/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Lingam.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/PermutationGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/SplitCasesSpec.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Lofs2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Mimbuild2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestDSep.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetradapp/model/MeasurementSimulatorParams.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphChange.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/UpdatedBayesIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/BasalInitializer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PossibleDsepFci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/RandomActiveLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PossibleDsepCfci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/StoredLagGraphParams.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/MmmbGraphRestricted.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LoadDataAndGraphs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/GeneralizedSemPm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/simulation/MeasurementSimulator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BayesUpdaterClassifier.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestSepset.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PurifyTetradBased2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/FactoredBayesStructuralEM.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/MultiDimIntTable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Dci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Gamma.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Hungarian.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetMap.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/CcdMax.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/TemplateExpander.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Triple.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ParamDescriptions.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/EndpointMatrixGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/DirichletDataSetProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ColtDataSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestIndexedLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/DefaultTetradLoggerConfig.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemOptimizerPowell.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Exponential.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Discrete.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/simulation/TestMeasurementSimulator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/IKnowledge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestConditionalCorrelation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IImages.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/EmBayesProperties.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BDeuScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/ParameterValues.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/StoredCellProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FactorAnalysis.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradLogger.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BffGes.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/MlBayesIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasDci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/IndependenceFact.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemBicScoreImages.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestCramerT.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/EvaluationExpression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PatternToDag.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ExpressionSignature.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Bff.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Glasso.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZBootstrap.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TimeSeriesUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/NodeType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/InverseCorrelation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Normal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestPolynomialTerm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestProbabilistic.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/LingamPattern.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemStdErrorEstimator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TestType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Discretizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/TimeSeriesData.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IntSextad.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/AndersonDarlingTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LinearSineSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/RegressionDataset.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IPurify.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/LaggedFactor.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/ScaleFree.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ExpressionInitializationException.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphConverter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/Regression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DirectedGraphIterator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/CptInvariantUpdater.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataReader.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/ExtraCategoryInterpolator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestRegression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/ApproximateUpdater.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasDeterministic.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Pc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/dbmi/algo/bayesian/constraint/inference/BayesianConstraintInferenceTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/CpcStable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Vcfas.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesImDistanceFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/ParameterPair.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Simulator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/csb/mgm/ProximalGradient.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/statistic/utils/ArrowConfusion.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/VerticalIntDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IonJoeModifications.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/GraphInitializer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/PolynomialFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/MixedDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Fas.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsConservative.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradLoggerConfig.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/NodeEqualityMode.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/VerticalDoubleDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Node.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MVPLikelihood.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/dbmi/algo/bayesian/constraint/inference/BCInference.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradSerializable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/CutoffFinder.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ByteDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MimUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TimeSeriesLagSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/AbstractExpression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/HitonMb.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/CovarianceMatrixOnTheFly.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/IndependenceFacts.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphGroupSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagIterator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/NumberObjectDataSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasStable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/DisplayNameHandler.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/EmBayesEstimator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/DiscreteProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemBicScoreImages2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Endpoint.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/BootstrapSampler.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DeltaTetradTest2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TetradTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Score.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Dag.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/LogNormal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LinearFisherModel.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsMinPValue.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/IDataReader.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/PreviousStepOnly.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Mbfs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/IntDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/DirichletEstimator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/Cyclic.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/TruncatedNormal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LoadContinuousDataAndSingleGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MbClassify.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemBicScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetProducer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/MeasuredLatentOnly.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/NoEdgesToSelf.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Ccd.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/SemSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BdeMetric.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/BoxDataSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DeltaTetradTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradVector.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ImpliedOrientation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MeekRulesPattern.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BicScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Fci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/BooleanGlassSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LoadContinuousDataAndGraphs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SearchLogUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PcPattern.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemGpScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/cluster/ClusteringAlgorithm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphNode.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Distribution.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/Context.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetradapp/model/BooleanGlassGenePm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BuildPureClusters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Knowledge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DiscretizationSpec.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IonLegalPairs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/Initializer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/VcpcFast.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DiscreteClassifier.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/StandardizedSemSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ChoiceGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestMixedMultipleTTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/TakesInitialGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ExpressionDescriptor.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MeekRules.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/statistic/utils/TailConfusion.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/SemThenDiscretize.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/kernel/KernelGaussian.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/JOptionUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Fang.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GPc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradAlgebra.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetradapp/model/GenePm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/DirectedEdgesOnly.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/MlBayesEstimator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Cefs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Beta.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TsFges2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/Integrator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/PolynomialTerm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GFci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/AbstractExpressionDescriptor.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Clusters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestTrekSep.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/LaggedEdge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/BigDataSetUtility.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Test.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PurifyTetradBased.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/LingUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BdeMetricCache.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/BasicLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Graph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestMulti.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/OrderedPair.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Ling.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestHsic.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/PointXy.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/Equation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/cluster/KMeans.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GSquareTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/OrientCollidersMaxP.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ExperimentalSetup.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/Transformation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ContinuousVariable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZConcatenateResiduals.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/LogisticRegression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Edges.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/Mmmb.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BffBeam.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/WFges.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZD.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FgesOrienter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/XdslXmlConstants.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsMaxPValuePossDsep.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ConstantExpression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestCorrelationT.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestConditionalGaussianLRT.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FciDsepLegalPairsCfci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesImProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestPolynomial.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TsFciOrient.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IBDeuScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BpcTetradPurifyWashdown.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ProbabilisticMAPIndependence.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/TakesData.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsMinScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestPartialCorrelation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/EstimateRank.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesProperties.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/KnowledgeTransferable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemBicScoreImages3.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/LingamPattern2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Pcd.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Fges.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SampleVcpcFast.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/IM.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/CombinationGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/csb/mgm/ConvexProximal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MbSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesPm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Fasts.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/RegressionResult.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MVPScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ISemBicScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/SemGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/RandomForward.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestChiSquare.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/RandomSampler.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/CellTable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/LegalPairs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestLaggedRegression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/csb/mgm/MGM.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/TriangularMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/DishModel.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/Function.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/StatUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DirichletScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemOptimizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/PM.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/Simulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsGreedy.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestRegressionAD.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Split.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/StoredCellProbsObs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataModelList.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IonHittingSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/session/SessionModel.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PermutationMatrixPair.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/ChiSquare.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/Scorer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ShiftSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/Mmhc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/ModelGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BinaryFunctionUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TsDagToPag.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagInPatternIterator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FindOneFactorClusters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Reorienter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ChiSquareTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Knowledge2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PurifyScoreBased.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/MultiGeneralAndersonDarlingTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/cluster/metrics/SquaredErrorLoss.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ResolveSepsets.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphScorer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsMaxPValue.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/RegressionCovariance.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BdeuScoreImages.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualLagGraphParams.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesXmlRenderer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/UpdateFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MimbuildTrek.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/SimpleRandomizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/kernel/KernelUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PcLocal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PcStable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestIndependenceFacts.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/RandomDistribution.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZGeneralizedInverse.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/RandomSingleFactorMim.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Variable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/ConnectionFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemPm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ParamDescription.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/RowSummingExactUpdater.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MeekRulesRestricted.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasLofs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DelimiterType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/RecursivePartialCorrelation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestDirichletScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/StandardizedSemIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/HasKnowledge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/csb/mgm/MixedUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GrowShrink.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Lofs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/BooleanGlassFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/NodePair.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ExpressionUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/CorrelationMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestDSepDiminishingPathStrengths.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/ModeInterpolator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TsGFci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/SingleValue.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/parser/Token.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DoubleDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/parser/ExpressionParser.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Vcpc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/ExpressionManager.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/WGfci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/PartialCorrelationPdf.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/GeneralSemSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/FruchtermanReingoldLayout.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemOptimizerRegression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FgesOld.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/EdgeListGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetMapDci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/MlBayesImObs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasStableConcurrentFdr.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagToPattern.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/Simulations.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Cfci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/QList.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/statistic/utils/SimulationPath.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/KnowledgeGroup.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedConnectivity.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/MixtureOfGaussians.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PcMaxLocal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ProbUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/Manipulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/NamingProtocol.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/GeneralAndersonDarlingTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/TimeLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ColtDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/ISemIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemBicScoreD.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataWriter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MbUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/TsFci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SemLikelihood2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/VcpcAlt.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataModel.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/KnowledgeBoxInput.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Lineizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/HitonVariant.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BpcAlgorithmType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/VariableSource.