Serialized Form (tetrad-lib 7.6.9-SNAPSHOT API)

Package edu.cmu.tetrad.algcomparison
- Class edu.cmu.tetrad.algcomparison.Comparison
  
  class Comparison extends Object implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    comparisonGraph
    
    Comparison.ComparisonGraph comparisonGraph
    
    The comparison graph type.
    
    dataPath
    
    String dataPath
    
    The data path.
    
    graphTypeUsed
    
    boolean[] graphTypeUsed
    
    The graph type used.
    
    knowledge
    
    Knowledge knowledge
    
    Represents a variable for storing knowledge.
    
    parallelism
    
    int parallelism
    
    The number of threads to use.
    
    resultsPath
    
    String resultsPath
    
    The result path.
    
    saveCPDAGs
    
    boolean saveCPDAGs
    
    Whether to save the CPDAGs.
    
    saveData
    
    boolean saveData
    
    Whether to save the data.
    
    saveGraphs
    
    boolean saveGraphs
    
    Whether to save the graphs.
    
    savePags
    
    boolean savePags
    
    Whether to save the PAGs.
    
    setAlgorithmKnowledge
    
    boolean setAlgorithmKnowledge
    
    True if knowledge should be set on the algorithms (if supplied).
    
    showUtilities
    
    boolean showUtilities
    
    Whether to show the utility calculations.
    
    sortByUtility
    
    boolean sortByUtility
    
    Whether to sort by utility.
    
    tabDelimitedTables
    
    boolean tabDelimitedTables
    
    Indicates whether the tables are tab-delimited.
Package edu.cmu.tetrad.algcomparison.algorithm
- Class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm
  
  class AbstractBootstrapAlgorithm extends Object implements Serializable
  - Serialized Fields
    
    count
    
    int count
    
    Bootstrap count, printed out to track bootstraps.
- Class edu.cmu.tetrad.algcomparison.algorithm.Algorithms
  
  class Algorithms extends Object implements Serializable
  
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  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    algorithms
    
    List<Algorithm> algorithms
    
    The list of algorithm.
- Class edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm
  
  class ExternalAlgorithm extends Object implements Serializable
  - Serialized Fields
    
    path
    
    String path
    
    The path to the external graph.
    
    simIndex
    
    int simIndex
    
    The index of the simulation.
    
    simulation
    
    Simulation simulation
    
    The simulation.
    
    usedParameters
    
    List<String> usedParameters
    
    The parameters used in the search.
- Class edu.cmu.tetrad.algcomparison.algorithm.FirstInflection
  
  class FirstInflection extends Object implements Serializable
  
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  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    high
    
    double high
    
    The high value for the parameter.
    
    increment
    
    double increment
    
    The increment for the parameter.
    
    low
    
    double low
    
    The low value for the parameter.
    
    parameter
    
    String parameter
    
    The parameter to vary.
- Class edu.cmu.tetrad.algcomparison.algorithm.StabilitySelection
  
  class StabilitySelection extends Object implements Serializable
  
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  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.StARS
  
  class StARS extends Object implements Serializable
  
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  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    high
    
    double high
    
    The high value for the parameter.
    
    low
    
    double low
    
    The low value for the parameter.
    
    parameter
    
    String parameter
    
    The parameter to vary.
Package edu.cmu.tetrad.algcomparison.algorithm.cluster
- Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Bpc
  
  class Bpc extends Object implements Serializable
  
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- Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Fofc
  
  class Fofc extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
- Class edu.cmu.tetrad.algcomparison.algorithm.cluster.Ftfc
  
  class Ftfc extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
Package edu.cmu.tetrad.algcomparison.algorithm.continuous.dag
- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma
  
  class Dagma extends AbstractBootstrapAlgorithm implements Serializable
  
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- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.DirectLingam
  
  class DirectLingam extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    score
    
    ScoreWrapper score
    
    The score.
- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Fask
  
  class Fask extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.FaskOrig
  
  class FaskOrig extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingam
  
  class IcaLingam extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    bHat
    
    Matrix bHat
    
    The bHat variable represents the estimated B matrix generated by the algorithm. The B matrix is a matrix that encodes the causal relationships between the variables in the data set. The bHat variable is implemented as an instance of the Matrix class from the Tetrad library. The Matrix class provides methods for creating and manipulating matrices.
    The bHat variable is a private member of the IcaLingam class and is accessible only within the class itself. It is initialized as an empty matrix during the construction of an instance of the IcaLingam algorithm.
    To retrieve the estimated B matrix generated by the algorithm, use the getBHat() method. This method returns a reference to the bHat variable, allowing access to the estimated B matrix.
- Class edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.IcaLingD
  
  class IcaLingD extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    stableBHats
    
    List<Matrix> stableBHats
    
    A list of stable B matrices generated by the algorithm.
    
    See Also:
    
    Matrix
    
    stableGraphs
    
    List<Graph> stableGraphs
    
    The stableGraphs variable represents a list of stable graphs generated by the algorithm. A stable graph is a directed graph that satisfies certain criteria and is considered to be a valid result of the algorithm. The list is implemented using the ArrayList class from the Java Collections Framework. The elements in the list are of type Graph, which represents a directed graph.
    The stableGraphs variable is a private member of the IcaLingD class and is accessible only within the class itself. It is initialized as an empty list during the construction of an instance of the IcaLingD algorithm.
    To retrieve the list of stable graphs generated by the algorithm, use the getStableGraphs() method. This method returns a reference to the stableGraphs variable, allowing access to the list of stable graphs.
    
    unstableBHats
    
    List<Matrix> unstableBHats
    
    Represents a list of unstable B matrices generated by the algorithm.
    
    unstableGraphs
    
    List<Graph> unstableGraphs
    
    Private variable to store a list of unstable graphs.
    This variable is used in the IcaLingD class to store a list of unstable graphs generated by the algorithm.
    
    See Also:
    
    IcaLingD
Package edu.cmu.tetrad.algcomparison.algorithm.multi
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated
  
  class FaskConcatenated extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskLofsConcatenated
  
  class FaskLofsConcatenated extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    rule
    
    Lofs.Rule rule
    
    The rule to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FaskVote
  
  class FaskVote extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FasLofs
  
  class FasLofs extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    rule
    
    Lofs.Rule rule
    
    The rule to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FciIod
  
  class FciIod extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.FgesConcatenated
  
  class FgesConcatenated extends Object implements Serializable
  
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  - Serialized Fields
    
    compareToTrue
    
    boolean compareToTrue
    
    True if the result should be compared to the true graph, false if to the CPDAG of the true graph.
    
    externalGraph
    
    Algorithm externalGraph
    
    The external graph.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.Images
  
  class Images extends Object implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.multi.ImagesBoss
  
  class ImagesBoss extends Object implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
Package edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss
  
  class Boss extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cpc
  
  class Cpc extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Cstar
  
  class Cstar extends Object implements Serializable
  
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  - Serialized Fields
    
    records
    
    LinkedList<Cstar.Record> records
    
    The records.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas
  
  class Fas extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges
  
  class Fges extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMb
  
  class FgesMb extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    targets
    
    List<Node> targets
    
    The targets.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FgesMeasurement
  
  class FgesMeasurement extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Grasp
  
  class Grasp extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pc
  
  class Pc extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Pcd
  
  class Pcd extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMax
  
  class PcMax extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.PcMb
  
  class PcMb extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    targets
    
    List<Node> targets
    
    The targets.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.RestrictedBoss
  
  class RestrictedBoss extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg
  
  class SingleGraphAlg extends Object implements Serializable
  
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  - Serialized Fields
    
    graph
    
    Graph graph
    
    The graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Sp
  
  class Sp extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
Package edu.cmu.tetrad.algcomparison.algorithm.oracle.pag
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.BossDot
  
  class BossDot extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.BossFci
  
  class BossFci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd
  
  class Ccd extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Cfci
  
  class Cfci extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.DmFcit
  
  class DmFcit extends AbstractBootstrapAlgorithm implements Serializable
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.DmFciT2
  
  class DmFciT2 extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.DmPc
  
  class DmPc extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fci
  
  class Fci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FciMax
  
  class FciMax extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Fcit
  
  class Fcit extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.FgesFci
  
  class FgesFci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci
  
  class Gfci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.GraspFci
  
  class GraspFci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci
  
  class PagSampleRfci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge
    
    test
    
    IndependenceWrapper test
    
    The probabilistic test
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Rfci
  
  class Rfci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    Represents the knowledge variable. This variable stores the knowledge associated with the given algorithm. The type of the variable is Knowledge.
    
