Serialized Form

Package edu.cmu.tetrad.algcomparison.algorithm

Class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm

class ExternalAlgorithm extends Object implements Serializable

Serialized Fields

path

String path

simIndex

int simIndex

simulation

Simulation simulation

usedParameters

List<String> usedParameters

Class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection

class FirstInflection extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

high

double high

increment

double increment

low

double low

parameter

String parameter

Class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection

class StabilitySelection extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

Class edu.cmu.tetrad.algcomparison.algorithm.StARS

class StARS extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

high

double high

low

double low

parameter

String parameter

Package edu.cmu.tetrad.algcomparison.algorithm.cluster

Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc

class Bpc extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc

class Fofc extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc

class Ftfc extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

Package edu.cmu.tetrad.algcomparison.algorithm.continuous.dag

Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma

class Dagma extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam

class DirectLingam extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam

class IcaLingam extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD

class IcaLingD extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

Package edu.cmu.tetrad.algcomparison.algorithm.external

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBnlearnMmhc

class ExternalAlgorithmBnlearnMmhc extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

extDir

String extDir

shortDescription

String shortDescription

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmBNTPc

class ExternalAlgorithmBNTPc extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

extDir

String extDir

shortDescription

String shortDescription

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmIntersection

class ExternalAlgorithmIntersection extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithms

ExternalAlgorithm[] algorithms

elapsed

long elapsed

shortDescription

String shortDescription

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgGes

class ExternalAlgorithmPcalgGes extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

extDir

String extDir

shortDescription

String shortDescription

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmPcalgPc

class ExternalAlgorithmPcalgPc extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

extDir

String extDir

shortDescription

String shortDescription

Class edu.cmu.tetrad.algcomparison.algorithm.external.ExternalAlgorithmTetrad

class ExternalAlgorithmTetrad extends ExternalAlgorithm implements Serializable

serialVersionUID:

23L

Serialized Fields

extDir

String extDir

shortDescription

String shortDescription

Package edu.cmu.tetrad.algcomparison.algorithm.mixed

Class edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm

class Mgm extends Object implements Serializable

serialVersionUID:

23L

Package edu.cmu.tetrad.algcomparison.algorithm.multi

Class edu.cmu.tetrad.algcomparison.algorithm.multi.Fask

class Fask extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated

class FaskConcatenated extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated

class FaskLofsConcatenated extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

rule

Lofs.Rule rule

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote

class FaskVote extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs

class FasLofs extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

rule

Lofs.Rule rule

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod

class FciIod extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated

class FgesConcatenated extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

compareToTrue

boolean compareToTrue

externalGraph

Algorithm externalGraph

knowledge

Knowledge knowledge

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.multi.Images

class Images extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

score

ScoreWrapper score

Package edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss

class Boss extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc

class Cpc extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas

class Fas extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges

class Fges extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

bootstrapGraphs

List<Graph> bootstrapGraphs

externalGraph

Graph externalGraph

knowledge

Knowledge knowledge

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb

class FgesMb extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

targetName

String targetName

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement

class FgesMeasurement extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.GesMe

class GesMe extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

compareToTrue

boolean compareToTrue

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp

class Grasp extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc

class Pc extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd

class Pcd extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcLingam

class PcLingam extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb

class PcMb extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

targets

List<Node> targets

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss

class RestrictedBoss extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

score

ScoreWrapper score

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg

class SingleGraphAlg extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

graph

Graph graph

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp

class Sp extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Bfci

class Bfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd

class Ccd extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci

class Cfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci

class Fci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax

class FciMax extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci

class Gfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci

class GraspFci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci

class PagSampleRfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci

class Rfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc

class RfciBsc extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci

class SpFci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci

class SvarFci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

test

IndependenceWrapper test

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci

class SvarGfci extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bootstrapGraphs

List<Graph> bootstrapGraphs

knowledge

Knowledge knowledge

score

ScoreWrapper score

test

IndependenceWrapper test

Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern

Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Cstar

class Cstar extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

records

LinkedList<Cstar.Record> records

score

ScoreWrapper score

test

IndependenceWrapper test

Package edu.cmu.tetrad.algcomparison.algorithm.other

Class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis

class FactorAnalysis extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso

class Glasso extends Object implements Serializable

serialVersionUID:

23L

Package edu.cmu.tetrad.algcomparison.algorithm.pairwise

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb

class Eb extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw

class FaskPw extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1

class R1 extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2

class R2 extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3

class R3 extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew

class Rskew extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE

class RskewE extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew

class Skew extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE

class SkewE extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh

class Tanh extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

algorithm

Algorithm algorithm

externalGraph

Graph externalGraph

Package edu.cmu.tetrad.algcomparison.graph

Class edu.cmu.tetrad.algcomparison.graph.Cyclic

class Cyclic extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.ErdosRenyi

class ErdosRenyi extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.RandomForward

class RandomForward extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.RandomSingleFactorMim

class RandomSingleFactorMim extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.RandomTwoFactorMim

class RandomTwoFactorMim extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.ScaleFree

class ScaleFree extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.graph.SingleGraph

class SingleGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

graph

Graph graph

Package edu.cmu.tetrad.algcomparison.independence

Class edu.cmu.tetrad.algcomparison.independence.BdeuTest

class BdeuTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.CciTest

class CciTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.ChiSquare

class ChiSquare extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT

class ConditionalGaussianLRT extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.DegenerateGaussianLRT

class DegenerateGaussianLRT extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.DiscreteBicTest

class DiscreteBicTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.FisherZ

class FisherZ extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.GICScoreTests

class GICScoreTests extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.Gsquare

class Gsquare extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.Kci

class Kci extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.MagSemBicTest

class MagSemBicTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.Mnlrlrt

class Mnlrlrt extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.MSeparationTest

class MSeparationTest extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

graph

Graph graph

Class edu.cmu.tetrad.algcomparison.independence.MultinomialLogisticRegressionWald

class MultinomialLogisticRegressionWald extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.Mvplrt

class Mvplrt extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.PoissonScoreTest

class PoissonScoreTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.PositiveCorr

class PositiveCorr extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest

class ProbabilisticTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.SemBicDTest

class SemBicDTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.SemBicTest

class SemBicTest extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.independence.UniformScatterTest

class UniformScatterTest extends Object implements Serializable

serialVersionUID:

23L

Package edu.cmu.tetrad.algcomparison.score

Class edu.cmu.tetrad.algcomparison.score.BdeuScore

class BdeuScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.CciScore

class CciScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore

class ConditionalGaussianBicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore

class DegenerateGaussianBicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore

class DiscreteBicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.EbicScore

class EbicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.FisherZScore

class FisherZScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.GicScores

class GicScores extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.MagSemBicScore

class MagSemBicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.MSeparationScore

class MSeparationScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

graph

Graph graph

Class edu.cmu.tetrad.algcomparison.score.MVPBicScore

class MVPBicScore extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.score.PoissonPriorScore

class PoissonPriorScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.PositiveCorrScore

class PositiveCorrScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.SemBicScore

class SemBicScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.SemBicScoreDeterministic

class SemBicScoreDeterministic extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore

class ZhangShenBoundScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataModel dataSet

Package edu.cmu.tetrad.algcomparison.simulation

Class edu.cmu.tetrad.algcomparison.simulation.BayesNetSimulation

class BayesNetSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

im

BayesIm im

ims

List<BayesIm> ims

pm

BayesPm pm

randomGraph

RandomGraph randomGraph

Class edu.cmu.tetrad.algcomparison.simulation.BooleanGlassSimulation

class BooleanGlassSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graph

Graph graph

randomGraph

RandomGraph randomGraph

Class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation

class ConditionalGaussianSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

coefHigh

double coefHigh

coefLow

double coefLow

coefSymmetric

boolean coefSymmetric

dataSets

List<DataSet> dataSets

dataType

DataType dataType

graphs

List<Graph> graphs

meanHigh

double meanHigh

meanLow

double meanLow

randomGraph

RandomGraph randomGraph

shuffledOrder

List<Node> shuffledOrder

varHigh

double varHigh

varLow

double varLow

Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation

class GeneralSemSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

im

GeneralizedSemIm im

ims

List<GeneralizedSemIm> ims

pm

GeneralizedSemPm pm

randomGraph

RandomGraph randomGraph

Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1

class GeneralSemSimulationSpecial1 extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

randomGraph

RandomGraph randomGraph

Class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation

class LeeHastieSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

dataType

DataType dataType

graphs

List<Graph> graphs

randomGraph

RandomGraph randomGraph

shuffledOrder

List<Node> shuffledOrder

Class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel

class LinearFisherModel extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

randomGraph

RandomGraph randomGraph

shocks

List<DataModel> shocks

Class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation

class LinearSineSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

betaHigh

double betaHigh

betaLow

double betaLow

dataSets

List<DataSet> dataSets

dataType

DataType dataType

gammaHigh

double gammaHigh

gammaLow

double gammaLow

graphs

List<Graph> graphs

interceptHigh

double interceptHigh

interceptLow

double interceptLow

linearHigh

double linearHigh

linearLow

double linearLow

randomGraph

RandomGraph randomGraph

shuffledOrder

List<Node> shuffledOrder

varHigh

double varHigh

varLow

double varLow

Class edu.cmu.tetrad.algcomparison.simulation.NLSemSimulation

class NLSemSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

randomGraph

RandomGraph randomGraph

Class edu.cmu.tetrad.algcomparison.simulation.SemSimulation

class SemSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

im

SemIm im

ims

List<SemIm> ims

pm

SemPm pm

randomGraph

RandomGraph randomGraph

seed

long seed

Class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize

class SemThenDiscretize extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

dataType

DataType dataType

graphs

List<Graph> graphs

randomGraph

RandomGraph randomGraph

shuffledOrder

List<Node> shuffledOrder

Class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation

class StandardizedSemSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

pm

SemPm pm

randomGraph

RandomGraph randomGraph

standardizedIm

StandardizedSemIm standardizedIm

Class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation

class TimeSeriesSemSimulation extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

