/Simulations.java

java/edu/cmu/tetrad/algcomparison/simulation/StandardizedSemSimulation.java

java/edu/cmu/tetrad/algcomparison/simulation/TimeSeriesSemSimulation.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyFN.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyFP.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyFPR.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyPrecision.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyRecall.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyTN.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyTP.java

java/edu/cmu/tetrad/algcomparison/statistic/AdjacencyTPR.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadFN.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadFP.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadPrecision.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadPrecisionCommonEdges.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadRecall.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadRecallCommonEdges.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadTN.java

java/edu/cmu/tetrad/algcomparison/statistic/ArrowheadTP.java

java/edu/cmu/tetrad/algcomparison/statistic/BicDiff.java

java/edu/cmu/tetrad/algcomparison/statistic/BicDiffPerRecord.java

java/edu/cmu/tetrad/algcomparison/statistic/BicEst.java

java/edu/cmu/tetrad/algcomparison/statistic/BicTrue.java

java/edu/cmu/tetrad/algcomparison/statistic/ElapsedTime.java

java/edu/cmu/tetrad/algcomparison/statistic/F1Adj.java

java/edu/cmu/tetrad/algcomparison/statistic/F1All.java

java/edu/cmu/tetrad/algcomparison/statistic/F1Arrow.java

java/edu/cmu/tetrad/algcomparison/statistic/GraphExactlyRight.java

java/edu/cmu/tetrad/algcomparison/statistic/MathewsCorrAdj.java

java/edu/cmu/tetrad/algcomparison/statistic/MathewsCorrArrow.java

java/edu/cmu/tetrad/algcomparison/statistic/NodesInCyclesPrecision.java

java/edu/cmu/tetrad/algcomparison/statistic/NodesInCyclesRecall.java

java/edu/cmu/tetrad/algcomparison/statistic/NumAmbiguousTriples.java

java/edu/cmu/tetrad/algcomparison/statistic/NumBidirectedEdges.java

java/edu/cmu/tetrad/algcomparison/statistic/NumberOfEdgesEst.java

java/edu/cmu/tetrad/algcomparison/statistic/NumberOfEdgesTrue.java

java/edu/cmu/tetrad/algcomparison/statistic/ParameterColumn.java

java/edu/cmu/tetrad/algcomparison/statistic/PercentAmbiguous.java

java/edu/cmu/tetrad/algcomparison/statistic/PercentBidirectedEdges.java

java/edu/cmu/tetrad/algcomparison/statistic/SHD.java

java/edu/cmu/tetrad/algcomparison/statistic/Statistic.java

java/edu/cmu/tetrad/algcomparison/statistic/Statistics.java

java/edu/cmu/tetrad/algcomparison/statistic/TailPrecision.java

java/edu/cmu/tetrad/algcomparison/statistic/TailRecall.java

java/edu/cmu/tetrad/algcomparison/statistic/TwoCycleFalseNegative.java

java/edu/cmu/tetrad/algcomparison/statistic/TwoCycleFalsePositive.java

java/edu/cmu/tetrad/algcomparison/statistic/TwoCyclePrecision.java

java/edu/cmu/tetrad/algcomparison/statistic/TwoCycleRecall.java

java/edu/cmu/tetrad/algcomparison/statistic/TwoCycleTruePositive.java

java/edu/cmu/tetrad/algcomparison/statistic/utils/AdjacencyConfusion.java

java/edu/cmu/tetrad/algcomparison/statistic/utils/ArrowConfusion.java

java/edu/cmu/tetrad/algcomparison/statistic/utils/SimulationPath.java

java/edu/cmu/tetrad/algcomparison/statistic/utils/TailConfusion.java

java/edu/cmu/tetrad/algcomparison/utils/HasKnowledge.java

java/edu/cmu/tetrad/algcomparison/utils/HasParameterValues.java

java/edu/cmu/tetrad/algcomparison/utils/HasParameters.java

java/edu/cmu/tetrad/algcomparison/utils/ParameterValues.java

java/edu/cmu/tetrad/algcomparison/utils/TakesData.java

java/edu/cmu/tetrad/algcomparison/utils/TakesIndependenceWrapper.java

java/edu/cmu/tetrad/algcomparison/utils/TakesInitialGraph.java

java/edu/cmu/tetrad/algcomparison/utils/UsesScoreWrapper.java

java/edu/cmu/tetrad/annotation/AbstractAnnotations.java

java/edu/cmu/tetrad/annotation/AlgType.java

java/edu/cmu/tetrad/annotation/Algorithm.java

java/edu/cmu/tetrad/annotation/AlgorithmAnnotations.java

java/edu/cmu/tetrad/annotation/AnnotatedClass.java

java/edu/cmu/tetrad/annotation/AnnotatedClassUtils.java

java/edu/cmu/tetrad/annotation/Bootstrapping.java

java/edu/cmu/tetrad/annotation/Experimental.java

java/edu/cmu/tetrad/annotation/Gaussian.java

java/edu/cmu/tetrad/annotation/Linear.java

java/edu/cmu/tetrad/annotation/Nonexecutable.java

java/edu/cmu/tetrad/annotation/Score.java

java/edu/cmu/tetrad/annotation/ScoreAnnotations.java

java/edu/cmu/tetrad/annotation/TestOfIndependence.java

java/edu/cmu/tetrad/annotation/TestOfIndependenceAnnotations.java

java/edu/cmu/tetrad/annotation/TimeSeries.java

java/edu/cmu/tetrad/annotation/UnmeasuredConfounder.java

java/edu/cmu/tetrad/bayes/ApproximateUpdater.java

java/edu/cmu/tetrad/bayes/BayesIm.java

java/edu/cmu/tetrad/bayes/BayesImDistanceFunction.java

java/edu/cmu/tetrad/bayes/BayesImProbs.java

java/edu/cmu/tetrad/bayes/BayesPm.java

java/edu/cmu/tetrad/bayes/BayesProperties.java

java/edu/cmu/tetrad/bayes/BayesUpdater.java

java/edu/cmu/tetrad/bayes/BayesUtils.java

java/edu/cmu/tetrad/bayes/BayesXmlParser.java

java/edu/cmu/tetrad/bayes/BayesXmlRenderer.java

java/edu/cmu/tetrad/bayes/BdeMetric.java

java/edu/cmu/tetrad/bayes/BdeMetricCache.java

java/edu/cmu/tetrad/bayes/CellTableProbs.java

java/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java

java/edu/cmu/tetrad/bayes/CptInvariantUpdater.java

java/edu/cmu/tetrad/bayes/DataSetProbs.java

java/edu/cmu/tetrad/bayes/DirichletBayesIm.java

java/edu/cmu/tetrad/bayes/DirichletDataSetProbs.java

java/edu/cmu/tetrad/bayes/DirichletEstimator.java

java/edu/cmu/tetrad/bayes/DiscreteProbs.java

java/edu/cmu/tetrad/bayes/EmBayesEstimator.java

java/edu/cmu/tetrad/bayes/EmBayesProperties.java

java/edu/cmu/tetrad/bayes/Evidence.java

java/edu/cmu/tetrad/bayes/ExtraCategoryInterpolator.java

java/edu/cmu/tetrad/bayes/FactoredBayesStructuralEM.java

java/edu/cmu/tetrad/bayes/Identifiability.java

java/edu/cmu/tetrad/bayes/IntAveDataSetProbs.java

java/edu/cmu/tetrad/bayes/IntMaxDataSetProbs.java

java/edu/cmu/tetrad/bayes/ManipulatingBayesUpdater.java

java/edu/cmu/tetrad/bayes/Manipulation.java

java/edu/cmu/tetrad/bayes/MlBayesEstimator.java