    See Also:
    
    Knowledge
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc
  
  class RfciBsc extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    Knowledge
    
    test
    
    IndependenceWrapper test
    
    Independence test; must the ProbabilisticTest.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SpFci
  
  class SpFci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence wrapper used for testing the independence between variables in a dataset.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarFci
  
  class SvarFci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    Represents the private variable `knowledge` in the class `SvarFci`.
    This variable stores the knowledge used by the `SvarFci` algorithm. The type of `knowledge` is `Knowledge`.
    
    See Also:
    
    SvarFci
    
    Knowledge
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
- Class edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.SvarGfci
  
  class SvarGfci extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
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  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    score
    
    ScoreWrapper score
    
    The score to use.
    
    test
    
    IndependenceWrapper test
    
    The independence test to use.
Package edu.cmu.tetrad.algcomparison.algorithm.other
- Class edu.cmu.tetrad.algcomparison.algorithm.other.FactorAnalysis
  
  class FactorAnalysis extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.algorithm.other.Glasso
  
  class Glasso extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
Package edu.cmu.tetrad.algcomparison.algorithm.pairwise
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Eb
  
  class Eb extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.FaskPw
  
  class FaskPw extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R1
  
  class R1 extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R2
  
  class R2 extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.R3
  
  class R3 extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Rskew
  
  class Rskew extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.RskewE
  
  class RskewE extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Skew
  
  class Skew extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.SkewE
  
  class SkewE extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
- Class edu.cmu.tetrad.algcomparison.algorithm.pairwise.Tanh
  
  class Tanh extends AbstractBootstrapAlgorithm implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    algorithm
    
    Algorithm algorithm
    
    The algorithm to use for the initial graph.
    
    externalGraph
    
    Graph externalGraph
    
    The external graph.
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
    
    The graph to be used.
Package edu.cmu.tetrad.algcomparison.independence
- Class edu.cmu.tetrad.algcomparison.independence.BasisFunctionLrt
  
  class BasisFunctionLrt 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.FisherZ
  
  class FisherZ 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.MSeparationTest
  
  class MSeparationTest extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    graph
    
    Graph graph
    
    The true 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.PoissonBicTest
  
  class PoissonBicTest extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.independence.ProbabilisticTest
  
  class ProbabilisticTest extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.independence.SemBicTest
  
  class SemBicTest extends Object implements Serializable
  
  serialVersionUID:
  
  23L
Package edu.cmu.tetrad.algcomparison.score
- Class edu.cmu.tetrad.algcomparison.score.BasisFunctionBicScore
  
  class BasisFunctionBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.BdeuScore
  
  class BdeuScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore
  
  class ConditionalGaussianBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.DegenerateGaussianBicScore
  
  class DegenerateGaussianBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.DiscreteBicScore
  
  class DiscreteBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.EbicScore
  
  class EbicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.GicScores
  
  class GicScores extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.MagDgBicScore
  
  class MagDgBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.MSepScore
  
  class MSepScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
    
    graph
    
    Graph graph
    
    The 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
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.SemBicScore
  
  class SemBicScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
- Class edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore
  
  class ZhangShenBoundScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataModel dataSet
    
    The data set.
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
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    im
    
    BayesIm im
    
    The Bayes IM.
    
    ims
    
    List<BayesIm> ims
    
    The Bayes IMs.
    
    pm
    
    BayesPm pm
    
    The Bayes PM.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
- Class edu.cmu.tetrad.algcomparison.simulation.CausalPerceptronNetwork
  
  class CausalPerceptronNetwork extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph generator.
- Class edu.cmu.tetrad.algcomparison.simulation.ConditionalGaussianSimulation
  
  class ConditionalGaussianSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    coefHigh
    
    double coefHigh
    
    The high coefficient.
    
    coefLow
    
    double coefLow
    
    The low coefficient.
    
    coefSymmetric
    
    boolean coefSymmetric
    
    Whether coefficients should be drawn equally from positive or negative values.
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    dataType
    
    DataType dataType
    
    The data type.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    meanHigh
    
    double meanHigh
    
    The high mean for variables.
    
    meanLow
    
    double meanLow
    
    The low mean for variables.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    shuffledOrder
    
    List<Node> shuffledOrder
    
    The shuffled order.
    
    varHigh
    
    double varHigh
    
    The high variance.
    
    varLow
    
    double varLow
    
    The low variance.
- Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulation
  
  class GeneralSemSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    im
    
    GeneralizedSemIm im
    
    Represents the GeneralizedSemIm object used for simulation.
    
    ims
    
    List<GeneralizedSemIm> ims
    
    The SEM IMs.
    
    pm
    
    GeneralizedSemPm pm
    
    The SEM PM.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
- Class edu.cmu.tetrad.algcomparison.simulation.GeneralSemSimulationSpecial1
  
  class GeneralSemSimulationSpecial1 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The graphs.
    
    graphs
    
    List<Graph> graphs
    
    The data sets.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
- Class edu.cmu.tetrad.algcomparison.simulation.GpSemSimulation
  
  class GpSemSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
- Class edu.cmu.tetrad.algcomparison.simulation.LeeHastieSimulation
  
  class LeeHastieSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    dataType
    
    DataType dataType
    
    The data type.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    shuffledOrder
    
    List<Node> shuffledOrder
    
    The shuffled order.
- Class edu.cmu.tetrad.algcomparison.simulation.LgMnarSimulation
  
  class LgMnarSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph generator.
- Class edu.cmu.tetrad.algcomparison.simulation.LinearFisherModel
  
  class LinearFisherModel extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    shocks
    
    List<DataModel> shocks
    
    The shocks.
- Class edu.cmu.tetrad.algcomparison.simulation.LinearSineSimulation
  
  class LinearSineSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    betaHigh
    
    double betaHigh
    
    The beta high.
    
    betaLow
    
    double betaLow
    
    The beta low.
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    dataType
    
    DataType dataType
    
    The data type.
    
    gammaHigh
    
    double gammaHigh
    
    The gamma high.
    
    gammaLow
    
    double gammaLow
    
    The gamma low.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    interceptHigh
    
    double interceptHigh
    
    The intercept high.
    
    interceptLow
    
    double interceptLow
    
    The intercept low.
    
    linearHigh
    
    double linearHigh
    
    The linear high.
    
    linearLow
    
    double linearLow
    
    The linear low.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    shuffledOrder
    
    List<Node> shuffledOrder
    
    The shuffled order.
    
    varHigh
    
    double varHigh
    
    The var high.
    