knowledge

Knowledge knowledge

randomGraph

RandomGraph randomGraph

Package edu.cmu.tetrad.algcomparison.statistic

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFn

class AdjacencyFn extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFp

class AdjacencyFp extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyFpr

class AdjacencyFpr extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyPrecision

class AdjacencyPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyRecall

class AdjacencyRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTn

class AdjacencyTn extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTp

class AdjacencyTp extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AdjacencyTpr

class AdjacencyTpr extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AncestorF1

class AncestorF1 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AncestorPrecision

class AncestorPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AncestorRecall

class AncestorRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AncestralPrecision

class AncestralPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AncestralRecall

class AncestralRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFn

class ArrowheadFn extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFp

class ArrowheadFp extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadFpr

class ArrowheadFpr extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecision

class ArrowheadPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadPrecisionCommonEdges

class ArrowheadPrecisionCommonEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecall

class ArrowheadRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadRecallCommonEdges

class ArrowheadRecallCommonEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTn

class ArrowheadTn extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ArrowheadTp

class ArrowheadTp extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeEst

class AverageDegreeEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.AverageDegreeTrue

class AverageDegreeTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BicDiff

class BicDiff extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

precomputeCovariances

boolean precomputeCovariances

Class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord

class BicDiffPerRecord extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

precomputeCovariances

boolean precomputeCovariances

Class edu.cmu.tetrad.algcomparison.statistic.BicEst

class BicEst extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

penaltyDiscount

double penaltyDiscount

precomputeCovariances

boolean precomputeCovariances

Class edu.cmu.tetrad.algcomparison.statistic.BicTrue

class BicTrue extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

precomputeCovariances

boolean precomputeCovariances

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedEst

class BidirectedEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedFP

class BidirectedFP extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedLatentPrecision

class BidirectedLatentPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedPrecision

class BidirectedPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedRecall

class BidirectedRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedTP

class BidirectedTP extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.BidirectedTrue

class BidirectedTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalseNegativeBidirected

class CommonAncestorFalseNegativeBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorFalsePositiveBidirected

class CommonAncestorFalsePositiveBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.CommonAncestorTruePositiveBidirected

class CommonAncestorTruePositiveBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.CommonMeasuredAncestorRecallBidirected

class CommonMeasuredAncestorRecallBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.CorrectSkeleton

class CorrectSkeleton extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathPrecision

class DefiniteDirectedPathPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.DefiniteDirectedPathRecall

class DefiniteDirectedPathRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.DensityEst

class DensityEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.DensityTrue

class DensityTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ElapsedCpuTime

class ElapsedCpuTime extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.F1Adj

class F1Adj extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.F1All

class F1All extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.F1Arrow

class F1Arrow extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.FalseNegativesAdjacencies

class FalseNegativesAdjacencies extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.FalsePositiveAdjacencies

class FalsePositiveAdjacencies extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative

class FractionDependentUnderAlternative extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull

class FractionDependentUnderNull extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight

class GraphExactlyRight extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalseNegativeBidirected

class LatentCommonAncestorFalseNegativeBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorFalsePositiveBidirected

class LatentCommonAncestorFalsePositiveBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorRecallBidirected

class LatentCommonAncestorRecallBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.LatentCommonAncestorTruePositiveBidirected

class LatentCommonAncestorTruePositiveBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.LegalPag

class LegalPag extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.MarkovAdequacyScore

class MarkovAdequacyScore extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrAdj

class MathewsCorrAdj extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.MathewsCorrArrow

class MathewsCorrArrow extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.MaximalityCondition

class MaximalityCondition extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition

class NoAlmostCyclicPathsCondition extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsInMagCondition

class NoAlmostCyclicPathsInMagCondition extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsCondition

class NoCyclicPathsCondition extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoCyclicPathsInMagCondition

class NoCyclicPathsInMagCondition extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesPrecision

class NodesInCyclesPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NodesInCyclesRecall

class NodesInCyclesRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NonancestorPrecision

class NonancestorPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NonancestorRecall

class NonancestorRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedF1

class NoSemidirectedF1 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedPrecision

class NoSemidirectedPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NoSemidirectedRecall

class NoSemidirectedRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumAmbiguousTriples

class NumAmbiguousTriples extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesEst

class NumberOfEdgesEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumberOfEdgesTrue

class NumberOfEdgesTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedBothNonancestorAncestor

class NumBidirectedBothNonancestorAncestor extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesEst

class NumBidirectedEdgesEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumBidirectedEdgesTrue

class NumBidirectedEdgesTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumColoredDD

class NumColoredDD extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumColoredNL

class NumColoredNL extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumColoredPD

class NumColoredPD extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumColoredPL

class NumColoredPL extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCommonMeasuredAncestorBidirected

class NumCommonMeasuredAncestorBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDefiniteDirectedEdgeAncestors

class NumCompatibleDefiniteDirectedEdgeAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeConfounded

class NumCompatibleDirectedEdgeConfounded extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleDirectedEdgeNonAncestors

class NumCompatibleDirectedEdgeNonAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleEdges

class NumCompatibleEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeAncestors

class NumCompatiblePossiblyDirectedEdgeAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatiblePossiblyDirectedEdgeNonAncestors

class NumCompatiblePossiblyDirectedEdgeNonAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleAncestors

class NumCompatibleVisibleAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCompatibleVisibleNonancestors

class NumCompatibleVisibleNonancestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectDDAncestors

class NumCorrectDDAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectPDAncestors

class NumCorrectPDAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectVisibleAncestors

class NumCorrectVisibleAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyDirected

class NumDefinitelyDirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDefinitelyNotDirectedPaths

class NumDefinitelyNotDirectedPaths extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeAncestors

class NumDirectedEdgeAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeBnaMeasuredCounfounded

class NumDirectedEdgeBnaMeasuredCounfounded extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNoMeasureAncestors

class NumDirectedEdgeNoMeasureAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeNotAncNotRev

class NumDirectedEdgeNotAncNotRev extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeReversed

class NumDirectedEdgeReversed extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdges

class NumDirectedEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedEdgeVisible

class NumDirectedEdgeVisible extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsEst

class NumDirectedPathsEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedPathsTrue

class NumDirectedPathsTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumDirectedShouldBePartiallyDirected

class NumDirectedShouldBePartiallyDirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectDDAncestors

class NumIncorrectDDAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectPDAncestors

class NumIncorrectPDAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumIncorrectVisibleAncestors

class NumIncorrectVisibleAncestors extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumLatentCommonAncestorBidirected

class NumLatentCommonAncestorBidirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumNondirectedEdges

class NumNondirectedEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumPartiallyOrientedEdges

class NumPartiallyOrientedEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumPossiblyDirected

class NumPossiblyDirected extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumUndirectedEdges

class NumUndirectedEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEst

class NumVisibleEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.OrientationPrecision

class OrientationPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.OrientationRecall

class OrientationRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyPrecision

class PagAdjacencyPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.PagAdjacencyRecall

class PagAdjacencyRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ParameterColumn

class ParameterColumn extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

parameter

String parameter

Class edu.cmu.tetrad.algcomparison.statistic.PercentAmbiguous

class PercentAmbiguous extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.PercentBidirectedEdges

class PercentBidirectedEdges extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedEst

class ProportionSemidirectedPathsNotReversedEst extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.ProportionSemidirectedPathsNotReversedTrue

class ProportionSemidirectedPathsNotReversedTrue extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.PvalueDistanceToAlpha

class PvalueDistanceToAlpha extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull

class PvalueUniformityUnderNull extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPathF1

class SemidirectedPathF1 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedPrecision

class SemidirectedPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.SemidirectedRecall

class SemidirectedRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance

class StructuralHammingDistance extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TailPrecision

class TailPrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TailRecall

class TailRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesArrows

class TrueDagFalseNegativesArrows extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalseNegativesTails

class TrueDagFalseNegativesTails extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveArrow

class TrueDagFalsePositiveArrow extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagFalsePositiveTails

class TrueDagFalsePositiveTails extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionArrow

class TrueDagPrecisionArrow extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagPrecisionTails

class TrueDagPrecisionTails extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallArrows

class TrueDagRecallArrows extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagRecallTails

class TrueDagRecallTails extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveArrow

class TrueDagTruePositiveArrow extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveDirectedPathNonancestor

class TrueDagTruePositiveDirectedPathNonancestor extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TrueDagTruePositiveTails

class TrueDagTruePositiveTails extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalseNegative

class TwoCycleFalseNegative extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleFalsePositive

class TwoCycleFalsePositive extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TwoCyclePrecision

class TwoCyclePrecision extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleRecall

class TwoCycleRecall extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.algcomparison.statistic.TwoCycleTruePositive

class TwoCycleTruePositive extends Object implements Serializable

serialVersionUID:

23L

Package edu.cmu.tetrad.annotation

Class edu.cmu.tetrad.annotation.AnnotatedClass

class AnnotatedClass extends Object implements Serializable

serialVersionUID:

5060798016477163171L

Serialized Fields

annotation

T extends Annotation annotation

clazz

Class clazz

Package edu.cmu.tetrad.bayes

Class edu.cmu.tetrad.bayes.ApproximateUpdater

class ApproximateUpdater extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The IM which this updater modifies.

Cannot be null.

counts

int[][] counts

Counts of data points for each variable value.

evidence

Evidence evidence

Stores evidence for all variables.

Cannot be null.

manipulatedBayesIm

BayesIm manipulatedBayesIm

This is the source BayesIm after manipulation; all data simulations should be taken from this.