java/edu/cmu/tetrad/bayes/MlBayesIm.java

java/edu/cmu/tetrad/bayes/MlBayesImObs.java

java/edu/cmu/tetrad/bayes/ModeInterpolator.java

java/edu/cmu/tetrad/bayes/ModelGenerator.java

java/edu/cmu/tetrad/bayes/OnTheFlyMarginalCalculator.java

java/edu/cmu/tetrad/bayes/Proposition.java

java/edu/cmu/tetrad/bayes/QList.java

java/edu/cmu/tetrad/bayes/RowSummingExactUpdater.java

java/edu/cmu/tetrad/bayes/StoredCellProbs.java

java/edu/cmu/tetrad/bayes/StoredCellProbsObs.java

java/edu/cmu/tetrad/bayes/UpdatedBayesIm.java

java/edu/cmu/tetrad/calculator/Transformation.java

java/edu/cmu/tetrad/calculator/expression/AbstractExpression.java

java/edu/cmu/tetrad/calculator/expression/AbstractExpressionDescriptor.java

java/edu/cmu/tetrad/calculator/expression/ConstantExpression.java

java/edu/cmu/tetrad/calculator/expression/Context.java

java/edu/cmu/tetrad/calculator/expression/Equation.java

java/edu/cmu/tetrad/calculator/expression/EvaluationExpression.java

java/edu/cmu/tetrad/calculator/expression/Expression.java

java/edu/cmu/tetrad/calculator/expression/ExpressionDescriptor.java

java/edu/cmu/tetrad/calculator/expression/ExpressionInitializationException.java

java/edu/cmu/tetrad/calculator/expression/ExpressionManager.java

java/edu/cmu/tetrad/calculator/expression/ExpressionSignature.java

java/edu/cmu/tetrad/calculator/expression/ExpressionUtils.java

java/edu/cmu/tetrad/calculator/expression/VariableExpression.java

java/edu/cmu/tetrad/calculator/parser/ExpressionLexer.java

java/edu/cmu/tetrad/calculator/parser/ExpressionParser.java

java/edu/cmu/tetrad/calculator/parser/Token.java

java/edu/cmu/tetrad/cluster/ClusteringAlgorithm.java

java/edu/cmu/tetrad/cluster/KMeans.java

java/edu/cmu/tetrad/cluster/metrics/Dissimilarity.java

java/edu/cmu/tetrad/cluster/metrics/SquaredErrorLoss.java

java/edu/cmu/tetrad/data/AbstractVariable.java

java/edu/cmu/tetrad/data/AndersonDarlingTest.java

java/edu/cmu/tetrad/data/BootstrapSampler.java

java/edu/cmu/tetrad/data/BoxDataSet.java

java/edu/cmu/tetrad/data/ByteDataBox.java

java/edu/cmu/tetrad/data/CaseExpander.java

java/edu/cmu/tetrad/data/CellTable.java

java/edu/cmu/tetrad/data/Clusters.java

java/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java

java/edu/cmu/tetrad/data/ContinuousVariable.java

java/edu/cmu/tetrad/data/CorrelationMatrix.java

java/edu/cmu/tetrad/data/CorrelationMatrixOnTheFly.java

java/edu/cmu/tetrad/data/CovarianceMatrix.java

java/edu/cmu/tetrad/data/Covariances.java

java/edu/cmu/tetrad/data/CovariancesDoubleForkJoin.java

java/edu/cmu/tetrad/data/DataBox.java

java/edu/cmu/tetrad/data/DataFilter.java

java/edu/cmu/tetrad/data/DataGraphUtils.java

java/edu/cmu/tetrad/data/DataModel.java

java/edu/cmu/tetrad/data/DataModelList.java

java/edu/cmu/tetrad/data/DataReader.java

java/edu/cmu/tetrad/data/DataSet.java

java/edu/cmu/tetrad/data/DataType.java

java/edu/cmu/tetrad/data/DataUtils.java

java/edu/cmu/tetrad/data/DataWriter.java

java/edu/cmu/tetrad/data/DelimiterType.java

java/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java

java/edu/cmu/tetrad/data/DiscreteVariable.java

java/edu/cmu/tetrad/data/DiscreteVariableType.java

java/edu/cmu/tetrad/data/DiscretizationSpec.java

java/edu/cmu/tetrad/data/Discretizer.java

java/edu/cmu/tetrad/data/DoubleDataBox.java

java/edu/cmu/tetrad/data/FloatDataBox.java

java/edu/cmu/tetrad/data/GeneralAndersonDarlingTest.java

java/edu/cmu/tetrad/data/Histogram.java

java/edu/cmu/tetrad/data/ICovarianceMatrix.java

java/edu/cmu/tetrad/data/IDataReader.java

java/edu/cmu/tetrad/data/IKnowledge.java

java/edu/cmu/tetrad/data/IndependenceFacts.java

java/edu/cmu/tetrad/data/IntDataBox.java

java/edu/cmu/tetrad/data/Knowledge2.java

java/edu/cmu/tetrad/data/KnowledgeBoxInput.java

java/edu/cmu/tetrad/data/KnowledgeEdge.java

java/edu/cmu/tetrad/data/KnowledgeGroup.java

java/edu/cmu/tetrad/data/KnowledgeTransferable.java

java/edu/cmu/tetrad/data/Lineizer.java

java/edu/cmu/tetrad/data/LogDataUtils.java

java/edu/cmu/tetrad/data/LongDataBox.java

java/edu/cmu/tetrad/data/MeanInterpolator.java

java/edu/cmu/tetrad/data/MixedDataBox.java

java/edu/cmu/tetrad/data/MultiGeneralAndersonDarlingTest.java

java/edu/cmu/tetrad/data/NumberObjectDataSet.java

java/edu/cmu/tetrad/data/RandomSampler.java

java/edu/cmu/tetrad/data/RegexTokenizer.java

java/edu/cmu/tetrad/data/ShortDataBox.java

java/edu/cmu/tetrad/data/ShortTriangularMatrix.java

java/edu/cmu/tetrad/data/Simulator.java

java/edu/cmu/tetrad/data/SplitCasesSpec.java

java/edu/cmu/tetrad/data/TimeSeriesData.java

java/edu/cmu/tetrad/data/TriangularMatrix.java

java/edu/cmu/tetrad/data/Variable.java

java/edu/cmu/tetrad/data/VariableSource.java

java/edu/cmu/tetrad/data/VerticalDoubleDataBox.java

java/edu/cmu/tetrad/data/VerticalIntDataBox.java

java/edu/cmu/tetrad/data/simulation/LoadContinuousDataAndGraphs.java

java/edu/cmu/tetrad/data/simulation/LoadContinuousDataAndSingleGraph.java

java/edu/cmu/tetrad/data/simulation/LoadContinuousDataSmithSim.java

java/edu/cmu/tetrad/data/simulation/LoadDataAndGraphs.java

java/edu/cmu/tetrad/data/simulation/LoadDataFromFileWithoutGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/akutsu/BoolSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/akutsu/LTestBoolSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/akutsu/LTestQnet3.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/akutsu/LTestSsys1.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/akutsu/RevealOutputGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/Biolingua.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/BiolinguaDigraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/BiolinguaRunner.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/Digraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/LTester.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/cm.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/correlMatrix.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/g.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/graph_gold.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/graph_paperfig1.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/ltm.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/biolingua/m.txt