    varLow
    
    double varLow
    
    The var low.
- Class edu.cmu.tetrad.algcomparison.simulation.NonlinearAdditiveNoiseModel
  
  class NonlinearAdditiveNoiseModel extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph generator.
- Class edu.cmu.tetrad.algcomparison.simulation.NonlinearFunctionsOfLinear
  
  class NonlinearFunctionsOfLinear extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph generator.
- Class edu.cmu.tetrad.algcomparison.simulation.PostnonlinearCausalModel
  
  class PostnonlinearCausalModel extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph generator.
- Class edu.cmu.tetrad.algcomparison.simulation.SemSimulation
  
  class SemSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    im
    
    SemIm im
    
    Represents a SemIm object used for simulation.
    
    ims
    
    List<SemIm> ims
    
    The SEM IMs.
    
    pm
    
    SemPm pm
    
    The SEM PM.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
- Class edu.cmu.tetrad.algcomparison.simulation.SemThenDiscretize
  
  class SemThenDiscretize extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    dataType
    
    DataType dataType
    
    The data type.
    
    graphs
    
    List<Graph> graphs
    
    The data sets.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    shuffledOrder
    
    List<Node> shuffledOrder
    
    The shuffled order.
- Class edu.cmu.tetrad.algcomparison.simulation.Simulations
  
  class Simulations extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    simulations
    
    List<Simulation> simulations
    
    The simulations.
- Class edu.cmu.tetrad.algcomparison.simulation.SingleDatasetSimulation
  
  class SingleDatasetSimulation extends Object implements Serializable
  - Serialized Fields
    
    dataSet
    
    DataSet dataSet
    
    The dataSet variable represents a single supplied data set.
- Class edu.cmu.tetrad.algcomparison.simulation.StandardizedSemSimulation
  
  class StandardizedSemSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    pm
    
    SemPm pm
    
    The SEM PM.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
    
    standardizedIm
    
    StandardizedSemIm standardizedIm
    
    The SEM IM.
- Class edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation
  
  class TimeSeriesSemSimulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The data sets.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge.
    
    randomGraph
    
    RandomGraph randomGraph
    
    The random graph.
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
    
    Whether to precompute covariances.
- Class edu.cmu.tetrad.algcomparison.statistic.BicDiffPerRecord
  
  class BicDiffPerRecord extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    precomputeCovariances
    
    boolean precomputeCovariances
    
    Whether to precompute covariances.
- Class edu.cmu.tetrad.algcomparison.statistic.BicEst
  
  class BicEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    precomputeCovariances
    
    boolean precomputeCovariances
    
    Whether to precompute covariances.
- Class edu.cmu.tetrad.algcomparison.statistic.BicTrue
  
  class BicTrue extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    precomputeCovariances
    
    boolean precomputeCovariances
    
    Whether to precompute covariances.
- 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.FBetaAdj
  
  class FBetaAdj extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    beta
    
    double beta
    
    The beta parameter.
- Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderAlternative
  
  class FractionDependentUnderAlternative extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    alpha
    
    double alpha
    
    The significance level for the independence tests.
- Class edu.cmu.tetrad.algcomparison.statistic.FractionDependentUnderNull
  
  class FractionDependentUnderNull extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    alpha
    
    double alpha
    
    The significance level.
- Class edu.cmu.tetrad.algcomparison.statistic.GraphExactlyRight
  
  class GraphExactlyRight extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.IdaAverageSquaredDistance
  
  class IdaAverageSquaredDistance extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    semIm
    
    SemIm semIm
    
    The true SEM IM. This stat can only be used if the true SEM IM is known.
- Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgMaxSquaredDiffEstTrue
  
  class IdaCheckAvgMaxSquaredDiffEstTrue extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgMinSquaredDiffEstTrue
  
  class IdaCheckAvgMinSquaredDiffEstTrue extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.IdaCheckAvgSquaredDifference
  
  class IdaCheckAvgSquaredDifference extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.IdaMaximumSquaredDifference
  
  class IdaMaximumSquaredDifference extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    semIm
    
    SemIm semIm
    
    The true SEM IM. This stat can only be used if the true SEM IM is known.
- Class edu.cmu.tetrad.algcomparison.statistic.IdaMinimumSquaredDifference
  
  class IdaMinimumSquaredDifference extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    semIm
    
    SemIm semIm
    
    The true SEM IM. This stat can only be used if the true SEM IM is known.
- Class edu.cmu.tetrad.algcomparison.statistic.ImpliedArrowOrientationRatioEst
  
  class ImpliedArrowOrientationRatioEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.ImpliedArrowOrientationRatioEst2
  
  class ImpliedArrowOrientationRatioEst2 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.ImpliedOrientationRatioEst
  
  class ImpliedOrientationRatioEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.ImpliesLegalMag
  
  class ImpliesLegalMag extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.KnowledgeSatisfied
  
  class KnowledgeSatisfied extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The `knowledge` variable represents a knowledge object. This variable is a private member of the `KnowledgeSatisfied` class, which implements the `Statistic` and `HasKnowledge` interfaces. It is used to measure whether the provided knowledge is satisfied for the estimated graph. It is initially set to `null`.
    
    See Also:
    
    KnowledgeSatisfied
    
    Statistic
    
    HasKnowledge
- 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.LegalCpdag
  
  class LegalCpdag 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.LocalGraphPrecision
  
  class LocalGraphPrecision extends Object implements Serializable
- Class edu.cmu.tetrad.algcomparison.statistic.LocalGraphRecall
  
  class LocalGraphRecall extends Object implements Serializable
- Class edu.cmu.tetrad.algcomparison.statistic.MagCgScore
  
  class MagCgScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.MagDgScore
  
  class MagDgScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.MagSemScore
  
  class MagSemScore extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAdPasses
  
  class MarkovCheckAdPasses extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Represents the type of conditioning set to be used in Markov checks for evaluating independence relationships in a graph or data set. The conditioning set determines which variables are conditioned on during independence tests, influencing the nature and scope of the independence facts being tested. This variable works in conjunction with IndependenceWrapper to perform statistical evaluations related to Markov property testing. Its specific type is defined by the ConditioningSetType enum, which provides various options such as GLOBAL_MARKOV, LOCAL_MARKOV, and others, each corresponding to a particular approach to selecting the conditioning set.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Provides an interface to independence tests for evaluating conditional independence relationships in a data set. It is used as a dependency for statistical computations and Markov checks within the containing class.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAdPassesBestOf10
  
  class MarkovCheckAdPassesBestOf10 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Represents the type of conditioning set employed during the Markov check for evaluating conditional independence relationships in a graph. The selected conditioning set type influences how variables are conditioned upon in independence tests.
    This variable is used to configure the scope and basis of the tests, providing flexibility to support various methodologies, such as local Markov properties or global Markov properties.
    Possible values are enumerated in the ConditioningSetType enum and include options such as GLOBAL_MARKOV, LOCAL_MARKOV, PARENTS_AND_NEIGHBORS, and others.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of IndependenceWrapper used to evaluate conditional independence relationships in a given data set. This object encapsulates the logic required for independence tests along with relevant parameters and descriptions of the data type being tested.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAndersonDarlingP
  
  class MarkovCheckAndersonDarlingP extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set employed during Markov checks. This variable determines how variables are conditioned in independence tests and is represented by the ConditioningSetType enumeration. The chosen conditioning set type dictates the methodology used to test for independence relationships in the context of graphical models.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Encapsulates and facilitates the execution of independence tests on datasets with specific configurations. This variable serves as a key component in determining dependencies or independencies among variables in statistical models, especially during the computation of the Markov check and Anderson-Darling P-value.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckAndersonDarlingPBestOf10
  