Class edu.cmu.tetrad.bayes.BayesImProbs

class BayesImProbs extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

Cannot be null.

variables

List<Node> variables

Cannot be null.

Class edu.cmu.tetrad.bayes.BayesPm

class BayesPm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

dag

Graph dag

The underlying graph that's being parameterized.

Cannot be null.

nodesToVariables

Map<Node,DiscreteVariable> nodesToVariables

The map from nodes to variables.

Cannot be null.

Class edu.cmu.tetrad.bayes.CptInvariantMarginalCalculator

class CptInvariantMarginalCalculator extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

Cannot be null.

evidence

Evidence evidence

Cannot be null.

storedMarginals

double[][] storedMarginals

Cannot be null.

updatedBayesIm

UpdatedBayesIm updatedBayesIm

Cannot be null.

Class edu.cmu.tetrad.bayes.CptInvariantUpdater

class CptInvariantUpdater extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The IM which this updater modifies.

Cannot be null.

cptInvariantMarginalCalculator

CptInvariantMarginalCalculator cptInvariantMarginalCalculator

The gadget that calculates marginals.

evidence

Evidence evidence

Stores evidence for all variables.

Cannot be null

manipulatedBayesIm

BayesIm manipulatedBayesIm

The manipulated Bayes IM--that is, bayesIm after the manipulations in evidence have been applied to it.

updatedBayesIm

UpdatedBayesIm updatedBayesIm

The IM after update.

Class edu.cmu.tetrad.bayes.DirichletBayesIm

class DirichletBayesIm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesPm

BayesPm bayesPm

The associated Bayes PM model.

nextRowTotal

double nextRowTotal

1.0000 The default row size for randomly creating new rows.

nodes

Node[] nodes

The array of nodes from the graph. Order is important.

parentDims

int[][] parentDims

The array of dimensionality (number of values for each node) for each of the subarrays of 'parents'.

parents

int[][] parents

The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important.

pseudocounts

double[][][] pseudocounts

The main data structure; stores the values of all of the pseudocounts for the Dirichlet Bayes net of the form row by row, for each node. The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM. If a pseudocount is -1, that means its value should be filled in manually.

Class edu.cmu.tetrad.bayes.Evidence

class Evidence extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

manipulation

Manipulation manipulation

A manipulation indicating how the bayes Im should be manipulated before updating.

proposition

Proposition proposition

A proposition stating what we know for each variable.

Cannot be null.

Class edu.cmu.tetrad.bayes.Identifiability

class Identifiability extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The BayesIm which this updater modifies.

Cannot be null.

debug

boolean debug

evidence

Evidence evidence

Stores evidence for all variables.

Cannot be null.

manipulatedBayesIm

BayesIm manipulatedBayesIm

The last manipulated BayesIm.

Can be null.

Class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm

class JunctionTreeAlgorithm extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

bayesIm

BayesIm bayesIm

bayesPm

BayesPm bayesPm

graphNodes

Node[] graphNodes

margins

double[][] margins

maxCardOrdering

Node[] maxCardOrdering

root

edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode root

treeNodes

Map<Node,edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode> treeNodes

Class edu.cmu.tetrad.bayes.JunctionTreeUpdater

class JunctionTreeUpdater extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The BayesIm which this updater modifies.

Cannot be null.

evidence

Evidence evidence

Stores evidence for all variables.

Cannot be null.

jta

JunctionTreeAlgorithm jta

Calculates probabilities from the manipulated Bayes IM.

Can be null.

manipulatedBayesIm

BayesIm manipulatedBayesIm

The last manipulated BayesIm.

Can be null.

updatedBayesIm

BayesIm updatedBayesIm

The BayesIm after update, if this was calculated.

Can be null.

Class edu.cmu.tetrad.bayes.Manipulation

class Manipulation extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

manipulated

boolean[] manipulated

An array indicating whether each variable in turn is manipulated.

Cannot be null.

variableSource

VariableSource variableSource

Class edu.cmu.tetrad.bayes.MlBayesIm

class MlBayesIm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesPm

BayesPm bayesPm

The associated Bayes PM model.

nodes

Node[] nodes

The array of nodes from the graph. Order is important.

parentDims

int[][] parentDims

The array of dimensionality (number of categories for each node) for each of the subarrays of 'parents'.

parents

int[][] parents

The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important.

probs

double[][][] probs

The main data structure; stores the values of all of the conditional probabilities for the Bayes net of the form P(N=v0 | P1=v1, P2=v2,...). The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM.

Class edu.cmu.tetrad.bayes.MlBayesImObs

class MlBayesImObs extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesImObs

BayesIm bayesImObs

bayesImRandomize

BayesIm bayesImRandomize

bayesPm

BayesPm bayesPm

The associated Bayes PM model.

jpd

StoredCellProbsObs jpd

nodes

Node[] nodes

The array of nodes from the graph. Order is important.

parentDims

int[][] parentDims

The array of dimensionality (number of categories for each node) for each of the subarrays of 'parents'.

parents

int[][] parents

The list of parents for each node from the graph. Order or nodes corresponds to the order of nodes in 'nodes', and order in subarrays is important.

probs

double[][][] probs

The main data structure; stores the values of all of the conditional probabilities for the Bayes net of the form P(N=v0 | P1=v1, P2=v2,...). The first dimension is the node N, in the order of 'nodes'. The second dimension is the row index for the table of parameters associated with node N; the third dimension is the column index. The row index is calculated by the function getRowIndex(int[] values) where 'values' is an array of numerical indices for each of the parent values; the order of the values in this array is the same as the order of node in 'parents'; the value indices are obtained from the Bayes PM for each node. The column is the index of the value of N, where this index is obtained from the Bayes PM.

Class edu.cmu.tetrad.bayes.Proposition

class Proposition extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

allowedCategories

boolean[][] allowedCategories

Cannot be null.

variableSource

VariableSource variableSource

Cannot be null.

Class edu.cmu.tetrad.bayes.RowSummingExactUpdater

class RowSummingExactUpdater extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The BayesIm which this updater modifies.

Cannot be null.

bayesImProbs

BayesImProbs bayesImProbs

Calculates probabilities from the manipulated Bayes IM.

Can be null.

evidence

Evidence evidence

Stores evidence for all variables.

Cannot be null.

manipulatedBayesIm

BayesIm manipulatedBayesIm

The last manipulated BayesIm.

Can be null.

updatedBayesIm

BayesIm updatedBayesIm

The BayesIm after update, if this was calculated.

Can be null.

Class edu.cmu.tetrad.bayes.StoredCellProbs

class StoredCellProbs extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

parentDims

int[] parentDims

probs

double[] probs

variables

List<Node> variables

Class edu.cmu.tetrad.bayes.StoredCellProbsObs

class StoredCellProbsObs extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

parentDims

int[] parentDims

probs

double[] probs

variables

List<Node> variables

Class edu.cmu.tetrad.bayes.UpdatedBayesIm

class UpdatedBayesIm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

affectedVars

boolean[] affectedVars

A boolean array that is true at a position if the node at that index is an ancestor or a child of one of the evidence variables.

Cannot be null.

bayesIm

BayesIm bayesIm

The wrapped BayesIm. Unmodified conditional probability values will be retrieved from here.

Cannot be null; must be evidence.getEstIm().

changedProbs

double[][][] changedProbs

Stores probs that change with respect to the underlying bayesIm, calculated on the fly.

Cannot be null.

evidence

Evidence evidence

The evidence updated on.

Cannot be null.

Package edu.cmu.tetrad.calculator.expression

Class edu.cmu.tetrad.calculator.expression.AbstractExpressionDescriptor.Signature

class Signature extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

arguments

String[] arguments

signature

String signature

Class edu.cmu.tetrad.calculator.expression.ConstantExpression

class ConstantExpression extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

The name of the constant or null if there isn't one. Constants with names are things like PI or E.

value

double value

THe value of the expression.

Class edu.cmu.tetrad.calculator.expression.EvaluationExpression

class EvaluationExpression extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

string

String string

The string you are testing the variable against.

variable

VariableExpression variable

The variable part of the expression.

Exception edu.cmu.tetrad.calculator.expression.ExpressionInitializationException

class ExpressionInitializationException extends Exception implements Serializable

Class edu.cmu.tetrad.calculator.expression.VariableExpression

class VariableExpression extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

variable

String variable

The variable that is being evaluated.

Package edu.cmu.tetrad.classify

Class edu.cmu.tetrad.classify.ClassifierBayesUpdaterDiscrete

class ClassifierBayesUpdaterDiscrete extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)

Throws:

IOException

ClassNotFoundException

Serialized Fields

bayesIm

BayesIm bayesIm

The BayesIm instance used to create an updater. Supplied as an argument to the constructor.

bayesImVars

List<Node> bayesImVars

classifications

int[] classifications

marginals

double[][] marginals

numCases

int numCases

percentCorrect

double percentCorrect

The percentage of correct estimates of the target variable. This will be set to a meaningful value upon completion of the crossTabulate method.

targetVariable

DiscreteVariable targetVariable

The target variable (inferred from its name).

testData

DataSet testData

The dataset to be classified.

totalUsableCases

int totalUsableCases

Package edu.cmu.tetrad.data

Class edu.cmu.tetrad.data.AbstractVariable

class AbstractVariable extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

Name of this variable.

Class edu.cmu.tetrad.data.BoxDataSet

class BoxDataSet extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

caseIds

Map<Integer,String> caseIds

Case ID's. These are strings associated with some or all of the cases of the dataset.

columnToTooltip

Map<String,String> columnToTooltip

dataBox

DataBox dataBox

The container storing the data. Rows are cases; columns are variables. The order of columns is coordinated with the order of variables in getVariables().

knowledge

Knowledge knowledge

The knowledge associated with this data.

multipliers

Map<Integer,Integer> multipliers

A map from cases to case multipliers. If a case is not in the domain of this map, its case multiplier is by default 1. This is the number of repetitions of the case in the dataset. The sample size is obtained by summing over these multipliers.

name

String name

The name of the data model. This is not used internally; it is only here in case an external class wants this dataset to have a name.

outputDelimiter

char outputDelimiter

The character used as a delimiter when the dataset is printed.

selection

Set<Node> selection

The set of selected variables.

variables

List<Node> variables

The list of variables. These correspond columnwise to the columns of data.