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/1c5g400tmeas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate1chisq.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate1meas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate1test.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate1thresh.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate2graph.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate2meas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate2test.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate3chisq.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate3graph.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2rate3meas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2ratemeas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/2ratetest.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/5g400tmeas.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/data/testmutual.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/ideker/ItkPredictorSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/ideker/LTestPredictorSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/ideker/ReadControl.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/ideker/ReadIdeker.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/package.html

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/reveal/LTestRevealSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/reveal/RevealEvaluator.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/reveal/RevealOutputGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/reveal/RevealSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/reveal/TestRevealEvaluator.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/AbstractNbComponent.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/BoolSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/LTestBoolSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/LTestReveal.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/LTestRevealSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbComponent.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbFunctionAnd.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbFunctionOr.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbFunctionSV.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbFunctionSum.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbGene.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbGeneAnd.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NbGeneOr.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/NetBuilderModel.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/RevealEvaluator.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/RevealOutputGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/RevealSearch.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/SimulateNetwork.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/SimulateNetworkMain.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/matearly1011.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/tstbool2nb1011.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/urchin/tstbool2nb10115.dat

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/BasicGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/BasicLTMatrix.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/BasicMatrix.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/LTMatrix.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/LTMatrixF.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/Matrix.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/MatrixF.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/OutputGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/SymMatrix.java

java/edu/cmu/tetrad/gene/tetrad/gene/algorithm/util/SymMatrixF.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/ActiveLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/DisplayNameHandler.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/LagGraphParams.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualActiveLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualLagGraphParams.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/RandomActiveLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/StoredLagGraphParams.java

java/edu/cmu/tetrad/gene/tetrad/gene/graph/package.html

java/edu/cmu/tetrad/gene/tetrad/gene/history/BasalInitializer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/BasicLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/BooleanFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/BooleanGlassFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/DishModel.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/GeneHistory.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/GraphInitializer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/GraphRandomizer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedConnectivity.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedParent.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/Initializer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/LagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/LaggedEdge.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/LaggedFactor.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/LinearFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/Polynomial.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/PolynomialFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/PolynomialTerm.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/PreviousStepOnly.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/RandomDistribution.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/SimpleRandomizer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestBooleanFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestIndexedConnectivity.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestIndexedLagGraph.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestPolynomial.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestPolynomialTerm.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/TestSimpleRandomizer.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/UpdateFunction.java