  class MarkovCheckAndersonDarlingPBestOf10 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used for Markov checks in statistical tests. This variable determines how the independence tests are conducted, influencing the set of variables considered to condition on when evaluating independence relationships in a graph.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of the IndependenceWrapper interface, which provides methods to assess statistical independence relationships in datasets. This wrapper is used in conjunction with various tests to evaluate dependencies and supports the execution of algorithms that rely on independence test results. Its specific implementation determines the behavior of the test and the parameters required for its execution.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckBinomialP
  
  class MarkovCheckBinomialP extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used for the Markov check in statistical evaluations. The conditioning set determines which variables are conditioned on when testing for independence or dependence among variables in a graph. It impacts the way independence facts are tested and interpreted, particularly in the context of causal modeling. Different types of conditioning sets correspond to distinct independence testing strategies, such as global or local tests.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Encapsulates an instance of an IndependenceWrapper, which provides methods to perform independence tests, retrieve test descriptions, manage data type requirements, and obtain associated parameters. This variable is central in conducting independence testing within the context of statistical evaluation for algorithms.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckBinomialPBestOf10
  
  class MarkovCheckBinomialPBestOf10 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used in the Markov check to assess conditional independence relationships within the graph. The conditioning set determines the subset of variables to condition on during independence testing, which impacts how independence and dependence relationships are evaluated based on the causal structure of the graph.
    This variable is integral to configuring the statistical computation of independence facts in the MarkovCheckBinomialPBestOf10 class.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Wrapper for independence tests used in statistical computations. This field represents the specific implementation of the IndependenceWrapper interface that supplies methods for determining independence between variables, describing the type of data involved, and retrieving test parameters.
    It is used to calculate statistical measures and perform conditional independence tests based on provided data and parameters.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckFractionDependentH0
  
  class MarkovCheckFractionDependentH0 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    The type of conditioning set used within the MarkovCheckFractionDependentH0 class to specify the approach for determining conditioning sets in statistical independence tests during Markov checks. This variable defines the strategy applied for selecting the conditioning sets, impacting how independence facts are tested and inferred. The selected ConditioningSetType determines how the contextual dependencies or independencies in a graph model are analyzed, as described by the available options in the ConditioningSetType enumeration.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of IndependenceWrapper that provides access to independence tests and related functionality for evaluating statistical independence in a dataset. Used as part of the Markov check process to determine if the p-values for an estimated graph are uniformly distributed.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckFractionDependentH1
  
  class MarkovCheckFractionDependentH1 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Represents the type of conditioning set used in the Markov check. This variable determines the strategy for selecting the set of variables to condition on when performing independence tests. The choice of conditioning set type impacts the interpretation of the independence or dependence facts discovered during the analysis.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Encapsulates an independence test and provides methods for accessing it based on the given data model and parameters. This wrapper abstracts different types of independence tests, making them accessible through a unified interface.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKolmogorovSmirnoffP
  
  class MarkovCheckKolmogorovSmirnoffP extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used in the Markov check. Determines how independence tests are conducted based on the graph structure by conditioning on a specific set of variables. The choice of the conditioning set type impacts the assessment of conditional independence and derived dependencies. This field is immutable and initialized during the instantiation of the MarkovCheckKolmogorovSmirnoffP class.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of the IndependenceWrapper interface that encapsulates the independence test logic. Used for generating and applying independence tests within the context of statistical calculations. The independenceWrapper field supplies a way to determine whether variables in data are independent, conditional on a provided conditioning set, and produces relevant test results.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKolmogorovSmirnoffPBestOf10
  
  class MarkovCheckKolmogorovSmirnoffPBestOf10 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set to be used for the Markov check in calculations. The conditioning set determines how independence facts are tested and is defined by the ConditioningSetType enum.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of the IndependenceWrapper interface used for conducting independence tests. This variable is critical for determining whether variables in a dataset are independent based on specified conditions. It enables the evaluation of statistical independence necessary for assessing the structure of causal graphs and for the execution of Markov-related validation checks.
    IndependenceWrapper provides methods for obtaining independence tests, retrieving test descriptions, handling parameter requirements, and verifying the compatibility of data types used for independence assessments. This interface serves as a foundational component in algorithms implementing statistical structure learning and evaluation.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKsPasses
  
  class MarkovCheckKsPasses extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used to evaluate conditional independence relationships during statistical tests in the Markov check process.
    The conditioning set determines the set of variables used in independence tests, impacting the assumptions made and the results of the Markov check. Different ConditioningSetTypes correspond to varying definitions of variable dependencies and independence implied by the graph, ranging from global to local contexts.
    This variable plays a critical role in selecting the appropriate conditioning technique to align with the statistical model under analysis.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of IndependenceWrapper used to encapsulate an independence testing algorithm for evaluating conditional independence relationships in statistical models.
    The IndependenceWrapper is responsible for performing independence tests, retrieving test descriptions, determining the required data types, and managing algorithm-specific parameters.
- Class edu.cmu.tetrad.algcomparison.statistic.MarkovCheckKsPassesBestOf10
  
  class MarkovCheckKsPassesBestOf10 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Represents the type of conditioning set used during the Markov checks in the context of statistical dependence testing. It specifies how variables are conditioned upon during independence tests and directly influences the results of the Markov checks. The type is defined by the ConditioningSetType enumeration, which includes various strategies for defining the conditioning set, such as GLOBAL_MARKOV, LOCAL_MARKOV, or MARKOV_BLANKET among others. This field is immutable and must be set during the initialization of the object.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of IndependenceWrapper used to encapsulate and perform independence tests on the dataset with specific configurations. This variable is intended to facilitate independence testing within the context of Markov check calculations and other statistical operations in the enclosing class.
- 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.Maximal
  
  class Maximal 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.McGetNumTestsH0
  
  class McGetNumTestsH0 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set to use when calculating independence tests within the context of the Markov check. This variable determines the approach used for conditioning on variables in the graph during statistical analysis.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    Encapsulates an implementation of the IndependenceWrapper interface used to perform independence tests on a dataset. This wrapper provides the ability to retrieve a specific implementation of the IndependenceTest depending on the given data model and test parameters.
    The independenceWrapper is used to integrate independence testing logic into classes that require customizable or interchangeable independence test implementations, such as the determination of conditional independence relationships in statistical models or algorithms.
- Class edu.cmu.tetrad.algcomparison.statistic.McGetNumTestsH1
  
  class McGetNumTestsH1 extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    conditioningSetType
    
    ConditioningSetType conditioningSetType
    
    Specifies the type of conditioning set used in the Markov check for evaluating independence or dependence relationships. This variable is associated with the configuration of the independence tests and determines how the conditioning set is constructed based on the selected type from the ConditioningSetType enum. The conditioning set influences the statistical properties of the independence tests performed during Markov checks.
    