Class edu.cmu.tetrad.data.ByteDataBox

class ByteDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

byte[][] data

The stored byte data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.Clusters

class Clusters extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

clusters

Map<String,Integer> clusters

This is used to store information on pure measurement models (when the graph is a measurement/structural model). The information is stored variable clusters, and is used by algorithm such as Purify and MIM Build (R. Silva, 04/2003)

names

Map<Integer,String> names

Node names.

numClusters

int numClusters

The number of clusters represented. If there is no fixed upper bound, set this to -1.

Class edu.cmu.tetrad.data.ContinuousDiscretizationSpec

class ContinuousDiscretizationSpec extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

breakpoints

double[] breakpoints

Breakpoints, for continuous data.

categories

List<String> categories

method

int method

The method used.

Class edu.cmu.tetrad.data.ContinuousVariable

class ContinuousVariable extends AbstractVariable implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

attributes

Map<String,Object> attributes

centerX

int centerX

The x coordinate of the center of the node.

centerY

int centerY

The y coordinate of the center of the node.

nodeType

NodeType nodeType

The node type.

nodeVariableType

NodeVariableType nodeVariableType

Node variable type (domain, interventional status, interventional value..) of this node variable

Class edu.cmu.tetrad.data.CorrelationMatrix

class CorrelationMatrix extends CovarianceMatrix implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.data.CorrelationMatrixOnTheFly

class CorrelationMatrixOnTheFly extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

cov

ICovarianceMatrix cov

matrixC

cern.colt.matrix.DoubleMatrix2D matrixC

Do not remove this field; it is needed for serialization.

selectedVariables

Set<Node> selectedVariables

The list of selected variables.

Cannot be null.

variables

List<Node> variables

The variables (in order) for this covariance matrix.

Cannot be null.

verbose

boolean verbose

Class edu.cmu.tetrad.data.CovarianceMatrix

class CovarianceMatrix extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

_covariancesMatrix

Matrix _covariancesMatrix

The wrapped covariance matrix data.

knowledge

Knowledge knowledge

The knowledge for this data.

Cannot be null.

name

String name

The name of the covariance matrix.

May be null.

sampleSize

int sampleSize

The size of the sample from which this covariance matrix was calculated.

Range > 0.

selectedVariables

Set<Node> selectedVariables

The list of selected variables.

Cannot be null.

variables

List<Node> variables

The variables (in order) for this covariance matrix.

Cannot be null.

Class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly

class CovarianceMatrixOnTheFly extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

knowledge

Knowledge knowledge

The knowledge for this data.

Cannot be null.

matrix

Matrix matrix

Stored matrix data. Should be square. This may be set by derived classes, but it must always be set to a legitimate covariance matrix.

Cannot be null. Must be symmetric and positive definite.

matrixC

cern.colt.matrix.DoubleMatrix2D matrixC

Do not remove this field; it is needed for serialization.

name

String name

The name of the covariance matrix.

May be null.

sampleSize

int sampleSize

The size of the sample from which this covariance matrix was calculated.

Range > 0.

selectedVariables

Set<Node> selectedVariables

The list of selected variables.

Cannot be null.

variables

List<Node> variables

The variables (in order) for this covariance matrix.

Cannot be null.

variances

double[] variances

vectors

double[][] vectors

verbose

boolean verbose

Class edu.cmu.tetrad.data.DataModelList

class DataModelList extends AbstractList<DataModel> implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

knowledge

Knowledge knowledge

The knowledge for this data.

modelList

List<DataModel> modelList

The list of models.

name

String name

The name of the DataModelList.

selectedModel

DataModel selectedModel

The selected model (may be null).

Class edu.cmu.tetrad.data.DelimiterType

class DelimiterType extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readResolve

Object readResolve()
            throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

ordinal

int ordinal

Class edu.cmu.tetrad.data.DiscreteDiscretizationSpec

class DiscreteDiscretizationSpec extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

categories

List<String> categories

remap

int[] remap

Discrete remapping of categories, for discrete data.

Class edu.cmu.tetrad.data.DiscreteVariable

class DiscreteVariable extends AbstractVariable implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

accommodateNewCategories

boolean accommodateNewCategories

True iff new variables should be allowed to be constructed to replace this one, accommodating new categories.

attributes

Map<String,Object> attributes

categoriesCopy

List<String> categoriesCopy

A copy of the category list is stored here for when the discrete variable is deserialized. On deserialization, STORED_CATEGORY_LISTS will be constructed if it hasn't been already, and this list will be looked up on the "bulletin board" to see if a permutation of it already exists.

categoryNamesDisplayed

boolean categoryNamesDisplayed

True iff the category categories for this variable should be displayed; false if the integer indices of categories should be displayed.

centerX

int centerX

The x coordinate of the center of the node.

centerY

int centerY

The y coordinate of the center of the node.

discreteVariableType

DiscreteVariableType discreteVariableType

The discreteVariableType of discrete variable this is.

nodeType

NodeType nodeType

The node discreteVariableType.

nodeVariableType

NodeVariableType nodeVariableType

Node variable type (domain, interventional status, interventional value, ...) of this node variable

Class edu.cmu.tetrad.data.DiscreteVariableType

class DiscreteVariableType extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readResolve

Object readResolve()
            throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

ordinal

int ordinal

Class edu.cmu.tetrad.data.DoubleDataBox

class DoubleDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

double[][] data

The stored double data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.FloatDataBox

class FloatDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

float[][] data

The stored float data.

Class edu.cmu.tetrad.data.IndependenceFacts

class IndependenceFacts extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

knowledge

Knowledge knowledge

name

String name

nodes

List<Node> nodes

unsortedFacts

Set<IndependenceFact> unsortedFacts

Class edu.cmu.tetrad.data.IntDataBox

class IntDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

int[][] data

The stored short data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.Knowledge

class Knowledge extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

defaultToKnowledgeLayout

boolean defaultToKnowledgeLayout

forbiddenRulesSpecs

Set<OrderedPair<Set<String>>> forbiddenRulesSpecs

knowledgeGroupRules

Map<KnowledgeGroup,OrderedPair<Set<String>>> knowledgeGroupRules

knowledgeGroups

List<KnowledgeGroup> knowledgeGroups

requiredRulesSpecs

Set<OrderedPair<Set<String>>> requiredRulesSpecs

tierSpecs

List<Set<String>> tierSpecs

variables

Set<String> variables

Class edu.cmu.tetrad.data.KnowledgeEdge

class KnowledgeEdge extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

from

String from

to

String to

Class edu.cmu.tetrad.data.KnowledgeGroup

class KnowledgeGroup extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

fromGroup

Set<String> fromGroup

The left group of variables.

- not null

toGroup

Set<String> toGroup

The right group of variables.

- not null

type

int type

The type of group that this is (currently either required or forbidden).

Class edu.cmu.tetrad.data.LongDataBox

class LongDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

long[][] data

The stored long data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.MixedDataBox

class MixedDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

continuousData

double[][] continuousData

discreteData

int[][] discreteData

numRows

int numRows

variables

List<Node> variables

Class edu.cmu.tetrad.data.NumberObjectDataSet

class NumberObjectDataSet extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

columnToTooltip

Map<String,String> columnToTooltip

data

Number[][] data

The container storing the data. Rows are cases; columns are variables. The order of columns is coordinated with the order of variables in getVariable().

knowledge

Knowledge knowledge

The knowledge associated with this data.

name

String name

The name of the data model. This is not used internally; it is only here in case an external class wants this dataset to have a name.

outputDelimiter

char outputDelimiter

The character used as a delimiter when the dataset is printed.

selection

Set<Node> selection

The set of selected variables.

variables

List<Node> variables

The list of variables. These correspond columnwise to the columns of data.

Class edu.cmu.tetrad.data.ShortDataBox

class ShortDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

short[][] data

The stored short data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.SplitCasesSpec

class SplitCasesSpec extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

breakpoints

int[] breakpoints

Breakpoints, for continuous data.

sampleSize

int sampleSize

Sample size.

splitNames

List<String> splitNames

Class edu.cmu.tetrad.data.TimeSeriesData

class TimeSeriesData extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

data2

Matrix data2

knowledge

Knowledge knowledge

name

String name

varNames

List<String> varNames

Class edu.cmu.tetrad.data.VerticalDoubleDataBox

class VerticalDoubleDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

double[][] data

The stored double data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Class edu.cmu.tetrad.data.VerticalIntDataBox

class VerticalIntDataBox extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

int[][] data

The stored int data.

numCols

int numCols

The number of columns (tracked because it may be zero).

numRows

int numRows

The number of rows (tracked because it may be zero).