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PopulationTetradTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/CpcOrienter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestIndexedConnectivity.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FastIca.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FgesD.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ProbFci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/GeneralizedSemIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestDrton.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/ParamComparison.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Nlo.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/GaussianPower.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GFciMax.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GwpResult.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FgesMb.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/ParamType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/TripleClassifier.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/regression/LogisticRegression2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SearchGraphUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/CpcLocal.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DMSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Sextad.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/kernel/Kernel.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZ.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/Histogram.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/LagGraphParams.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/Expression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZPercentIndependent.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/TimeSeriesSemSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ConditionalGaussianScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PurifySextadBased.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/LongDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/RandomUtil.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/parser/ExpressionLexer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesUpdater.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/LagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/statistic/utils/AdjacencyConfusion.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetradapp/model/BooleanGlassGeneIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/CaseExpander.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FindTwoFactorClusters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/IambnPc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsPossibleDsep.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/CovarianceMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/MisclassificationUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/csb/mgm/IndTestMultinomialAJ.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/InterIamb.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/DirichletBayesIm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesXmlParser.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/IntMaxDataSetProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/AbstractVariable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestGSquare.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsSet.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/Parameters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/LogDataUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Cci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LoadContinuousDataSmithSim.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/AdLeafTree.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/ManipulatingBayesUpdater.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MimAdjacencySearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DeltaSextadTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagToPag2.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/KnowledgeEdge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/AtMostOneEdgePerPair.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Cpc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/calculator/expression/VariableExpression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Kpc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BinaryFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Jcpc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemEstimator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/Proposition.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ScoredIndTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FciOrient.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/pitt/dbmi/algo/bayesian/constraint/inference/BayesianConstraintInference.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZRecursive.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ConditionalGaussianOtherScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphGroup.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/RandomGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ConditionalGaussianOtherLikelihood.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestMultinomialLogisticRegression.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasFdr.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/AdTrees.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphWithParameters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/LagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SampleVcpc.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/HasParameters.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/RandomTwoFactorMim.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ClusterUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsMaxScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/JsonUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/GeneralSemSimulationSpecial1.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/SemOptimizerEm.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/OnTheFlyMarginalCalculator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/BayesNetSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/Evidence.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestSimpleRandomizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/Parameter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/DirectedUndirectedOnly.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/ConditionalGaussianSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Ion.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/Polynomial.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestProbabilisticVerbose.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Uniform.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ShortTriangularMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/DataSetProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/LayeredDrawing.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/GraphRandomizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestKciMatlab.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/CombinationIterator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/Edge.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ShortDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/MeanInterpolator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/LocalDiscreteScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PagUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/CellTableProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/BDeScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DiscreteVariableType.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MVPBicScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Purify.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestTimeSeries.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/Mapping.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/RegexTokenizer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ArrUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/IntAveDataSetProbs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/GeneHistory.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DiscreteTetradTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PossibleGraphicalChangeFinder.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphGeneratorRandomNumEdges.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradLoggerEvent.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Poisson.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FciDsepLegalPairs.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MixedBicScore.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FciMax.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/DepthChoiceGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradSerializableExcluded.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/mb/Iamb.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/InArrowImpliesNonancestor.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/FloatDataBox.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TextTable.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Tetrad.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/LargeScaleSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/MatrixUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataGraphUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ConditionalGaussianLikelihood.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/dist/Indicator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ScoredGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/LinearFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/ForkJoinPoolInstance.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Washdown.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/Rfci.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LeeHastieSimulation.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/GraphSearch.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/BayesUtils.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/GraphConstraint.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FciOrientT.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/ContinuousTetradTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/MagToPag.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/XdslXmlParser.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/IndexedParent.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/FasStableConcurrent.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IFas.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TaskManager.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/graph/SingleGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/EdgeListGraphSingleConnections.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PossibleDConnectingPath.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/ActiveLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagSepsets.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/TestBooleanFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/history/BooleanFunction.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/IndexedMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/gene/tetrad/gene/graph/ManualActiveLagGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/simulation/LoadDataFromFileWithoutGraph.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/cluster/metrics/Dissimilarity.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/LocalScoreCache.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/algcomparison/utils/HasParameterValues.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/EFang.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/DataUtility.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/sem/DagScorer.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/NumberFormatUtil.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/KamadaKawaiLayout.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/DagToPag.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/PcMax.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/graph/UniformGraphGenerator.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndTestFisherZFisherPValue.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/IndependenceTest.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/util/TetradLoggerListener.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/ICovarianceMatrix.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/search/SepsetsConservativeMajority.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DataFilter.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/bayes/Identifiability.java
/Users/nea24/Box Sync/Benos/R-MGM/java/tetradLite/src/edu/cmu/tetrad/data/DiscreteVariable.java