    independenceWrapper
    
    IndependenceWrapper independenceWrapper
    
    An instance of the IndependenceWrapper interface used to perform independence tests in the context of statistical computations and graph evaluations. It provides the necessary methods to retrieve and configure independence tests, as well as to obtain a description of the specific independence testing algorithm being employed.
- Class edu.cmu.tetrad.algcomparison.statistic.NoAlmostCyclicPathsCondition
  
  class NoAlmostCyclicPathsCondition 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.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.NumberArrowsEst
  
  class NumberArrowsEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberArrowsNotInUnshieldedCollidersEst
  
  class NumberArrowsNotInUnshieldedCollidersEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberCollidersEst
  
  class NumberCollidersEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesEst
  
  class NumberEdgesEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesInCollidersEst
  
  class NumberEdgesInCollidersEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesInUnshieldedCollidersEst
  
  class NumberEdgesInUnshieldedCollidersEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberEdgesTrue
  
  class NumberEdgesTrue 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.NumberTailsEst
  
  class NumberTailsEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumberUnshieldedCollidersEst
  
  class NumberUnshieldedCollidersEst 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.NumCompatibleVisibleNonancestors
  
  class NumCompatibleVisibleNonancestors extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumCorrectBidirected
  
  class NumCorrectBidirected 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.NumCorrectVisibleEdges
  
  class NumCorrectVisibleEdges extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumCoveringAdjacenciesInPag
  
  class NumCoveringAdjacenciesInPag 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.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.NumEdgeInEstInTrue
  
  class NumEdgeInEstInTrue extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumGenuineAdjacenciesInPag
  
  class NumGenuineAdjacenciesInPag 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.NumParametersEst
  
  class NumParametersEst 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.NumVisibleEdgeEst
  
  class NumVisibleEdgeEst extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEdges
  
  class NumVisibleEdges extends Object implements Serializable
  
  serialVersionUID:
  
  23L
- Class edu.cmu.tetrad.algcomparison.statistic.NumVisibleEdgeTrue
  
  class NumVisibleEdgeTrue 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
    
    The name of the parameter to list. If this parameter does not exist, '*' is output.
- 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
    
    The significance level for the independence tests.
- Class edu.cmu.tetrad.algcomparison.statistic.PvalueUniformityUnderNull
  
  class PvalueUniformityUnderNull extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    alpha
    
    double alpha
    
    The significance level for the independence tests.
- 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.Statistics
  
  class Statistics extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    statistics
    
    List<Statistic> statistics
    
    The list of statistics.
    
    weights
    
    Map<Statistic,Double> weights
    
    The utility weights for the statistics.
- Class edu.cmu.tetrad.algcomparison.statistic.StructuralHammingDistance
  
  class StructuralHammingDistance extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    compareToCpdag
    
    boolean compareToCpdag
    
    Indicates whether the Structural Hamming Distance (SHD) calculation should be based on the CPDAG (Completed Partially Directed Acyclic Graph) form of the true graph rather than its original PDAG (Partially Directed Acyclic Graph) form. When set to true, the SHD computation compares the estimated graph to the CPDAG of the true graph; otherwise, it compares the estimated graph to the true PDAG.
- 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
    
    AnnotatedClass represents a class along with its associated annotation.
    
    clazz
    
    Class<?> clazz
    
    Represents a Class used as a parameter to an AnnotatedClass object. It is stored as a private final member in the AnnotatedClass class.
    Example usage:
    
    AnnotatedClass<MyAnnotation> annotatedClass = new AnnotatedClass<>(MyClass.class, myAnnotation); Class<?> clazz = annotatedClass.clazz();
    
    See Also:
    
    AnnotatedClass
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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    Represents a variable of the BayesIm class.
    
    variables
    
    List<Node> variables
    
    Represents a list of nodes.
- Class edu.cmu.tetrad.bayes.BayesPm
  
  class BayesPm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The Bayes net.
    
    evidence
    
    Evidence evidence
    
    The evidence.
    
    storedMarginals
    
    double[][] storedMarginals
    
    The stored marginals.
    
    updatedBayesIm
    
    UpdatedBayesIm updatedBayesIm
    
    The updated Bayes net.
- Class edu.cmu.tetrad.bayes.CptInvariantUpdater
  
  class CptInvariantUpdater extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.CptMapCounts
  
  class CptMapCounts extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    cellCounts
    
    Map<Integer,Integer> cellCounts
    
    Constructs a new count map, a map from a unique integer index for a particular node to the count for that value, where 0's are not stored.
    
    numColumns
    
    int numColumns
    
    The number of columns in the table.
    
    numRows
    
    int numRows
    
    The number of rows in the table.
    
    priorCount
    
    double priorCount
    
    The prior count for all cells. '0' is maximimum likelihood estimate.
    
    rowCounts
    
    Map<Integer,Integer> rowCounts
    
    Constructs a new row count map, a map from a unique integer index for a particular node to the count for that row, where 0's are not stored.
- Class edu.cmu.tetrad.bayes.CptMapProbs
  
  class CptMapProbs extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    map
    
    Map<Integer,Double> map
    
    Constructs a new probability map, a map from a unique integer index for a particular node to the probability of that node taking on that value, where NaN's are not stored.
    
    numColumns
    
    int numColumns
    
    The number of columns in the table.
    
    numRows
    
    int numRows
    
    The number of rows in the table.
- Class edu.cmu.tetrad.bayes.DirichletBayesIm
  
  class DirichletBayesIm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
- Class edu.cmu.tetrad.bayes.Identifiability
  
  class Identifiability extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The BayesIm which this updater modifies.
    
    debug
    
    boolean debug
    
    The last manipulated BayesIm.
    
    evidence
    
    Evidence evidence
    
    Stores evidence for all variables.
    
    manipulatedBayesIm
    
    BayesIm manipulatedBayesIm
    
    The last manipulated BayesIm.
- Class edu.cmu.tetrad.bayes.JunctionTreeAlgorithm
  
  class JunctionTreeAlgorithm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The BayesIm.
    
    bayesPm
    
    BayesPm bayesPm
    
    The BayesPm.
    
    graphNodes
    
    Node[] graphNodes
    
    The nodes in the graph.
    
    margins
    
    double[][] margins
    
    The marginal probabilities of the nodes.
    
    maxCardOrdering
    
    Node[] maxCardOrdering
    
    The maximum cardinality ordering of the nodes.
    
    root
    
    edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode root
    
    The root of the junction tree.
    
    treeNodes
    
    Map<Node,edu.cmu.tetrad.bayes.JunctionTreeAlgorithm.TreeNode> treeNodes
    
    The tree nodes.
- Class edu.cmu.tetrad.bayes.JunctionTreeUpdater
  
  class JunctionTreeUpdater extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The BayesIm which this updater modifies.
    
    evidence
    
    Evidence evidence
    
    Stores evidence for all variables.
    
    jta
    
    JunctionTreeAlgorithm jta
    
    Calculates probabilities from the manipulated Bayes IM.
    
    manipulatedBayesIm
    
    BayesIm manipulatedBayesIm
    
    The last manipulated BayesIm.
    
    updatedBayesIm
    
    BayesIm updatedBayesIm
    
    The BayesIm after update, if this was calculated.
- Class edu.cmu.tetrad.bayes.Manipulation
  
  class Manipulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    manipulated
    
    boolean[] manipulated
    
    An array indicating whether each variable in turn is manipulated.
    
    variableSource
    
    VariableSource variableSource
    
    The variable source for which this manipulation is defined.
- Class edu.cmu.tetrad.bayes.MlBayesIm
  
  class MlBayesIm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesPm
    
    BayesPm bayesPm
    
    The associated Bayes PM model.
    
    cptMapType
    
    MlBayesIm.CptMapType cptMapType
    
    The type of CPT map used to store the probabilities.
    
    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.
    
    probMatrices
    
    CptMap[] probMatrices
    
    The array of CPT maps for each node. The index of the node corresponds to the index of the probability map in this array. Replaces the probs array.
    