Package edu.cmu.tetrad.data.simulation

Class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndGraphs

class LoadContinuousDataAndGraphs extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graphs

List<Graph> graphs

path

String path

usedParameters

List<String> usedParameters

Class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph

class LoadContinuousDataAndSingleGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graph

Graph graph

parametersValues

Parameters parametersValues

path

String path

usedParameters

List<String> usedParameters

Class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim

class LoadContinuousDataSmithSim extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

graph

Graph graph

parametersValues

Parameters parametersValues

path

String path

usedParameters

List<String> usedParameters

Class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs

class LoadDataAndGraphs extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSets

List<DataSet> dataSets

description

String description

graphs

List<Graph> graphs

path

String path

usedParameters

List<String> usedParameters

Class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph

class LoadDataFromFileWithoutGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

dataSet

DataSet dataSet

parameterValues

Map<String,Object> parameterValues

path

String path

Package edu.cmu.tetrad.graph

Class edu.cmu.tetrad.graph.Dag

class Dag extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)

Throws:

IOException

ClassNotFoundException

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

graph

Graph graph

underLineTriples

Set<Triple> underLineTriples

Class edu.cmu.tetrad.graph.Edge

class Edge extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)

Throws:

IOException

ClassNotFoundException

Serialized Fields

bold

boolean bold

edgeTypeProbabilities

List<EdgeTypeProbability> edgeTypeProbabilities

endpoint1

Endpoint endpoint1

endpoint2

Endpoint endpoint2

highlighted

boolean highlighted

node1

Node node1

node2

Node node2

probability

double probability

properties

List<Edge.Property> properties

Class edu.cmu.tetrad.graph.EdgeListGraph

class EdgeListGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)

Throws:

IOException

ClassNotFoundException

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

attributes

Map<String,Object> attributes

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

edgeLists

Map<Node,Set<Edge>> edgeLists

Map from each node to the List of edges connected to that node.

edgesSet

Set<Edge> edgesSet

The edges in the graph.

namesHash

Map<String,Node> namesHash

A hash from node names to nodes;

nodes

List<Node> nodes

A list of the nodes in the graph, in the order in which they were added.

underLineTriples

Set<Triple> underLineTriples

Class edu.cmu.tetrad.graph.EdgeTypeProbability

class EdgeTypeProbability extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

edgeType

EdgeTypeProbability.EdgeType edgeType

probability

double probability

properties

List<Edge.Property> properties

Class edu.cmu.tetrad.graph.GraphNode

class GraphNode extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

attributes

Map<String,Object> attributes

centerX

int centerX

The x coordinate of the center of the node.

centerY

int centerY

The y coordinate of the center of the node.

name

String name

The name of the node.

nodeType

NodeType nodeType

The type of the node.

See Also:

• NodeType

nodeVariableType

NodeVariableType nodeVariableType

Node variable type (domain, interventional status, interventional value..) of this node variable

Class edu.cmu.tetrad.graph.IndependenceFact

class IndependenceFact extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

_z

Set<Node> _z

x

Node x

y

Node y

Class edu.cmu.tetrad.graph.LagGraph

class LagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

attributes

Map<String,Object> attributes

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

graph

Dag graph

laggedVariables

Map<String,List<Node>> laggedVariables

paths

Paths paths

underLineTriples

Set<Triple> underLineTriples

variables

List<String> variables

Class edu.cmu.tetrad.graph.NodeType

class NodeType extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readResolve

Object readResolve()
            throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

ordinal

int ordinal

Class edu.cmu.tetrad.graph.OrderedPair

class OrderedPair extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

first

E first

The "First" node.

second

E second

The "second" node.

Class edu.cmu.tetrad.graph.Paths

class Paths extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

graph

Graph graph

Class edu.cmu.tetrad.graph.SemGraph

class SemGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.)

Throws:

IOException

ClassNotFoundException

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

attributes

Map<String,Object> attributes

cpdag

boolean cpdag

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

errorNodes

Map<Node,Node> errorNodes

A map from nodes to their error nodes, if they exist. This includes variables nodes to their error nodes and error nodes to themselves. Added because looking them up in the graph was not scalable.

graph

Graph graph

The underlying graph that stores all the information. This needs to be an EdgeListGraph or something at least that can allow nodes to quickly be added or removed.

pag

boolean pag

paths

Paths paths

showErrorTerms

boolean showErrorTerms

True if error terms for exogenous terms should be shown.

underLineTriples

Set<Triple> underLineTriples

Class edu.cmu.tetrad.graph.TimeLagGraph

class TimeLagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

attributes

Map<String,Object> attributes

cpdag

boolean cpdag

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

graph

EdgeListGraph graph

lag0Nodes

List<Node> lag0Nodes

maxLag

int maxLag

numInitialLags

int numInitialLags

pag

boolean pag

paths

Paths paths

underLineTriples

Set<Triple> underLineTriples

Class edu.cmu.tetrad.graph.Triple

class Triple extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

x

Node x

y

Node y

z

Node z

Class edu.cmu.tetrad.graph.Underlines

class Underlines extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

ambiguousTriples

Set<Triple> ambiguousTriples

dottedUnderLineTriples

Set<Triple> dottedUnderLineTriples

graph

Graph graph

underLineTriples

Set<Triple> underLineTriples

Package edu.cmu.tetrad.regression

Class edu.cmu.tetrad.regression.LogisticRegression

class LogisticRegression extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

alpha

double alpha

The default alpha level which may be specified otherwise in the GUI

dataCols

double[][] dataCols

The data converted into column major, to avoid unnecessary copying.

dataSet

DataSet dataSet

The data set that was supplied.

rows

int[] rows

Class edu.cmu.tetrad.regression.LogisticRegression.Result

class Result extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

chiSq

double chiSq

coefs

double[] coefs

intercept

double intercept

logLikelihood

double logLikelihood

numRegressors

int numRegressors

ny0

int ny0

ny1

int ny1

probs

double[] probs

regressorNames

List<String> regressorNames

stdErrs

double[] stdErrs

target

String target

xMeans

double[] xMeans

xStdDevs

double[] xStdDevs

Class edu.cmu.tetrad.regression.RegressionResult

class RegressionResult extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Alpha value to determine significance.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

b

double[] b

The array of regression coefficients.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

n

int n

The number of data points.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

p

double[] p

The array of p-values for the regression coefficients.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

r2

double r2

R square value.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

regressorNames

String[] regressorNames

Regressor names.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

res

Vector res

The residuals.

rss

double rss

Residual sums of squares.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

se

double[] se

Standard errors of the coefficients

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

t

double[] t

The array of t-statistics for the regression coefficients.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

zeroInterceptAssumed

boolean zeroInterceptAssumed

True iff this model assumes a zero intercept.

See Also:

• RegressionResult(boolean, java.lang.String[], int, double[], double[], double[], double[], double, double, double, edu.cmu.tetrad.util.Vector)

Package edu.cmu.tetrad.search

Class edu.cmu.tetrad.search.Cstar.Record

class Record extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

causeNode

Node causeNode

effect

double effect

numCauses

int numCauses

numEffects

int numEffects

pi

double pi

target

Node target

Package edu.cmu.tetrad.search.score

Class edu.cmu.tetrad.search.score.ScoredGraph

class ScoredGraph extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

graph

Graph graph

score

Double score

Package edu.cmu.tetrad.search.test

Class edu.cmu.tetrad.search.test.IndependenceResult

class IndependenceResult extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

fact

IndependenceFact fact

indep

boolean indep

pValue

double pValue

score

double score

Package edu.cmu.tetrad.search.utils

Class edu.cmu.tetrad.search.utils.SepsetMap

class SepsetMap extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help).

Throws:

IOException

ClassNotFoundException

Serialized Fields

parents

Map<Node,HashSet<Node>> parents

pValues

Map<Set<Node>,Double> pValues

sepsets

Map<Set<Node>,Set<Node>> sepsets

Class edu.cmu.tetrad.search.utils.Sextad

class Sextad extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

i

int i

j

int j

k

int k

l

int l

m

int m

n

int n

Package edu.cmu.tetrad.search.work_in_progress

Class edu.cmu.tetrad.search.work_in_progress.Sextad

class Sextad extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

i

Node i

j

Node j

k

Node k

l

Node l

m

Node m

n

Node n

Package edu.cmu.tetrad.sem

Class edu.cmu.tetrad.sem.DagScorer

class DagScorer extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

covMatrix

ICovarianceMatrix covMatrix

dag

Graph dag

dataSet

DataSet dataSet

edgeCoef

Matrix edgeCoef

errorCovar

Matrix errorCovar

fml

double fml

implCovarMeasC

Matrix implCovarMeasC

logDetSample

double logDetSample

sampleCovar

Matrix sampleCovar

variables

List<Node> variables

Class edu.cmu.tetrad.sem.GeneralizedSemIm

class GeneralizedSemIm extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

guaranteeIid

boolean guaranteeIid

parameterValues

Map<String,Double> parameterValues

A map from freeParameters names to their values--these form the context for evaluating expressions. Variables do not appear in this list. All freeParameters are double-valued.

pm

GeneralizedSemPm pm

The wrapped PM, that holds all of the expressions and structure for the model.

Class edu.cmu.tetrad.sem.GeneralizedSemPm

class GeneralizedSemPm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help).

Throws:

IOException

ClassNotFoundException

Serialized Fields

errorNodes

List<Node> errorNodes

The error nodes.

errorsTemplate

String errorsTemplate

The stored template for error terms.

graph

SemGraph graph

The structural model graph that this sem parametric model is based on.

Cannot be null.

measuredNodes

List<Node> measuredNodes

The measured nodes.

namesToNodes

Map<String,Node> namesToNodes

A map from names to nodes, speedup.

nodeExpressions

Map<Node,Expression> nodeExpressions

The map from variable nodes to equations.

nodeExpressionStrings

Map<Node,String> nodeExpressionStrings

The String representations of equations that were set.

nodes

List<Node> nodes

The list of all nodes (unmodifiable).

Cannot be null.

parameterEstimationInitializationExpressions

Map<String,Expression> parameterEstimationInitializationExpressions

Distributions from which initial values for freeParameters are drawn.

parameterEstimationInitializationExpressionStrings

Map<String,String> parameterEstimationInitializationExpressionStrings

String representations of initial parameter distributions. A map from parameter names to expression strings.

parameterExpressions

Map<String,Expression> parameterExpressions

Distributions from which initial values for freeParameters are drawn.

parameterExpressionStrings

Map<String,String> parameterExpressionStrings

String representations of initial parameter distributions. A map from parameter names to expression strings.

parametersEstimationInitializationTemplate

String parametersEstimationInitializationTemplate

The stored template for freeParameters.

parametersTemplate

String parametersTemplate

The stored template for freeParameters.

parameterSubscript

Map<String,Integer> parameterSubscript

referencedNodes

Map<Node,Set<Node>> referencedNodes

The nodes of the model, variable nodes or error nodes, mapped to the other nodes that they are associated with.

referencedParameters

Map<String,Set<Node>> referencedParameters

The freeParameters in the model, mapped to the nodes that they are associated with. Each parameter may be associated with more than one node. When freeParameters are removed from an equation or error distribution, the associated nodes should be removed from the relevant set in this map, and if the set is empty, the parameter should be removed from the map. Also, before adding a parameter to this map, it must be checked whether a parameter by the same name already exists. If one such parameter by the same name already exists, that one should be used instead of the new one. This is needed both to avoid confusion and to allow freeParameters to be reused in different parts of the interface, creating equality constraints.