java/edu/cmu/tetrad/gene/tetrad/gene/history/package.html

java/edu/cmu/tetrad/gene/tetrad/gene/history/package2.html

java/edu/cmu/tetrad/gene/tetrad/gene/history/package3.html

java/edu/cmu/tetrad/gene/tetrad/gene/simexp/LinearSimExp1.java

java/edu/cmu/tetrad/gene/tetrad/gene/simexp/package.html

java/edu/cmu/tetrad/gene/tetrad/gene/simulation/MeasurementSimulator.java

java/edu/cmu/tetrad/gene/tetrad/gene/simulation/TestMeasurementSimulator.java

java/edu/cmu/tetrad/gene/tetrad/gene/simulation/package.html

java/edu/cmu/tetrad/gene/tetrad/gene/util/HandleyConvert.java

java/edu/cmu/tetrad/gene/tetrad/gene/util/package.html

java/edu/cmu/tetrad/gene/tetradapp/model/BooleanGlassGeneIm.java

java/edu/cmu/tetrad/gene/tetradapp/model/BooleanGlassGenePm.java

java/edu/cmu/tetrad/gene/tetradapp/model/GenePm.java

java/edu/cmu/tetrad/gene/tetradapp/model/MeasurementSimulatorParams.java

java/edu/cmu/tetrad/graph/AtMostOneEdgePerPair.java

java/edu/cmu/tetrad/graph/Dag.java

java/edu/cmu/tetrad/graph/DirectedEdgesOnly.java

java/edu/cmu/tetrad/graph/DirectedUndirectedOnly.java

java/edu/cmu/tetrad/graph/Edge.java

java/edu/cmu/tetrad/graph/EdgeListGraph.java

java/edu/cmu/tetrad/graph/EdgeListGraphSingleConnections.java

java/edu/cmu/tetrad/graph/EdgeTypeProbability.java

java/edu/cmu/tetrad/graph/Edges.java

java/edu/cmu/tetrad/graph/Endpoint.java

java/edu/cmu/tetrad/graph/EndpointMatrixGraph.java

java/edu/cmu/tetrad/graph/FruchtermanReingoldLayout.java

java/edu/cmu/tetrad/graph/Graph.java

java/edu/cmu/tetrad/graph/GraphConstraint.java

java/edu/cmu/tetrad/graph/GraphConverter.java

java/edu/cmu/tetrad/graph/GraphGeneratorRandomNumEdges.java

java/edu/cmu/tetrad/graph/GraphGroup.java

java/edu/cmu/tetrad/graph/GraphNode.java

java/edu/cmu/tetrad/graph/GraphUtils.java

java/edu/cmu/tetrad/graph/InArrowImpliesNonancestor.java

java/edu/cmu/tetrad/graph/IndependenceFact.java

java/edu/cmu/tetrad/graph/KamadaKawaiLayout.java

java/edu/cmu/tetrad/graph/LagGraph.java

java/edu/cmu/tetrad/graph/LayeredDrawing.java

java/edu/cmu/tetrad/graph/MeasuredLatentOnly.java

java/edu/cmu/tetrad/graph/MisclassificationUtils.java

java/edu/cmu/tetrad/graph/NoEdgesToSelf.java

java/edu/cmu/tetrad/graph/Node.java

java/edu/cmu/tetrad/graph/NodeEqualityMode.java

java/edu/cmu/tetrad/graph/NodePair.java

java/edu/cmu/tetrad/graph/NodeType.java

java/edu/cmu/tetrad/graph/NodeVariableType.java

java/edu/cmu/tetrad/graph/OrderedPair.java

java/edu/cmu/tetrad/graph/SemGraph.java

java/edu/cmu/tetrad/graph/TimeLagGraph.java

java/edu/cmu/tetrad/graph/Triple.java

java/edu/cmu/tetrad/graph/TripleClassifier.java

java/edu/cmu/tetrad/graph/UniformGraphGenerator.java

java/edu/cmu/tetrad/latest/LatestClient.java

java/edu/cmu/tetrad/latest/SoftwareVersion.java

java/edu/cmu/tetrad/performance/Comparison.java

java/edu/cmu/tetrad/performance/Comparison2.java

java/edu/cmu/tetrad/performance/ComparisonParameters.java

java/edu/cmu/tetrad/performance/ComparisonResult.java

java/edu/cmu/tetrad/performance/ComparisonScript.java

java/edu/cmu/tetrad/performance/ExploreComparison.java

java/edu/cmu/tetrad/performance/PerformanceTests.java

java/edu/cmu/tetrad/performance/PerformanceTestsDan.java

java/edu/cmu/tetrad/performance/readme_ComparisonScript.txt

java/edu/cmu/tetrad/regression/LogisticRegression.java

java/edu/cmu/tetrad/regression/LogisticRegression2.java

java/edu/cmu/tetrad/regression/LogisticRegressionResult.java

java/edu/cmu/tetrad/regression/Regression.java

java/edu/cmu/tetrad/regression/RegressionCovariance.java

java/edu/cmu/tetrad/regression/RegressionDataset.java

java/edu/cmu/tetrad/regression/RegressionDatasetGeneralized.java

java/edu/cmu/tetrad/regression/RegressionPlane.java

java/edu/cmu/tetrad/regression/RegressionResult.java

java/edu/cmu/tetrad/regression/RegressionUtils.java

java/edu/cmu/tetrad/search/AdLeafTree.java

java/edu/cmu/tetrad/search/AdTrees.java

java/edu/cmu/tetrad/search/BDeScore.java

java/edu/cmu/tetrad/search/BDeuScore.java

java/edu/cmu/tetrad/search/BayesUpdaterClassifier.java

java/edu/cmu/tetrad/search/BdeuScoreImages.java

java/edu/cmu/tetrad/search/Bff.java

java/edu/cmu/tetrad/search/BffBeam.java

java/edu/cmu/tetrad/search/BffGes.java

java/edu/cmu/tetrad/search/BicScore.java

java/edu/cmu/tetrad/search/BinaryFunction.java

java/edu/cmu/tetrad/search/BinaryFunctionUtils.java

java/edu/cmu/tetrad/search/BpcAlgorithmType.java

java/edu/cmu/tetrad/search/BpcTetradPurifyWashdown.java

java/edu/cmu/tetrad/search/BuildPureClusters.java

java/edu/cmu/tetrad/search/Ccd.java

java/edu/cmu/tetrad/search/CcdMax.java

java/edu/cmu/tetrad/search/Cefs.java

java/edu/cmu/tetrad/search/Cfci.java

java/edu/cmu/tetrad/search/ChiSquareTest.java

java/edu/cmu/tetrad/search/ClusterUtils.java

java/edu/cmu/tetrad/search/ConditionalCorrelationIndependence.java

java/edu/cmu/tetrad/search/ConditionalGaussianLikelihood.java

java/edu/cmu/tetrad/search/ConditionalGaussianOtherLikelihood.java

java/edu/cmu/tetrad/search/ConditionalGaussianOtherScore.java

java/edu/cmu/tetrad/search/ConditionalGaussianScore.java

java/edu/cmu/tetrad/search/ContinuousTetradTest.java

java/edu/cmu/tetrad/search/Cpc.java

java/edu/cmu/tetrad/search/CpcLocal.java

java/edu/cmu/tetrad/search/CpcOrienter.java

java/edu/cmu/tetrad/search/CpcStable.java

java/edu/cmu/tetrad/search/DMSearch.java

java/edu/cmu/tetrad/search/DagInPatternIterator.java

java/edu/cmu/tetrad/search/DagIterator.java

java/edu/cmu/tetrad/search/DagSepsets.java

java/edu/cmu/tetrad/search/DagToPag.java

java/edu/cmu/tetrad/search/DagToPag2.java

java/edu/cmu/tetrad/search/DagToPattern.java