    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.
    This is kept here for backward compatibility. The new way of storing the probabilities is in the probMatrices array.
- Class edu.cmu.tetrad.bayes.MlBayesImObs
  
  class MlBayesImObs extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bayesImObs
    
    BayesIm bayesImObs
    
    BayesIm containing only the observed variables. Only used to 1) construct propositions (mapped from the original allowUnfaithfulness bayesIm) in Identifiability 2) to avoid summing over rows in jpd when only the latent variables have changed values (only sum when all the latent variables have value 0) This is a MlBayesIm instead of a MlBayesImObs because otherwise there will be an infinite loop attempting to creating the MlBayesImObs
    
    bayesImRandomize
    
    BayesIm bayesImRandomize
    
    a regular MlBayesIm used to create randomized CPDs so that the values can be marginalized to a consistent observed jpd
    
    bayesPm
    
    BayesPm bayesPm
    
    The associated Bayes PM model.
    
    jpd
    
    StoredCellProbsObs jpd
    
    joint probability table
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    allowedCategories
    
    boolean[][] allowedCategories
    
    An array indicating whether each category for each variable is allowed.
    
    variableSource
    
    VariableSource variableSource
    
    The Bayes IM that this is a proposition for.
- 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The BayesIm which this updater modifies.
    
    bayesImProbs
    
    BayesImProbs bayesImProbs
    
    Calculates probabilities from the manipulated Bayes IM.
    
    evidence
    
    Evidence evidence
    
    Stores evidence for all variables.
    
    manipulatedBayesIm
    
    BayesIm manipulatedBayesIm
    
    The last manipulated BayesIm.
    
    updatedBayesIm
    
    BayesIm updatedBayesIm
    
    The BayesIm after update, if this was calculated.
- Class edu.cmu.tetrad.bayes.StoredCellProbs
  
  class StoredCellProbs extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    parentDims
    
    int[] parentDims
    
    The parent dimensions of the table.
    
    probs
    
    double[] probs
    
    The cell probabilities.
    
    variables
    
    List<Node> variables
    
    The variables for which this table stores cell probabilities.
- Class edu.cmu.tetrad.bayes.StoredCellProbsObs
  
  class StoredCellProbsObs extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    parentDims
    
    int[] parentDims
    
    The number of values for each parent.
    
    probs
    
    double[] probs
    
    The probabilities.
    
    variables
    
    List<Node> variables
    
    The variables for which the cell probabilities are stored.
- 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.
    
    Parameters:
    
    s - a ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - 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.
    
    bayesIm
    
    BayesIm bayesIm
    
    The wrapped BayesIm. Unmodified conditional probability values will be retrieved from here.
    
    changedProbs
    
    double[][][] changedProbs
    
    Stores probs that change with respect to the underlying bayesIm, calculated on the fly.
    
    evidence
    
    Evidence evidence
    
    The evidence updated on.
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
    
    The function name.
    
    signature
    
    String signature
    
    The signature string.
- 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 Class 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.)
    
    Parameters:
    
    s - The input stream.
    
    Throws:
    
    IOException - If an IO error occurs.
    
    ClassNotFoundException - If a class is not found.
  - Serialized Fields
    
    bayesIm
    
    BayesIm bayesIm
    
    The BayesIm instance used to create an updater. Supplied as an argument to the constructor.
    
    bayesImVars
    
    List<Node> bayesImVars
    
    The variables in the dataset to be classified. These should be the same variables as in the training dataset according to the "equals" method of DiscreteVariable.
    
    classifications
    
    int[] classifications
    
    The classifications of the target variable.
    
    marginals
    
    double[][] marginals
    
    The marginals.
    
    numCases
    
    int numCases
    
    The number of cases in the dataset.
    
    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
    
    The number of usable cases in the dataset.
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.
    
    selectionBias
    
    boolean selectionBias
    
    True just in case this node is a selection bias node.
- Class edu.cmu.tetrad.data.BoxDataSet
  
  class BoxDataSet extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    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.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    breakpoints
    
    double[] breakpoints
    
    Breakpoints, for continuous data.
    
    categories
    
    List<String> categories
    
    Categories, for discrete data.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    attributes
    
    Map<String,Object> attributes
    
    The node type.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    cov
    
    ICovarianceMatrix cov
    
    The covariance matrix. Cannot be null. Must be symmetric and positive definite.
    
    variables
    
    List<Node> variables
    
    The variables (in order) for this covariance matrix.
    
    verbose
    
    boolean verbose
    
    Whether to print out verbose messages.
- Class edu.cmu.tetrad.data.CovarianceMatrix
  
  class CovarianceMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    _covariancesMatrix
    
    Matrix _covariancesMatrix
    
    The wrapped covariance matrix data.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge for this data.
    
    name
    
    String name
    
    The name of the covariance matrix.
    
    sampleSize
    
    int sampleSize
    
    The size of the sample from which this covariance matrix was calculated.
    
    selectedVariables
    
    Set<Node> selectedVariables
    
    The list of selected variables.
    
    variables
    
    List<Node> variables
    
    The variables (in order) for this covariance matrix.
- Class edu.cmu.tetrad.data.CovarianceMatrixOnTheFly
  
  class CovarianceMatrixOnTheFly extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge for this data.
    
    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.
    
    name
    
    String name
    
    The name of the covariance matrix.
    
    sampleSize
    
    int sampleSize
    
    The size of the sample from which this covariance matrix was calculated.
    
    selectedVariables
    
    Set<Node> selectedVariables
    
    The list of selected variables.
    
    variables
    
    List<Node> variables
    
    The variables (in order) for this covariance matrix.
    
    variances
    
    double[] variances
    
    The variances of the variables.
    
    vectors
    
    double[][] vectors
    
    The vectors for the variables.
    
    verbose
    
    boolean verbose
    
    Whether to print out verbose information.
- Class edu.cmu.tetrad.data.DataModelList
  
  class DataModelList extends AbstractList<DataModel> implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    readResolve
    
    Object readResolve() throws ObjectStreamException
    
    readResolve.
    
    Throws:
    
    ObjectStreamException - if any.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    ordinal
    
    int ordinal
    
    The ordinal of this type.
- Class edu.cmu.tetrad.data.DiscreteDiscretizationSpec
  
  class DiscreteDiscretizationSpec extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    categories
    
    List<String> categories
    
    Categories, for discrete data.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    Attributes of the node.
    
    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
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    readResolve
    
    Object readResolve() throws ObjectStreamException
    
    Returns the ordinal of this type.
    
    Throws:
    
    ObjectStreamException - if any.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    ordinal
    
    int ordinal
    
    The ordinal of this type.
- 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
    
    The knowledge.
    
    name
    
    String name
    
    The name of the independence facts.
    
    nodes
    
    List<Node> nodes
    
    The nodes in the graph.
    
    unsortedFacts
    
    Set<IndependenceFact> unsortedFacts
    
    The unsorted facts.
- 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
    
    The default to knowledge layout.
    
    forbiddenRulesSpecs
    
    List<OrderedPair<Set<String>>> forbiddenRulesSpecs
    
    This needs to be a list for backward compatibility. Need to check when adding a new spec whether it's already in the list.
    
    knowledgeGroupRules
    
    Map<KnowledgeGroup,OrderedPair<Set<String>>> knowledgeGroupRules
    
    The knowledge group rules.
    
    knowledgeGroups
    
    List<KnowledgeGroup> knowledgeGroups
    
    The knowledge groups.
    
    requiredRulesSpecs
    
    List<OrderedPair<Set<String>>> requiredRulesSpecs
    
    This needs to be a list for backward compatibility. Need to check when adding a new spec whether it's already in the list.
    
    tierSpecs
    
    List<Set<String>> tierSpecs
    
    The tier specs.
    
    variables
    
    Set<String> variables
    
    The variable names.
- Class edu.cmu.tetrad.data.KnowledgeEdge
  
  class KnowledgeEdge extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    from
    
    String from
    
    The tail node of the edge.
    
    to
    
    String to
    
    The head node of the edge.
- Class edu.cmu.tetrad.data.KnowledgeGroup
  
  class KnowledgeGroup extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    fromGroup
    
    Set<String> fromGroup
    
    The left group of variables.
    
    toGroup
    
    Set<String> toGroup
    
    The right group of variables.
    