Cannot be null.

startsWithParametersEstimationInitializationTemplates

Map<String,String> startsWithParametersEstimationInitializationTemplates

A map from initial name strings to parameter templates.

startsWithParametersTemplates

Map<String,String> startsWithParametersTemplates

A map from initial name strings to parameter templates.

variableNames

List<String> variableNames

The list of variable names.

variableNodes

List<Node> variableNodes

The latent and measured nodes.

variablesTemplate

String variablesTemplate

The stored template for variables.

Class edu.cmu.tetrad.sem.Mapping

class Mapping extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

a

Matrix a

The 2D double array whose element at (i, j) to be manipulated.

Can't be null.

i

int i

The left-hand coordinate of a[i][j].

Any value.

j

int j

The right-hand coordinate of a[i][j].

Any value.

parameter

Parameter parameter

The parameter this mapping maps.

Can't be null.

semIm

ISemIm semIm

The SemIm for which this is a mapping.

Can't be null.

Class edu.cmu.tetrad.sem.ParamConstraint

class ParamConstraint extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

number

double number

param2

Parameter param2

semIm

SemIm semIm

type

ParamConstraintType type

Class edu.cmu.tetrad.sem.ParamConstraintType

class ParamConstraintType extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readResolve

Object readResolve()
            throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

ordinal

int ordinal

Class edu.cmu.tetrad.sem.Parameter

class Parameter extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

distribution

Distribution distribution

If this parameter is initialized randomly, the initial value is drawn from this distribution.

Cannot be null.

fixed

boolean fixed

True iff this parameter is fixed in estimation.

Any value.

initializedRandomly

boolean initializedRandomly

True iff this parameter should be initialized randomly.

Any value.

name

String name

The name of the parameter.

Cannot be null.

nodeA

Node nodeA

One of the anchor endpoints specifying the parameter this is.

Cannot be null.

nodeB

Node nodeB

One of the anchor endpoints specifying the parameter this is.

Cannot be null.

startingValue

double startingValue

If this parameter is either fixed or not initialized randomly, returns its starting value.

Any value.

type

ParamType type

The type of parameter--coefficient, covariance, or variance.

Cannot be null. Should be ParamType.VAR if nodeA != nodeB and ParamType.COVAR if nodeA == nodeB.

Class edu.cmu.tetrad.sem.ParameterPair

class ParameterPair extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

a

Parameter a

The first element of the ordered pair. Can be null.

May be null.

b

Parameter b

The second element of the ordered pair. Can be null.

May be null.

Class edu.cmu.tetrad.sem.ParamType

class ParamType extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readResolve

Object readResolve()
            throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

ordinal

int ordinal

Class edu.cmu.tetrad.sem.SemEstimator

class SemEstimator extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

covMatrix

ICovarianceMatrix covMatrix

The covariance matrix used to estimate the SemIm. Note that the variables names in the covariance matrix must be in the same order as the variable names in the semPm.

Cannot be null.

dataSet

DataSet dataSet

The data set being estimated from (needed to calculate means of variables). May be null in which case means are set to zero.

Can be null.

estimatedSem

SemIm estimatedSem

The most recently estimated model, or null if no model has been estimated yet.

Can be null.

numRestarts

int numRestarts

scoreType

ScoreType scoreType

semOptimizer

SemOptimizer semOptimizer

The algorithm that minimizes the fitting function for the SEM.

semPm

SemPm semPm

The SemPm containing the graph and the freeParameters to be estimated.

Cannot be null.

Class edu.cmu.tetrad.sem.SemEstimatorGibbsParams

class SemEstimatorGibbsParams extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

flatPrior

boolean flatPrior

numIterations

int numIterations

startIm

SemIm startIm

stretch

double stretch

tolerance

double tolerance

Class edu.cmu.tetrad.sem.SemEvidence

class SemEvidence extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

manipulation

SemManipulation manipulation

A manipulation indicating how the bayes Im should be manipulated before updating.

proposition

SemProposition proposition

A proposition stating what we know for each variable.

Cannot be null.

semIm

SemIm semIm

Bayes IM that this is evidence for.

Class edu.cmu.tetrad.sem.SemIm

class SemIm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

cyclic

boolean cyclic

True just in case the graph for the SEM is cyclic.

cyclicChecked

boolean cyclicChecked

True just in case cyclicity has already been checked.

distributions

Map<Node,Distribution> distributions

Stores a distribution for each variable. Initialized to N(0, 1) for each.

edgeCoef

Matrix edgeCoef

Matrix of edge coefficients. edgeCoefC[i][j] is the coefficient of the edge from getVariableNodes().get(i) to getVariableNodes().get(j), or 0.0 if this edge is not in the graph. The values of these may be changed, but the array itself may not.

Cannot be null.

errCovar

Matrix errCovar

Matrix of error covariances. errCovar[i][j] is the covariance of the error term of getExoNodes().get(i) and getExoNodes().get(j), with the special case (duh!) that errCovar[i][i] is the variance of getExoNodes.get(i). The values of these may be changed, but the array itself may not.

Cannot be null.

errorParam1

double errorParam1

errorParam2

double errorParam2

estimated

boolean estimated

True iff this SemIm is estimated.

Any value.

fixedMappings

List<Mapping> fixedMappings

The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedParameters.

Cannot be null.

fixedParameters

List<Parameter> fixedParameters

The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedMappings.

Cannot be null.

freeMappings

List<Mapping> freeMappings

The list of freeMappings. This is an unmodifiable list. It is fixed (up to order) by the SemPm. This must be in the same order as this.freeParameters.

Cannot be null.

freeParameters

List<Parameter> freeParameters

The list of free freeParameters (Unmodifiable). This must be in the same order as this.freeMappings.

Cannot be null.

functions

Map<Node,ConnectionFunction> functions

Stores the connection functions of specified nodes.

implCovar

Matrix implCovar

Replaced by implCovarC. Please do not delete. Required for serialization backward compatibility.

meanParameters

List<Parameter> meanParameters

The list of mean freeParameters (Unmodifiable). This must be in the same order as variableMeans.

measuredNodes

List<Node> measuredNodes

The list of measured variableNodes from the semPm. (Unmodifiable.)

Cannot be null.

numRandomCalls

int numRandomCalls

parameterBoundsEnforced

boolean parameterBoundsEnforced

True iff setting freeParameters to out-of-bound values throws exceptions.

Any value.

params

Parameters params

Parameters to help guide how values are chosen for freeParameters.

sampleCovarC

Matrix sampleCovarC

Replaced by sampleCovar. Please do not delete. Required for serialization backward compatibility.

sampleCovInv

Matrix sampleCovInv

sampleSize

int sampleSize

The sample size.

Range >= 0.

scoreType

ScoreType scoreType

semPm

SemPm semPm

The Sem PM containing the graph and the freeParameters to be estimated. For now a defensive copy of this is not being constructed, since it is not used anywhere in the code except in the the constructor and in its accessor method. If somebody changes it, it's their own fault, but it won't affect this class.

Cannot be null.

standardErrors

double[] standardErrors

Stores the standard errors for the freeParameters. May be null.

Can be null.

variableMeans

double[] variableMeans

Means of variables. These will not be counted for purposes of calculating degrees of freedom, since the increase in dof is exactly balanced by a decrease in dof.

Cannot be null.

variableMeansStdDev

double[] variableMeansStdDev

Standard Deviations of means. Needed to calculate standard errors.

Cannot be null.

variableNodes

List<Node> variableNodes

The list of measured and latent variableNodes for the semPm. (Unmodifiable.)

Cannot be null.

variablesHash

Map<Node,Integer> variablesHash

Class edu.cmu.tetrad.sem.SemManipulation

class SemManipulation extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

manipulated

boolean[] manipulated

An array indicating whether each variable in turn is manipulated.

Cannot be null.

semIm

SemIm semIm

Bayes IM that this is evidence for.

Cannot be null.

Class edu.cmu.tetrad.sem.SemOptimizerEm

class SemOptimizerEm extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

errorParent

Node[] errorParent

expectedCov

Matrix expectedCov

graph

SemGraph graph

idxLatent

int[] idxLatent

idxObserved

int[] idxObserved

nodeParentsCov

double[][] nodeParentsCov

numLatent

int numLatent

numObserved

int numObserved

numRestarts

int numRestarts

parents

int[][] parents

parentsCov

double[][][] parentsCov

semIm

SemIm semIm

yCov

Matrix yCov

yCovModel

Matrix yCovModel

yzCovModel

Matrix yzCovModel

zCovModel

Matrix zCovModel

Class edu.cmu.tetrad.sem.SemOptimizerPowell

class SemOptimizerPowell extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

numRestarts

int numRestarts

Class edu.cmu.tetrad.sem.SemOptimizerRegression

class SemOptimizerRegression extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

numRestarts

int numRestarts

Class edu.cmu.tetrad.sem.SemOptimizerRicf

class SemOptimizerRicf extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

numRestarts

int numRestarts

Class edu.cmu.tetrad.sem.SemOptimizerScattershot

class SemOptimizerScattershot extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

numRestarts

int numRestarts

Class edu.cmu.tetrad.sem.SemPm

class SemPm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

bIndex

int bIndex

The index of the most recent "B" parameter. (These are edge coefficients.)

Range >= 0.

graph

SemGraph graph

The structural model graph that this sem parametric model is based on.

Cannot be null.

mIndex

int mIndex

The index of the most recent "M" parameter. (These are means.)