java/edu/cmu/tetrad/search/Dci.java

java/edu/cmu/tetrad/search/DegenerateGaussianScore.java

java/edu/cmu/tetrad/search/DeltaSextadTest.java

java/edu/cmu/tetrad/search/DeltaTetradTest.java

java/edu/cmu/tetrad/search/DeltaTetradTest2.java

java/edu/cmu/tetrad/search/DirectedGraphIterator.java

java/edu/cmu/tetrad/search/DirichletScore.java

java/edu/cmu/tetrad/search/DiscreteClassifier.java

java/edu/cmu/tetrad/search/DiscreteMixedLikelihood.java

java/edu/cmu/tetrad/search/DiscreteMixedScore.java

java/edu/cmu/tetrad/search/DiscreteTetradTest.java

java/edu/cmu/tetrad/search/EstimateRank.java

java/edu/cmu/tetrad/search/ExperimentalSetup.java

java/edu/cmu/tetrad/search/FactorAnalysis.java

java/edu/cmu/tetrad/search/Fas.java

java/edu/cmu/tetrad/search/FasConcurrent.java

java/edu/cmu/tetrad/search/FasDci.java

java/edu/cmu/tetrad/search/FasDeterministic.java

java/edu/cmu/tetrad/search/FasFdr.java

java/edu/cmu/tetrad/search/FasLofs.java

java/edu/cmu/tetrad/search/FasStable.java

java/edu/cmu/tetrad/search/FasStableConcurrentFdr.java

java/edu/cmu/tetrad/search/Fask.java

java/edu/cmu/tetrad/search/FastIca.java

java/edu/cmu/tetrad/search/Fasts.java

java/edu/cmu/tetrad/search/Fci.java

java/edu/cmu/tetrad/search/FciDsepLegalPairs.java

java/edu/cmu/tetrad/search/FciDsepLegalPairsCfci.java

java/edu/cmu/tetrad/search/FciMax.java

java/edu/cmu/tetrad/search/FciOrient.java

java/edu/cmu/tetrad/search/FciOrientT.java

java/edu/cmu/tetrad/search/Fges.java

java/edu/cmu/tetrad/search/Fges2.java

java/edu/cmu/tetrad/search/FgesD.java

java/edu/cmu/tetrad/search/FgesMb.java

java/edu/cmu/tetrad/search/FgesOld.java

java/edu/cmu/tetrad/search/FgesOrienter.java

java/edu/cmu/tetrad/search/FindOneFactorClusters.java

java/edu/cmu/tetrad/search/FindTwoFactorClusters.java

java/edu/cmu/tetrad/search/GFci.java

java/edu/cmu/tetrad/search/GFciMax.java

java/edu/cmu/tetrad/search/GPc.java

java/edu/cmu/tetrad/search/GSquareTest.java

java/edu/cmu/tetrad/search/Glasso.java

java/edu/cmu/tetrad/search/GraphChange.java

java/edu/cmu/tetrad/search/GraphGroupSearch.java

java/edu/cmu/tetrad/search/GraphScore.java

java/edu/cmu/tetrad/search/GraphScorer.java

java/edu/cmu/tetrad/search/GraphSearch.java

java/edu/cmu/tetrad/search/GraphWithParameters.java

java/edu/cmu/tetrad/search/GrowShrink.java

java/edu/cmu/tetrad/search/GwpResult.java

java/edu/cmu/tetrad/search/Hungarian.java

java/edu/cmu/tetrad/search/IBDeuScore.java

java/edu/cmu/tetrad/search/IFas.java

java/edu/cmu/tetrad/search/IImages.java

java/edu/cmu/tetrad/search/IPurify.java

java/edu/cmu/tetrad/search/ISemBicScore.java

java/edu/cmu/tetrad/search/ImpliedOrientation.java

java/edu/cmu/tetrad/search/IndTestChiSquare.java

java/edu/cmu/tetrad/search/IndTestConditionalCorrelation.java

java/edu/cmu/tetrad/search/IndTestConditionalGaussianLRT.java

java/edu/cmu/tetrad/search/IndTestCorrelationT.java

java/edu/cmu/tetrad/search/IndTestCramerT.java

java/edu/cmu/tetrad/search/IndTestDSep.java

java/edu/cmu/tetrad/search/IndTestDSepDiminishingPathStrengths.java

java/edu/cmu/tetrad/search/IndTestDegenerateGaussianLRT.java

java/edu/cmu/tetrad/search/IndTestDirichletScore.java

java/edu/cmu/tetrad/search/IndTestDrton.java

java/edu/cmu/tetrad/search/IndTestFisherZ.java

java/edu/cmu/tetrad/search/IndTestFisherZBootstrap.java

java/edu/cmu/tetrad/search/IndTestFisherZConcatenateResiduals.java

java/edu/cmu/tetrad/search/IndTestFisherZD.java

java/edu/cmu/tetrad/search/IndTestFisherZFisherPValue.java

java/edu/cmu/tetrad/search/IndTestFisherZGeneralizedInverse.java

java/edu/cmu/tetrad/search/IndTestFisherZPercentIndependent.java

java/edu/cmu/tetrad/search/IndTestFisherZRecursive.java

java/edu/cmu/tetrad/search/IndTestGSquare.java

java/edu/cmu/tetrad/search/IndTestHsic.java

java/edu/cmu/tetrad/search/IndTestIndependenceFacts.java

java/edu/cmu/tetrad/search/IndTestKciMatlab.java

java/edu/cmu/tetrad/search/IndTestLaggedRegression.java

java/edu/cmu/tetrad/search/IndTestMNLRLRT.java

java/edu/cmu/tetrad/search/IndTestMVPLRT.java

java/edu/cmu/tetrad/search/IndTestMixedMultipleTTest.java

java/edu/cmu/tetrad/search/IndTestMulti.java

java/edu/cmu/tetrad/search/IndTestMultinomialLogisticRegression.java

java/edu/cmu/tetrad/search/IndTestPartialCorrelation.java

java/edu/cmu/tetrad/search/IndTestPositiveCorr.java

java/edu/cmu/tetrad/search/IndTestProbabilistic.java

java/edu/cmu/tetrad/search/IndTestProbabilisticVerbose.java

java/edu/cmu/tetrad/search/IndTestRegression.java

java/edu/cmu/tetrad/search/IndTestRegressionAD.java

java/edu/cmu/tetrad/search/IndTestScore.java

java/edu/cmu/tetrad/search/IndTestSepset.java

java/edu/cmu/tetrad/search/IndTestTimeSeries.java

java/edu/cmu/tetrad/search/IndTestTrekSep.java

java/edu/cmu/tetrad/search/IndTestType.java

java/edu/cmu/tetrad/search/IndependenceTest.java

java/edu/cmu/tetrad/search/IntSextad.java

java/edu/cmu/tetrad/search/InverseCorrelation.java

java/edu/cmu/tetrad/search/Ion.java

java/edu/cmu/tetrad/search/IonHittingSet.java

java/edu/cmu/tetrad/search/IonJoeModifications.java

java/edu/cmu/tetrad/search/IonLegalPairs.java

java/edu/cmu/tetrad/search/Jcpc.java

java/edu/cmu/tetrad/search/Kci.java

java/edu/cmu/tetrad/search/Kpc.java

java/edu/cmu/tetrad/search/LegalPairs.java

java/edu/cmu/tetrad/search/Ling.java

java/edu/cmu/tetrad/search/Lingam.java

java/edu/cmu/tetrad/search/LingamPattern.java

java/edu/cmu/tetrad/search/LingamPattern2.java

java/edu/cmu/tetrad/search/LocalDiscreteScore.java

java/edu/cmu/tetrad/search/LocalScoreCache.java

java/edu/cmu/tetrad/search/Lofs.java

java/edu/cmu/tetrad/search/Lofs2.java