    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
    
    The continuous data.
    
    discreteData
    
    int[][] discreteData
    
    The discrete data.
    
    numRows
    
    int numRows
    
    The number of rows in the dataset.
    
    variables
    
    List<Node> variables
    
    The variables in the dataset.
- Class edu.cmu.tetrad.data.NumberObjectDataSet
  
  class NumberObjectDataSet extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    columnToTooltip
    
    Map<String,String> columnToTooltip
    
    The map from column names to tooltips.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    breakpoints
    
    int[] breakpoints
    
    Breakpoints, for continuous data.
    
    sampleSize
    
    int sampleSize
    
    Sample size.
    
    splitNames
    
    List<String> splitNames
    
    Split names.
- Class edu.cmu.tetrad.data.TimeSeriesData
  
  class TimeSeriesData extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    data2
    
    Matrix data2
    
    The data.
    
    knowledge
    
    Knowledge knowledge
    
    The knowledge about the data.
    
    name
    
    String name
    
    The name of the data.
    
    varNames
    
    List<String> varNames
    
    The names of the variables.
- 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
    
    The data sets.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    path
    
    String path
    
    The path.
    
    usedParameters
    
    List<String> usedParameters
    
    The used parameters.
- Class edu.cmu.tetrad.data.simulation.LoadContinuousDataAndSingleGraph
  
  class LoadContinuousDataAndSingleGraph extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graph
    
    Graph graph
    
    The graph.
    
    parametersValues
    
    Parameters parametersValues
    
    The parameters values.
    
    path
    
    String path
    
    The path.
    
    usedParameters
    
    List<String> usedParameters
    
    The used parameters.
- Class edu.cmu.tetrad.data.simulation.LoadContinuousDataSmithSim
  
  class LoadContinuousDataSmithSim extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    graph
    
    Graph graph
    
    The graph.
    
    parametersValues
    
    Parameters parametersValues
    
    The parameters values.
    
    path
    
    String path
    
    The path.
    
    usedParameters
    
    List<String> usedParameters
    
    The used parameters.
- Class edu.cmu.tetrad.data.simulation.LoadDataAndGraphs
  
  class LoadDataAndGraphs extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSets
    
    List<DataSet> dataSets
    
    The data sets.
    
    description
    
    String description
    
    The description.
    
    graphs
    
    List<Graph> graphs
    
    The graphs.
    
    path
    
    String path
    
    The path.
    
    usedParameters
    
    List<String> usedParameters
    
    The used parameters.
- Class edu.cmu.tetrad.data.simulation.LoadDataFromFileWithoutGraph
  
  class LoadDataFromFileWithoutGraph extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    dataSet
    
    DataSet dataSet
    
    The data set.
    
    parameterValues
    
    Map<String,Object> parameterValues
    
    The parameter values.
    
    path
    
    String path
    
    The 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.)
    
    Parameters:
    
    s - The object input stream.
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The set of ambiguous triples.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The set of dotted underline triples.
    
    graph
    
    Graph graph
    
    The graph.
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The set of underline triples.
- Class edu.cmu.tetrad.graph.Edge
  
  class Edge extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    bold
    
    boolean bold
    
    Whether the edge is bold.
    
    edgeTypeProbabilities
    
    List<EdgeTypeProbability> edgeTypeProbabilities
    
    The edge type probabilities.
    
    endpoint1
    
    Endpoint endpoint1
    
    The endpoint at the first node.
    
    endpoint2
    
    Endpoint endpoint2
    
    The endpoint at the second node.
    
    highlighted
    
    boolean highlighted
    
    Whether the edge is highlighted.
    
    node1
    
    Node node1
    
    The first node.
    
    node2
    
    Node node2
    
    The second node.
    
    probability
    
    double probability
    
    The probability.
    
    properties
    
    List<Edge.Property> properties
    
    The 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.)
    
    Parameters:
    
    s - a ObjectInputStream object
    
    Throws:
    
    IOException - if any.
    
    ClassNotFoundException - if any.
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The ambiguous triples.
    
    ancestorCache
    
    Map<org.apache.commons.lang3.tuple.Pair<Node,Node>,Boolean> ancestorCache
    
    The cache for the ancestor relationships
    
    attributes
    
    Map<String,Object> attributes
    
    The attributes.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The dotted underline triples.
    
    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.
    
    parentsHash
    
    Map<Node,List<Node>> parentsHash
    
    The parents hash.
    
    semidirectedPathCache
    
    Map<org.apache.commons.lang3.tuple.Pair<Node,Node>,Boolean> semidirectedPathCache
    
    The cache for the semidirected path relationships
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The underline triples.
- Class edu.cmu.tetrad.graph.EdgeTypeProbability
  
  class EdgeTypeProbability extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    edgeType
    
    EdgeTypeProbability.EdgeType edgeType
    
    The edge type.
    
    probability
    
    double probability
    
    The probability.
    
    properties
    
    List<Edge.Property> properties
    
    The 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.
    
    Parameters:
    
    s - The input stream.
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    attributes
    
    Map<String,Object> attributes
    
    The attributes of the node.
    
    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
    
    selectionBias
    
    boolean selectionBias
    
    Whether the node is selected as a bias node.
- Class edu.cmu.tetrad.graph.IndependenceFact
  
  class IndependenceFact extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    _z
    
    Set<Node> _z
    
    The conditioning set.
    
    x
    
    Node x
    
    The first node conditioned nodes.
    
    y
    
    Node y
    
    The second conditioned node.
- Class edu.cmu.tetrad.graph.LagGraph
  
  class LagGraph extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The set of ambiguous triples.
    
    attributes
    
    Map<String,Object> attributes
    
    The map from variables to their attributes.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The set of dotted underline triples.
    
    graph
    
    Dag graph
    
    The graph.
    
    laggedVariables
    
    Map<String,List<Node>> laggedVariables
    
    The map from variables to their lagged variables.
    
    paths
    
    Paths paths
    
    The paths
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The set of underline triples.
    
    variables
    
    List<String> variables
    
    The list of variables in the getModel time lag.
- Class edu.cmu.tetrad.graph.OrderedPair
  
  class OrderedPair extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    graph
    
    Graph graph
    
    The 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.)
    
    Parameters:
    
    s - The object input stream.
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The ambiguous triples.
    
    attributes
    
    Map<String,Object> attributes
    
    The attributes of the graph.
    
    cpdag
    
    boolean cpdag
    
    True if the graph is a CPDAG.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The dotted underlines.
    