Range >= 0.

nodes

List<Node> nodes

The list of all nodes (unmodifiable).

Cannot be null.

paramComparisons

Map<ParameterPair,ParamComparison> paramComparisons

The set of parameter comparisons.

Cannot be null.

parameters

List<Parameter> parameters

The list of Parameters (unmodifiable).

Cannot be null.

tIndex

int tIndex

The index of the most recent "T" parameter. (These are variance and covariance terms.)

Range >= 0.

variableNodes

List<Node> variableNodes

The list of variable nodes (unmodifiable).

Cannot be null.

Class edu.cmu.tetrad.sem.SemProposition

class SemProposition extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

semIm

SemIm semIm

Cannot be null.

values

double[] values

Cannot be null.

Class edu.cmu.tetrad.sem.SemUpdater

class SemUpdater extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

evidence

SemEvidence evidence

semIm

SemIm semIm

Class edu.cmu.tetrad.sem.StandardizedSemIm

class StandardizedSemIm extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

edgeCoef

Matrix edgeCoef

edgeParameters

Map<Edge,Double> edgeParameters

A map from edges in the graph to their coefficients. These are the only freeParameters in the model. This includes coefficients for directed as well as bidirected edges.

editingEdge

Edge editingEdge

errorCovar

Matrix errorCovar

errorVariances

Map<Node,Double> errorVariances

implCovar

Matrix implCovar

A map from error nodes in the graph to their error variances. These are not freeParameters in the model; their values are always calculated as residual variances, under the constraint that the variances of each variable must be 1.

implCovarMeas

Matrix implCovarMeas

range

StandardizedSemIm.ParameterRange range

sampleSize

int sampleSize

semGraph

SemGraph semGraph

The graph of the model. Stored internally because it must be ensured that the error terms are showing.

semPm

SemPm semPm

The SEM model.

Class edu.cmu.tetrad.sem.StandardizedSemIm.ParameterRange

class ParameterRange extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

coef

double coef

edge

Edge edge

high

double high

low

double low

Package edu.cmu.tetrad.session

Exception edu.cmu.tetrad.session.CouldNotCreateModelException

class CouldNotCreateModelException extends Exception implements Serializable

Serialized Fields

modelClass

Class modelClass

Class edu.cmu.tetrad.session.Session

class Session extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

name

String name

The name of the session.

Can't be null.

nodes

List<SessionNode> nodes

The session nodes, stored as a Set of nodes.

Can't be null.

Class edu.cmu.tetrad.session.SessionEvent

class SessionEvent extends EventObject implements Serializable

Serialized Fields

child

SessionNode child

node

SessionNode node

parent

SessionNode parent

type

int type

Class edu.cmu.tetrad.session.SessionNode

class SessionNode extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

attributes

Map<String,Object> attributes

boxType

String boxType

The (optional) name of this session node.

Cannot be null.

children

Set<SessionNode> children

The set of children of this node--a Set of SessionNodes. Must be kept in sync with sets of parents in the child nodes.

Cannot be null.

displayName

String displayName

The display name of the session node.

Cannot be null.

lastModelClass

Class lastModelClass

The class of the last model created.

Can be null.

loggerConfig

TetradLoggerConfig loggerConfig

model

SessionModel model

The model itself. Once this is created, another model cannot be created until this one is explicitly destroyed.

Can be null.

modelClasses

Class[] modelClasses

The possible classes this SessionNode can use to construct models.

Cannot be null.

modelParamTypes

Class[] modelParamTypes

When a model is created, we keep a reference to its param types in order to determine, should the need arise, whether one of the objects used to create the model has been destroyed.

Can be null.

nextEdgeAddAllowed

boolean nextEdgeAddAllowed

True iff the next edge should not be added. (Included for GUI user control.) Reset to true every time an edge is added; edge adds must be disallowed individually. To disallow the next edge add, set to false.

Any value.

nodeVariableType

NodeVariableType nodeVariableType

Node variable type (domain, interventional status, interventional value..) of this node variable

oldModel

SessionModel oldModel

Stores a reference to the previous model so that information from it can be used to initialize a new model.

Can be null.

parameters

Parameters parameters

paramMap

Map<Class,Parameters> paramMap

A map from model classes to parameter objects.

Cannot be null.

parents

Set<SessionNode> parents

The set of parents of this node--a Set of SessionNodes. Must be kept in sync with sets of children in the parent nodes.

Cannot be null.

repetition

int repetition

The number of times this session node should be executed (in depth first order) in a simulation edu.cmu.tetrad.study.

Range > 0.

Class edu.cmu.tetrad.session.Type1

class Type1 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type10

class Type10 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type11

class Type11 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type12

class Type12 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type2

class Type2 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type3

class Type3 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type4

class Type4 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type5

class Type5 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type6

class Type6 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type7

class Type7 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type8

class Type8 extends Object implements Serializable

serialVersionUID:

23L

Class edu.cmu.tetrad.session.Type9

class Type9 extends Object implements Serializable

serialVersionUID:

23L

Package edu.cmu.tetrad.study.gene.tetrad.gene.graph

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ActiveLagGraph

class ActiveLagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

lagGraph

LagGraph lagGraph

Underlying graph representing the update graph.

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualActiveLagGraph

class ManualActiveLagGraph extends ActiveLagGraph implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraph

class ManualLagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

lagGraph

BasicLagGraph lagGraph

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.ManualLagGraphParams

class ManualLagGraphParams extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

mlag

int mlag

The maximum lag of the lag graph.

varsPerInd

int varsPerInd

The number of variables per individual.

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.RandomActiveLagGraph

class RandomActiveLagGraph extends ActiveLagGraph implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

Class edu.cmu.tetrad.study.gene.tetrad.gene.graph.StoredLagGraphParams

class StoredLagGraphParams extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

filename

String filename

The filename of the stored lag graph.

Package edu.cmu.tetrad.study.gene.tetrad.gene.history

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer

class BasalInitializer extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

basalExpression

double basalExpression

The average expression level that all unregulated genes are initialized to.

initStDev

double initStDev

The standard deviation of a normal distribution N(basalExpression, sem.D.) that random initial values for unregulated genes are set to.

updateFunction

UpdateFunction updateFunction

The update function this is initializing for.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BasicLagGraph

class BasicLagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

connectivity

SortedMap<String,SortedSet<LaggedFactor>> connectivity

For each factor, stores the set of lagged factors which map into it. (Maps Strings to SortedSets of Strings.) This is the main data structure for the graph.

locations

Map<String,PointXy> locations

Stores the locations of the points for a directed graph.

maxLagAllowable

int maxLagAllowable

The maximum allowable lag. edges may not be added with lags greater than this. The value must be >= 1.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanFunction

class BooleanFunction extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

lookupTable

boolean[] lookupTable

The stored boolean function. The order of the rows (for the given parents array, for two parents) is 00, 01, 10, 11, and so on for higher numbers of parents.

parents

IndexedParent[] parents

The array of parents for the stored boolean function.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction

class BooleanGlassFunction extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

basalExpression

double basalExpression

The basalExpression for determining whether history expression levels should be mapped to "true" or "false" for purposes of looking up output values in the Boolean function table.

booleanFunctions

BooleanFunction[] booleanFunctions

Stores a boolean function for each factor from a preselected set of lagged factors to the given factor.

booleanInfluenceRate

double booleanInfluenceRate

The rate at which the F function (with outputs -1 and +1) affects the update for a gene.

connectivity

IndexedLagGraph connectivity

The indexed connectivity "snapshot" of the lag graph.

decayRate

double decayRate

The rate at which expression levels for a gene tend to return to basal level.

errorDistributions

Distribution[] errorDistributions

Error distributions from which errors are drawn for each of the factors.

lowerBound

double lowerBound

The lower bound for expression levels. Expression levels that wander below this bound will be set to this bound.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.DishModel

class DishModel extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

dishBumps

double[] dishBumps

An array of dish bumps for each dish.

dishBumpStDev

double dishBumpStDev

The standard deviation of the normal distribution from which dish bump values are drawn, in percent. The distribution has a mean of 100%.

dishNumber

int dishNumber

The number of the getModel dish.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory

class GeneHistory extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

dishModel

DishModel dishModel

A model of the differences in expression levels due to the particular dish a sample is taken from.

historyArray

double[][] historyArray

A history of time slices of values for each factor, extending back as far as is necessary for the update function to be applied properly (that is, from maxlag up to 0, the getModel time step). Note that the firs subscript is the time slice, whereas the second subscript is the expression level for each gene.

initializer

Initializer initializer

The initializer for the history.

initSync

boolean initSync

Indicates whether initialization should be synchronized or not. If it's synchronized, then the same (or almost the same) set of initial random values are used each time the initialize() method is called. Otherwise, a new set of random values is chosen each time. Note that this is a "first pass" attempt at "shocking" the simulated cells.

step

int step

The getModel time step, which is the number of steps after the initialization period. In other words, time step 0 is the first update step after the initialization, or the first step at which the Glass updating function has been applied. (Markov process.)

syncInitialization

double[][] syncInitialization

A stored copy of the initial values for the history array, to be used if synchronized initialization is desired. If synchonized initialization is selected, then on the first pass through the initialization method, this array is calculated, and for each individual simulated, the history array for that individual is initialized using values from this array.

updateFunction

UpdateFunction updateFunction

The update function for the history.

updatePeriods

int[] updatePeriods

To simulate asynchronous updating, update periods for each factor are allowed to be different. (Note: this was a brilliant idea somebody had a long time ago that has never yet been used. jdramsey 2/22/02)

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedConnectivity

class IndexedConnectivity extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

factors

List<String> factors

The factors in the graph, in the order that they are used.

parents

IndexedParent[][] parents

The graph that this "snapshot" of indexedConnectivity was taken from.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedLagGraph

class IndexedLagGraph extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

factors

List<String> factors

The factors in the graph, in the order that they are used.

parents

IndexedParent[][] parents

The graph that this "snapshot" of indexedLagGraph was taken from.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.IndexedParent

class IndexedParent extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

index

int index

The index of the parent.

lag

int lag

The lag of the parent.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedEdge

class LaggedEdge extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

factor

String factor

laggedFactor

LaggedFactor laggedFactor

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LaggedFactor

class LaggedFactor extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

factor

String factor

The name of the factor.

lag

int lag

The number of time steps back for the lagged factor.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.LinearFunction

class LinearFunction extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

polynomialFunction

PolynomialFunction polynomialFunction

The wrapped polynomial function that's doing all the work.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.Polynomial

class Polynomial extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

terms

List<PolynomialTerm> terms

The terms of the polynomial.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialFunction

class PolynomialFunction extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

connectivity

IndexedLagGraph connectivity

The "snapshot" indexed connectivity of the initial lag graph.

errorDistributions

Distribution[] errorDistributions

Error distributions from which errors are drawn for each of the factors.

polynomials

Polynomial[] polynomials

The polynomials of each factor given its parents.