java/edu/cmu/tetrad/search/MNLRLikelihood.java

java/edu/cmu/tetrad/search/MNLRScore.java

java/edu/cmu/tetrad/search/MVPBicScore.java

java/edu/cmu/tetrad/search/MVPLikelihood.java

java/edu/cmu/tetrad/search/MVPScore.java

java/edu/cmu/tetrad/search/MagToPag.java

java/edu/cmu/tetrad/search/MbClassify.java

java/edu/cmu/tetrad/search/MbSearch.java

java/edu/cmu/tetrad/search/MbUtils.java

java/edu/cmu/tetrad/search/Mbfs.java

java/edu/cmu/tetrad/search/MeekRules.java

java/edu/cmu/tetrad/search/MeekRulesPattern.java

java/edu/cmu/tetrad/search/MeekRulesRestricted.java

java/edu/cmu/tetrad/search/MimAdjacencySearch.java

java/edu/cmu/tetrad/search/MimUtils.java

java/edu/cmu/tetrad/search/Mimbuild2.java

java/edu/cmu/tetrad/search/MimbuildTrek.java

java/edu/cmu/tetrad/search/MixedBicScore.java

java/edu/cmu/tetrad/search/MultiFask.java

java/edu/cmu/tetrad/search/OrientCollidersMaxP.java

java/edu/cmu/tetrad/search/PagUtils.java

java/edu/cmu/tetrad/search/PatternToDag.java

java/edu/cmu/tetrad/search/Pc.java

java/edu/cmu/tetrad/search/PcAll.java

java/edu/cmu/tetrad/search/PcLocal.java

java/edu/cmu/tetrad/search/PcPattern.java

java/edu/cmu/tetrad/search/PcStable.java

java/edu/cmu/tetrad/search/PcStableMax.java

java/edu/cmu/tetrad/search/PcStableMaxLocal.java

java/edu/cmu/tetrad/search/Pcd.java

java/edu/cmu/tetrad/search/PermutationMatrixPair.java

java/edu/cmu/tetrad/search/Peter1Score.java

java/edu/cmu/tetrad/search/PeterScore.java

java/edu/cmu/tetrad/search/PopulationTetradTest.java

java/edu/cmu/tetrad/search/PossibleDConnectingPath.java

java/edu/cmu/tetrad/search/PossibleDsepCfci.java

java/edu/cmu/tetrad/search/PossibleDsepFci.java

java/edu/cmu/tetrad/search/PossibleGraphicalChangeFinder.java

java/edu/cmu/tetrad/search/ProbFci.java

java/edu/cmu/tetrad/search/ProbabilisticMAPIndependence.java

java/edu/cmu/tetrad/search/Purify.java

java/edu/cmu/tetrad/search/PurifyScoreBased.java

java/edu/cmu/tetrad/search/PurifySextadBased.java

java/edu/cmu/tetrad/search/PurifyTetradBased.java

java/edu/cmu/tetrad/search/PurifyTetradBased2.java

java/edu/cmu/tetrad/search/RBExperiments.java

java/edu/cmu/tetrad/search/RecursivePartialCorrelation.java

java/edu/cmu/tetrad/search/Reorienter.java

java/edu/cmu/tetrad/search/ResolveSepsets.java

java/edu/cmu/tetrad/search/Rfci.java

java/edu/cmu/tetrad/search/SampleVcpc.java

java/edu/cmu/tetrad/search/SampleVcpcFast.java

java/edu/cmu/tetrad/search/Score.java

java/edu/cmu/tetrad/search/ScoreForFact.java

java/edu/cmu/tetrad/search/ScoredGraph.java

java/edu/cmu/tetrad/search/ScoredIndTest.java

java/edu/cmu/tetrad/search/SearchGraphUtils.java

java/edu/cmu/tetrad/search/SearchLogUtils.java

java/edu/cmu/tetrad/search/SemBicScore.java

java/edu/cmu/tetrad/search/SemBicScoreDeterministic.java

java/edu/cmu/tetrad/search/SemBicScoreImages.java

java/edu/cmu/tetrad/search/SemBicScoreImages2.java

java/edu/cmu/tetrad/search/SemBicScoreImages3.java

java/edu/cmu/tetrad/search/SemBicScoreMultiFas.java

java/edu/cmu/tetrad/search/SemBicScorer.java

java/edu/cmu/tetrad/search/SemGpScore.java

java/edu/cmu/tetrad/search/SemLikelihood2.java

java/edu/cmu/tetrad/search/SepsetMap.java

java/edu/cmu/tetrad/search/SepsetMapDci.java

java/edu/cmu/tetrad/search/SepsetProducer.java

java/edu/cmu/tetrad/search/SepsetsConservative.java

java/edu/cmu/tetrad/search/SepsetsConservativeMajority.java

java/edu/cmu/tetrad/search/SepsetsGreedy.java

java/edu/cmu/tetrad/search/SepsetsMaxPValue.java

java/edu/cmu/tetrad/search/SepsetsMaxPValuePossDsep.java

java/edu/cmu/tetrad/search/SepsetsMaxScore.java

java/edu/cmu/tetrad/search/SepsetsMinPValue.java

java/edu/cmu/tetrad/search/SepsetsMinScore.java

java/edu/cmu/tetrad/search/SepsetsPossibleDsep.java

java/edu/cmu/tetrad/search/SepsetsSet.java

java/edu/cmu/tetrad/search/Sextad.java

java/edu/cmu/tetrad/search/ShiftSearch.java

java/edu/cmu/tetrad/search/Test.java

java/edu/cmu/tetrad/search/TestType.java

java/edu/cmu/tetrad/search/Tetrad.java

java/edu/cmu/tetrad/search/TetradTest.java

java/edu/cmu/tetrad/search/TimeSeriesLagSearch.java

java/edu/cmu/tetrad/search/TimeSeriesUtils.java

java/edu/cmu/tetrad/search/TsDagToPag.java

java/edu/cmu/tetrad/search/TsFci.java

java/edu/cmu/tetrad/search/TsFciOrient.java

java/edu/cmu/tetrad/search/TsFges2.java

java/edu/cmu/tetrad/search/TsGFci.java

java/edu/cmu/tetrad/search/Vcfas.java

java/edu/cmu/tetrad/search/Vcpc.java

java/edu/cmu/tetrad/search/VcpcAlt.java

java/edu/cmu/tetrad/search/VcpcFast.java

java/edu/cmu/tetrad/search/WFges.java

java/edu/cmu/tetrad/search/WGfci.java

java/edu/cmu/tetrad/search/Washdown.java

java/edu/cmu/tetrad/search/XdslXmlConstants.java

java/edu/cmu/tetrad/search/XdslXmlParser.java

java/edu/cmu/tetrad/search/kernel/Kernel.java

java/edu/cmu/tetrad/search/kernel/KernelGaussian.java

java/edu/cmu/tetrad/search/kernel/KernelUtils.java

java/edu/cmu/tetrad/search/mb/HitonMb.java

java/edu/cmu/tetrad/search/mb/HitonVariant.java

java/edu/cmu/tetrad/search/mb/Iamb.java

java/edu/cmu/tetrad/search/mb/IambnPc.java

java/edu/cmu/tetrad/search/mb/InterIamb.java

java/edu/cmu/tetrad/search/mb/Mmhc.java

java/edu/cmu/tetrad/search/mb/Mmmb.java

java/edu/cmu/tetrad/search/mb/MmmbGraphRestricted.java

java/edu/cmu/tetrad/sem/ConnectionFunction.java

java/edu/cmu/tetrad/sem/DagScorer.java

java/edu/cmu/tetrad/sem/EmpiricalCdf.java

java/edu/cmu/tetrad/sem/EmpiricalDistributionForExpression.java

java/edu/cmu/tetrad/sem/GeneralizedSemEstimator.java

java/edu/cmu/tetrad/sem/GeneralizedSemIm.java

java/edu/cmu/tetrad/sem/GeneralizedSemPm.java

java/edu/cmu/tetrad/sem/ISemIm.java

java/edu/cmu/tetrad/sem/LargeScaleSimulation.java

java/edu/cmu/tetrad/sem/Mapping.java

java/edu/cmu/tetrad/sem/ParamComparison.java

java/edu/cmu/tetrad/sem/ParamConstraint.java

java/edu/cmu/tetrad/sem/ParamConstraintType.java

java/edu/cmu/tetrad/sem/ParamType.java

java/edu/cmu/tetrad/sem/Parameter.java

java/edu/cmu/tetrad/sem/ParameterPair.java

java/edu/cmu/tetrad/sem/ReidentifyVariables.java

java/edu/cmu/tetrad/sem/Ricf.java

java/edu/cmu/tetrad/sem/ScoreType.java

java/edu/cmu/tetrad/sem/Scorer.java

java/edu/cmu/tetrad/sem/SemEstimator.java

java/edu/cmu/tetrad/sem/SemEstimatorGibbs.java

java/edu/cmu/tetrad/sem/SemEstimatorGibbsParams.java

java/edu/cmu/tetrad/sem/SemEvidence.java

java/edu/cmu/tetrad/sem/SemIm.java

java/edu/cmu/tetrad/sem/SemManipulation.java

java/edu/cmu/tetrad/sem/SemOptimizer.java

java/edu/cmu/tetrad/sem/SemOptimizerEm.java

java/edu/cmu/tetrad/sem/SemOptimizerPowell.java

java/edu/cmu/tetrad/sem/SemOptimizerRegression.java

java/edu/cmu/tetrad/sem/SemOptimizerRicf.java

java/edu/cmu/tetrad/sem/SemOptimizerScattershot.java

java/edu/cmu/tetrad/sem/SemPm.java

java/edu/cmu/tetrad/sem/SemProposition.java

java/edu/cmu/tetrad/sem/SemStdErrorEstimator.java

java/edu/cmu/tetrad/sem/SemUpdater.java

java/edu/cmu/tetrad/sem/SemXmlConstants.java

java/edu/cmu/tetrad/sem/SemXmlParser.java

java/edu/cmu/tetrad/sem/SemXmlRenderer.java

java/edu/cmu/tetrad/sem/StandardizedSemIm.java

java/edu/cmu/tetrad/sem/TemplateExpander.java

java/edu/cmu/tetrad/sem/Tsls.java

java/edu/cmu/tetrad/session/CouldNotCreateModelException.java

java/edu/cmu/tetrad/session/DelegatesEditing.java

java/edu/cmu/tetrad/session/DoNotAddOldModel.java

java/edu/cmu/tetrad/session/Executable.java

java/edu/cmu/tetrad/session/ExecutionRestarter.java

java/edu/cmu/tetrad/session/ModificationRegistery.java

java/edu/cmu/tetrad/session/ParamsResettable.java

java/edu/cmu/tetrad/session/Session.java

java/edu/cmu/tetrad/session/SessionAdapter.java

java/edu/cmu/tetrad/session/SessionEvent.java

java/edu/cmu/tetrad/session/SessionListener.java

java/edu/cmu/tetrad/session/SessionModel.java

java/edu/cmu/tetrad/session/SessionNode.java

java/edu/cmu/tetrad/session/SessionSupport.java

java/edu/cmu/tetrad/session/SimulationParamsSource.java

java/edu/cmu/tetrad/session/SimulationStudy.java

java/edu/cmu/tetrad/session/Type1.java

java/edu/cmu/tetrad/session/Type10.java

java/edu/cmu/tetrad/session/Type11.java

java/edu/cmu/tetrad/session/Type12.java

java/edu/cmu/tetrad/session/Type2.java

java/edu/cmu/tetrad/session/Type3.java

java/edu/cmu/tetrad/session/Type4.java

java/edu/cmu/tetrad/session/Type5.java

java/edu/cmu/tetrad/session/Type6.java

java/edu/cmu/tetrad/session/Type7.java

java/edu/cmu/tetrad/session/Type8.java

java/edu/cmu/tetrad/session/Type9.java

java/edu/cmu/tetrad/simulation/Gdistance.java

java/edu/cmu/tetrad/simulation/GdistanceApply.java

java/edu/cmu/tetrad/simulation/GdistanceRandom.java

java/edu/cmu/tetrad/simulation/GdistanceRandomApply.java

java/edu/cmu/tetrad/simulation/GdistanceTest.java

java/edu/cmu/tetrad/simulation/GdistanceUtils.java

java/edu/cmu/tetrad/simulation/Hsim.java

java/edu/cmu/tetrad/simulation/HsimAutoC.java

java/edu/cmu/tetrad/simulation/HsimAutoRun.java

java/edu/cmu/tetrad/simulation/HsimCompareRepeat.java

java/edu/cmu/tetrad/simulation/HsimContinuous.java

java/edu/cmu/tetrad/simulation/HsimEvalFromData.java

java/edu/cmu/tetrad/simulation/HsimRepeatAC.java

java/edu/cmu/tetrad/simulation/HsimRepeatAuto.java

java/edu/cmu/tetrad/simulation/HsimRepeatAutoRun.java

java/edu/cmu/tetrad/simulation/HsimRobustCompare.java

java/edu/cmu/tetrad/simulation/HsimRun.java

java/edu/cmu/tetrad/simulation/HsimSchedule.java

java/edu/cmu/tetrad/simulation/HsimStudy.java

java/edu/cmu/tetrad/simulation/HsimStudyAuto.java

java/edu/cmu/tetrad/simulation/HsimUtils.java

java/edu/cmu/tetrad/simulation/PRAOerrors.java

java/edu/cmu/tetrad/simulation/ReadMe

java/edu/cmu/tetrad/simulation/Vicinity.java

java/edu/cmu/tetrad/stat/RealVariance.java

java/edu/cmu/tetrad/stat/RealVarianceVector.java

java/edu/cmu/tetrad/stat/RealVarianceVectorForkJoin.java

java/edu/cmu/tetrad/stat/Variance.java

java/edu/cmu/tetrad/stat/VarianceVector.java

java/edu/cmu/tetrad/stat/VarianceVectorForkJoin.java

java/edu/cmu/tetrad/stat/correlation/Covariance.java

java/edu/cmu/tetrad/stat/correlation/CovarianceMatrix.java

java/edu/cmu/tetrad/stat/correlation/RealCovariance.java

java/edu/cmu/tetrad/stat/correlation/RealCovarianceMatrix.java

java/edu/cmu/tetrad/stat/correlation/RealCovarianceMatrixForkJoin.java

java/edu/cmu/tetrad/study/BryanSensitivityStudy.java

java/edu/cmu/tetrad/study/Conditions/Condition1.java

java/edu/cmu/tetrad/study/Conditions/Condition2.java

java/edu/cmu/tetrad/study/ExampleCompareFromFiles.java

java/edu/cmu/tetrad/study/ExampleCompareSimulation.java

java/edu/cmu/tetrad/study/ExampleCompareSimulationDiscrete.java

java/edu/cmu/tetrad/study/ExampleFirstInflection.java

java/edu/cmu/tetrad/study/ExampleSave.java

java/edu/cmu/tetrad/study/ExampleStARS.java

java/edu/cmu/tetrad/study/LingamStudy.java

java/edu/cmu/tetrad/study/README

java/edu/cmu/tetrad/util/AlgorithmDescriptions.java

java/edu/cmu/tetrad/util/ArrUtils.java

java/edu/cmu/tetrad/util/ChoiceGenerator.java

java/edu/cmu/tetrad/util/CombinationGenerator.java

java/edu/cmu/tetrad/util/CombinationIterator.java

java/edu/cmu/tetrad/util/CutoffFinder.java

java/edu/cmu/tetrad/util/DataConvertUtils.java

java/edu/cmu/tetrad/util/DataUtility.java

java/edu/cmu/tetrad/util/DefaultTetradLoggerConfig.java

java/edu/cmu/tetrad/util/DelimiterUtils.java