Class edu.cmu.tetrad.study.gene.tetrad.gene.history.PolynomialTerm

class PolynomialTerm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

coefficient

double coefficient

The coefficient of the term.

variables

int[] variables

The variables of the term.

Package edu.cmu.tetrad.study.gene.tetrad.gene.simulation

Class edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator

class MeasurementSimulator extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

cellNumber

int cellNumber

chipChipVariability

double chipChipVariability

dishDishVariability

double dishDishVariability

dishNumber

int dishNumber

firstStepStored

int firstStepStored

history

GeneHistory history

interval

int interval

measuredData

double[][][] measuredData

numCellsPerDish

int numCellsPerDish

numDishes

int numDishes

numSamplesPerDish

int numSamplesPerDish

parameters

Parameters parameters

pixelDigitalization

double pixelDigitalization

rawData

double[][][] rawData

sampleSampleVariability

double sampleSampleVariability

stepsGenerated

int stepsGenerated

timeSteps

int[] timeSteps

Package edu.cmu.tetrad.study.gene.tetradapp.model

Class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGeneIm

class BooleanGlassGeneIm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

genePm

BooleanGlassGenePm genePm

Cannot be null.

glassFunction

BooleanGlassFunction glassFunction

Cannot be null.

history

GeneHistory history

Cannot be null.

initializer

BasalInitializer initializer

Cannot be null.

name

String name

Can be null.

simulator

MeasurementSimulatorParams simulator

Cannot be null.

Class edu.cmu.tetrad.study.gene.tetradapp.model.BooleanGlassGenePm

class BooleanGlassGenePm extends GenePm implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

Can be null.n

Class edu.cmu.tetrad.study.gene.tetradapp.model.GenePm

class GenePm extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

lagGraph

LagGraph lagGraph

The wrapped lag workbench.

Cannot be null.

Class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams

class MeasurementSimulatorParams extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

includeDishAndChipVariables

boolean includeDishAndChipVariables

simulator

MeasurementSimulator simulator

Cannot be null.

Package edu.cmu.tetrad.util

Class edu.cmu.tetrad.util.DefaultTetradLoggerConfig

class DefaultTetradLoggerConfig extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

active

Set<String> active

The event ids that are currently active.

events

List<TetradLoggerConfig.Event> events

The events that are supported.

Class edu.cmu.tetrad.util.DefaultTetradLoggerConfig.DefaultEvent

class DefaultEvent extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

description

String description

id

String id

Class edu.cmu.tetrad.util.Matrix

class Matrix extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

apacheData

org.apache.commons.math3.linear.RealMatrix apacheData

m

int m

n

int n

Class edu.cmu.tetrad.util.Matrix2

class Matrix2 extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

apacheData

org.apache.commons.math3.linear.RealMatrix apacheData

m

int m

n

int n

Class edu.cmu.tetrad.util.Parameters

class Parameters extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

overriddenParameters

Map<String,Object> overriddenParameters

parameters

Map<String,Object[]> parameters

usedParameters

Set<String> usedParameters

Class edu.cmu.tetrad.util.PartialCorrelationPdf

class PartialCorrelationPdf extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

constant

double constant

The aggregate value of the constant expression in the distribution function for zero partial correlation.

k

int k

Number of compared variables--that is, 2 + (#conditioning variables).

n

int n

Number of data points in the sample.

outsideExp

double outsideExp

The power to which the variable expression is raised in the distribution function for zero partial correlation.

Class edu.cmu.tetrad.util.PointXy

class PointXy extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

x

int x

The x coordinate.

y

int y

The y coordinate.

Class edu.cmu.tetrad.util.TetradLogger.EmptyConfig

class EmptyConfig extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

active

boolean active

Class edu.cmu.tetrad.util.TetradLoggerEvent

class TetradLoggerEvent extends EventObject implements Serializable

Serialized Fields

config

TetradLoggerConfig config

Class edu.cmu.tetrad.util.Vector

class Vector extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

data

org.apache.commons.math3.linear.RealVector data

Class edu.cmu.tetrad.util.Version

class Version extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

incrementalRelease

int incrementalRelease

The incremental release number. In release a.b.c-d, d. This number increases without bound until the next major version, minor version, or minor subversion release, at which point is goes back to zero. If it is zero, release a.b.c.dx may be referred to as a.b.c.

With maven snapshots the incremental release number refers to the snapshot build date. If this field is SNAPSHOT it is set to max int

Range greater than or equal to 0.

majorVersion

int majorVersion

The major version number. In release a.b.c-d, a. At time of creating this class, it's 4, and the minor version is 3. This should increase only for truly substantial and essentially complete new releases of Tetrad.

Range greater than or equal to 0.

minorSubversion

int minorSubversion

The minor release number. In release a.b.c-d, c. This number increases without bound until the next major or minor release, at which point it goes back to zero.

Range greater than or equal to 0.

minorVersion

int minorVersion

The minor version number. In release a.b.c-d, b. This number increases without bound until the next major release, at which point it goes back to zero.

Range greater than or equal to 0.

Package edu.cmu.tetrad.util.dist

Class edu.cmu.tetrad.util.dist.Beta

class Beta extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

Ibid.

beta

double beta

Ibid.

Class edu.cmu.tetrad.util.dist.ChiSquare

class ChiSquare extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Parameters:

s - Ibid.

Throws:

IOException - If the stream cannot be read.

ClassNotFoundException - If the class of an object in the stream is not in the project.

Serialized Fields

df

double df

The stored degees of freedom. Needed because the wrapped distribution does not provide getters for its parameters.

Class edu.cmu.tetrad.util.dist.Discrete

class Discrete extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

p

double[] p

Class edu.cmu.tetrad.util.dist.Exponential

class Exponential extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

lambda

double lambda

Class edu.cmu.tetrad.util.dist.Gamma

class Gamma extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

alpha

double alpha

lambda

double lambda

Class edu.cmu.tetrad.util.dist.GaussianPower

class GaussianPower extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

name

String name

power

double power

sd

double sd

Class edu.cmu.tetrad.util.dist.Indicator

class Indicator extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

p

double p

Class edu.cmu.tetrad.util.dist.LogNormal

class LogNormal extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

sd

double sd

Class edu.cmu.tetrad.util.dist.MixtureOfGaussians

class MixtureOfGaussians extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

a

double a

mean1

double mean1

mean2

double mean2

sd1

double sd1

sd2

double sd2

Class edu.cmu.tetrad.util.dist.Normal

class Normal extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Parameters:

s - What it says.

Throws:

IOException - If the stream cannot be read.

ClassNotFoundException - if a the class of an object in the input cannot be found.

Serialized Fields

mean

double mean

The mean of the distribution.

sd

double sd

The standard deviation of the distribution.

Class edu.cmu.tetrad.util.dist.Poisson

class Poisson extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

mean

double mean

Class edu.cmu.tetrad.util.dist.SingleValue

class SingleValue extends Object implements Serializable

serialVersionUID:

23L

Serialized Fields

value

double value

Class edu.cmu.tetrad.util.dist.Split

class Split extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Parameters:

s - the stream to read from.

Throws:

IOException - If the stream cannot be read.

ClassNotFoundException - If the class of an object in the stream is not in the project.

Serialized Fields

a

double a

b

double b

Class edu.cmu.tetrad.util.dist.TruncatedNormal

class TruncatedNormal extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Parameters:

s - What it says.

Throws:

IOException - If the stream cannot be read.

ClassNotFoundException - if a the class of an object in the input cannot be found.

Serialized Fields

high

double high

The standard devision of the distribution.

low

double low

The standard devision of the distribution.

mean

double mean

The mean of the distribution.

sd

double sd

The standard devision of the distribution.

Class edu.cmu.tetrad.util.dist.Uniform

class Uniform extends Object implements Serializable

serialVersionUID:

23L

Serialization Methods

readObject

private void readObject(ObjectInputStream s)
                 throws IOException,
ClassNotFoundException

Adds semantic checks to the default deserialization method. This method must have the standard signature for a readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any semantic checks can be specified and do not need to stay the same from version to version. A readObject method of this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.

Throws:

IOException

ClassNotFoundException

Serialized Fields

a

double a

The lower bound of the range from which numbers are drawn uniformly.

b

double b

The upper bound of the range from which numbers are drawn uniformly.

Package edu.pitt.isp.sverchkov.data

Class edu.pitt.isp.sverchkov.data.AdTree

class AdTree extends edu.pitt.isp.sverchkov.data.AdTreeHelper implements Serializable

Serialized Fields

attributeLookup

Map<A,Integer> attributeLookup

attributes

List<A> attributes

root

edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode root

values

List<AdTree<A,V>.edu.pitt.isp.sverchkov.data.AdTree.VHelper> values

Class edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode

class CountNode extends Object implements Serializable

Serialized Fields

attr

int attr

count

int count

vary

edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode[] vary

Class edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode

class VaryNode extends Object implements Serializable

Serialized Fields

mcv

int mcv

values

edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode[] values