java/edu/cmu/tetrad/util/DepthChoiceGenerator.java

java/edu/cmu/tetrad/util/Experimental.java

java/edu/cmu/tetrad/util/ForkJoinPoolInstance.java

java/edu/cmu/tetrad/util/Function.java

java/edu/cmu/tetrad/util/IM.java

java/edu/cmu/tetrad/util/IndependenceTestDescriptions.java

java/edu/cmu/tetrad/util/IndexedMatrix.java

java/edu/cmu/tetrad/util/Integrator.java

java/edu/cmu/tetrad/util/JOptionUtils.java

java/edu/cmu/tetrad/util/JsonUtils.java

java/edu/cmu/tetrad/util/LingUtils.java

java/edu/cmu/tetrad/util/LogUtils.java

java/edu/cmu/tetrad/util/MathUtils.java

java/edu/cmu/tetrad/util/MatrixUtils.java

java/edu/cmu/tetrad/util/Memorable.java

java/edu/cmu/tetrad/util/MultiDimIntTable.java

java/edu/cmu/tetrad/util/MultidataUtils.java

java/edu/cmu/tetrad/util/NamingProtocol.java

java/edu/cmu/tetrad/util/NumberFormatUtil.java

java/edu/cmu/tetrad/util/PM.java

java/edu/cmu/tetrad/util/ParamDescription.java

java/edu/cmu/tetrad/util/ParamDescriptions.java

java/edu/cmu/tetrad/util/ParameterUtils.java

java/edu/cmu/tetrad/util/Parameters.java

java/edu/cmu/tetrad/util/Params.java

java/edu/cmu/tetrad/util/PartialCorrelationPdf.java

java/edu/cmu/tetrad/util/PermutationGenerator.java

java/edu/cmu/tetrad/util/Point.java

java/edu/cmu/tetrad/util/PointXy.java

java/edu/cmu/tetrad/util/ProbUtils.java

java/edu/cmu/tetrad/util/RandomUtil.java

java/edu/cmu/tetrad/util/RocCalculator.java

java/edu/cmu/tetrad/util/ScoreDescriptions.java

java/edu/cmu/tetrad/util/SelectionGenerator.java

java/edu/cmu/tetrad/util/StatUtils.java

java/edu/cmu/tetrad/util/TaskManager.java

java/edu/cmu/tetrad/util/TetradAlgebra.java

java/edu/cmu/tetrad/util/TetradLogger.java

java/edu/cmu/tetrad/util/TetradLoggerConfig.java

java/edu/cmu/tetrad/util/TetradLoggerEvent.java

java/edu/cmu/tetrad/util/TetradLoggerListener.java

java/edu/cmu/tetrad/util/TetradMatrix.java

java/edu/cmu/tetrad/util/TetradProperties.java

java/edu/cmu/tetrad/util/TetradSerializable.java

java/edu/cmu/tetrad/util/TetradSerializableExcluded.java

java/edu/cmu/tetrad/util/TetradSerializableUtils.java

java/edu/cmu/tetrad/util/TetradVector.java

java/edu/cmu/tetrad/util/TextTable.java

java/edu/cmu/tetrad/util/Unmarshallable.java

java/edu/cmu/tetrad/util/Version.java

java/edu/cmu/tetrad/util/dist/Beta.java

java/edu/cmu/tetrad/util/dist/ChiSquare.java

java/edu/cmu/tetrad/util/dist/Discrete.java

java/edu/cmu/tetrad/util/dist/Distribution.java

java/edu/cmu/tetrad/util/dist/Exponential.java

java/edu/cmu/tetrad/util/dist/Gamma.java

java/edu/cmu/tetrad/util/dist/GaussianPower.java

java/edu/cmu/tetrad/util/dist/Indicator.java

java/edu/cmu/tetrad/util/dist/LogNormal.java

java/edu/cmu/tetrad/util/dist/MixtureOfGaussians.java

java/edu/cmu/tetrad/util/dist/Normal.java

java/edu/cmu/tetrad/util/dist/Poisson.java

java/edu/cmu/tetrad/util/dist/SingleValue.java

java/edu/cmu/tetrad/util/dist/Split.java

java/edu/cmu/tetrad/util/dist/TruncatedNormal.java

java/edu/cmu/tetrad/util/dist/Uniform.java

java/edu/pitt/csb/mgm/ConvexProximal.java

java/edu/pitt/csb/mgm/EigenDecomposition.java

java/edu/pitt/csb/mgm/ExampleMixedSearch.java

java/edu/pitt/csb/mgm/ExploreIndepTests.java

java/edu/pitt/csb/mgm/HessenbergTransformer.java

java/edu/pitt/csb/mgm/IndTestMultinomialLogisticRegressionWald.java

java/edu/pitt/csb/mgm/MGM.java

java/edu/pitt/csb/mgm/MixedUtils.java

java/edu/pitt/csb/mgm/ProximalGradient.java

java/edu/pitt/csb/mgm/SchurTransformer.java

java/edu/pitt/csb/mgm/TriDiagonalTransformer.java

java/edu/pitt/csb/mgm/test_data/DAG_0_data.txt

java/edu/pitt/csb/mgm/test_data/DAG_0_graph.txt

java/edu/pitt/csb/mgm/test_data/med_test_C.txt

java/edu/pitt/csb/mgm/test_data/med_test_D.txt

java/edu/pitt/csb/mgm/test_data/med_true_graph.txt

java/edu/pitt/csb/mgm/test_data/small_test_C.txt

java/edu/pitt/csb/mgm/test_data/small_test_D.txt

java/edu/pitt/csb/stability/DataGraphSearch.java

java/edu/pitt/csb/stability/SearchWrappers.java

java/edu/pitt/csb/stability/StabilityUtils.java

java/edu/pitt/dbmi/algo/bayesian/constraint/inference/BCCausalInference.java

java/edu/pitt/dbmi/algo/bayesian/constraint/inference/BCInference.java

java/edu/pitt/dbmi/algo/bayesian/constraint/inference/BayesianConstraintInference.java

java/edu/pitt/dbmi/algo/bayesian/constraint/inference/BayesianConstraintInferenceTest.java

java/edu/pitt/dbmi/algo/bayesian/constraint/search/RfciBsc.java

java/edu/pitt/dbmi/algo/resampling/GeneralResamplingSearch.java

java/edu/pitt/dbmi/algo/resampling/GeneralResamplingTest.java

java/edu/pitt/dbmi/algo/resampling/ResamplingEdgeEnsemble.java

java/edu/pitt/dbmi/algo/resampling/task/GeneralResamplingSearchRunnable.java

java/edu/pitt/isp/sverchkov/data/ADTree.java

java/edu/pitt/isp/sverchkov/data/ADTreeHelper.java

java/edu/pitt/isp/sverchkov/data/ADTreeTest.java

java/edu/pitt/isp/sverchkov/data/DataTable.java

java/edu/pitt/isp/sverchkov/data/DataTableImpl.java

java/edu/pitt/isp/sverchkov/data/DataTools.java

java/jgpml/CSVtoMatrix.java

java/jgpml/GaussianProcess.java

java/jgpml/LICENCE

java/jgpml/README

java/jgpml/covariancefunctions/CovLINard.java

java/jgpml/covariancefunctions/CovLINone.java

java/jgpml/covariancefunctions/CovNNone.java

java/jgpml/covariancefunctions/CovNNoneNoise.java

java/jgpml/covariancefunctions/CovNoise.java

java/jgpml/covariancefunctions/CovSEard.java

java/jgpml/covariancefunctions/CovSEiso.java

java/jgpml/covariancefunctions/CovSum.java

java/jgpml/covariancefunctions/CovarianceFunction.java

java/jgpml/covariancefunctions/MatrixOperations.java

man/.Rapp.history

man/.Rhistory

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