    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
    
    True if the graph is a PAG.
    
    paths
    
    Paths paths
    
    The paths of the graph.
    
    showErrorTerms
    
    boolean showErrorTerms
    
    True if error terms for exogenous terms should be shown.
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The underlines.
- Class edu.cmu.tetrad.graph.TimeLagGraph
  
  class TimeLagGraph extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The set of ambiguous triples.
    
    attributes
    
    Map<String,Object> attributes
    
    A node in a time lag graph.
    
    cpdag
    
    boolean cpdag
    
    Whether the graph is a CPDAG.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The set of dotted underlined triples.
    
    graph
    
    EdgeListGraph graph
    
    A node in a time lag graph.
    
    lag0Nodes
    
    List<Node> lag0Nodes
    
    The nodes in lag 0.
    
    maxLag
    
    int maxLag
    
    The maximum lag.
    
    numInitialLags
    
    int numInitialLags
    
    The number of initial lags.
    
    pag
    
    boolean pag
    
    Whether the graph is a PAG.
    
    paths
    
    Paths paths
    
    The paths in the graph.
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The set of underlined triples.
- Class edu.cmu.tetrad.graph.Triple
  
  class Triple extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    x
    
    Node x
    
    The first node in the triple.
    
    y
    
    Node y
    
    The second node in the triple.
    
    z
    
    Node z
    
    The third node in the triple.
- Class edu.cmu.tetrad.graph.Underlines
  
  class Underlines extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    ambiguousTriples
    
    Set<Triple> ambiguousTriples
    
    The ambiguous triples.
    
    dottedUnderLineTriples
    
    Set<Triple> dottedUnderLineTriples
    
    The dotted underlines.
    
    graph
    
    Graph graph
    
    The graph.
    
    underLineTriples
    
    Set<Triple> underLineTriples
    
    The underlines.
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.
    
    Parameters:
    
    s - a ObjectInputStream object
    
    Throws:
    
    IOException - if an error occurs
    
    ClassNotFoundException - if an error occurs
  - 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
    
    The rows in the data used for regression.
- Class edu.cmu.tetrad.regression.LogisticRegression.Result
  
  class Result extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    alpha
    
    double alpha
    
    The alpha level.
    
    chiSq
    
    double chiSq
    
    The chi square statistic.
    
    coefs
    
    double[] coefs
    
    The array of regression coefficients.
    
    intercept
    
    double intercept
    
    The intercept.
    
    logLikelihood
    
    double logLikelihood
    
    The log likelihood of the regression.
    
    numRegressors
    
    int numRegressors
    
    The number of regressors.
    
    ny0
    
    int ny0
    
    The number of cases with target = 0.
    
    ny1
    
    int ny1
    
    The number of cases with target = 1.
    
    probs
    
    double[] probs
    
    The array of coefP-values for the regression coefficients.
    
    regressorNames
    
    List<String> regressorNames
    
    The names of the regressors.
    
    stdErrs
    
    double[] stdErrs
    
    The array of standard errors for the regression coefficients.
    
    target
    
    String target
    
    The target.
    
    xMeans
    
    double[] xMeans
    
    The array of means.
    
    xStdDevs
    
    double[] xStdDevs
    
    The array of standard devs.
- Class edu.cmu.tetrad.regression.RegressionResult
  
  class RegressionResult extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    The cause node.
    
    effect
    
    double effect
    
    The minimum effect size of the predictor on the target across subsamples calculated by IDA.
    
    numCauses
    
    int numCauses
    
    The number of possible causes of the target.
    
    numEffects
    
    int numEffects
    
    The number of possible effects of the target.
    
    pi
    
    double pi
    
    The percentage of the time the predictor is a cause of the target across subsamples.
    
    target
    
    Node target
    
    The effect node.
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
    
    The graph.
    
    score
    
    Double score
    
    The score.
Package edu.cmu.tetrad.search.test
- Class edu.cmu.tetrad.search.test.IndependenceResult
  
  class IndependenceResult extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    fact
    
    IndependenceFact fact
    
    The fact itself.
    
    indep
    
    boolean indep
    
    The conditional independence result, true if the fact holds, false if not.
    
    isValid
    
    boolean isValid
    
    Whether the result is valid or not. A test is not valid if the test is not able to determine whether the fact holds or not.
    
    pValue
    
    double pValue
    
    The p-values of the independence result, under the null (independence) hypothesis.
    
    score
    
    double score
    
    The score of the test, which is alpha - p if the test returns a p-value or else a bump if the test is based on a score.
Package edu.cmu.tetrad.search.utils
- Class edu.cmu.tetrad.search.utils.AlmostCycleRemover
  
  class AlmostCycleRemover extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    B
    
    Map<Node,Set<Edge>> B
    
    A map of nodes to bidirected edges for them.
    
    M
    
    Map<Node,Set<Node>> M
    
    A map of nodes to parents oriented by triples for them.
    
    T
    
    Map<Node,Set<Triple>> T
    
    A map of nodes to triples for them.
- 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).
    
    Parameters:
    
    s - a ObjectInputStream object
    
    Throws:
    
    IOException - if an error occurs
    
    ClassNotFoundException - if an error occurs
  - Serialized Fields
    
    parents
    
    Map<Node,HashSet<Node>> parents
    
    The map from pairs of nodes to separating sets.
    
    pValues
    
    Map<Set<Node>,Double> pValues
    
    The map from pairs of nodes to p-values.
    
    sepsets
    
    Map<Set<Node>,Set<Node>> sepsets
    
    The map from pairs of nodes to separating sets.
- Class edu.cmu.tetrad.search.utils.Sextad
  
  class Sextad extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    i
    
    int i
    
    The first node.
    
    j
    
    int j
    
    The second node.
    
    k
    
    int k
    
    The third node.
    
    l
    
    int l
    
    The fourth node.
    
    m
    
    int m
    
    The fifth node.
    
    n
    
    int n
    
    The sixth node.
- Record Class edu.cmu.tetrad.search.utils.TetradInt
  
  class TetradInt extends Record implements Serializable
  - Serialized Fields
    
    i
    
    int i
    
    The field for the i record component.
    
    j
    
    int j
    
    The field for the j record component.
    
    k
    
    int k
    
    The field for the k record component.
    
    l
    
    int l
    
    The field for the l record component.
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
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    i
    
    Node i
    
    The first node in the sextad.
    
    j
    
    Node j
    
    The second node in the sextad.
    
    k
    
    Node k
    
    The third node in the sextad.
    
    l
    
    Node l
    
    The fourth node in the sextad.
    
    m
    
    Node m
    
    The fifth node in the sextad.
    
    n
    
    Node n
    
    The sixth node in the sextad.
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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    covMatrix
    
    ICovarianceMatrix covMatrix
    
    The covariance matrix.
    
    dag
    
    Graph dag
    
    The DAG.
    
    dataSet
    
    DataSet dataSet
    
    The data set.
    
    edgeCoef
    
    Matrix edgeCoef
    
    The edge coefficients.
    
    errorCovar
    
    Matrix errorCovar
    
    The error covariance.
    
    fml
    
    double fml
    
    The fml score.
    
    implCovarMeasC
    
    Matrix implCovarMeasC
    
    The implied covariance matrix for the measured variables.
    
    logDetSample
    
    double logDetSample
    
    The log determinant of the sample covariance matrix.
    
    sampleCovar
    
    Matrix sampleCovar
    
    The sample covariance.
    
    variables
    
    List<Node> variables
    
    The variables.
- Class edu.cmu.tetrad.sem.GeneralizedSemIm
  
  class GeneralizedSemIm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    guaranteeIid
    
    boolean guaranteeIid
    
    Whether to guarantee that the IID is preserved when simulating data.
    
    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 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    A map from names to nodes, speedup.
    
    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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    number
    
    double number
    
    The number of the constraint.
    
    param2
    
    Parameter param2
    
    The first parameter.
    
    semIm
    
    SemIm semIm
    
    The SEM.
    
    type
    
    ParamConstraintType type
    
    The type of the constraint.
- Class edu.cmu.tetrad.sem.Parameter
  
  class Parameter extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.SemEstimator
  
  class SemEstimator extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
    
    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.
    
    estimatedSem
    
    SemIm estimatedSem
    
    The most recently estimated model, or null if no model has been estimated yet.
    
    numRestarts
    
    int numRestarts
    
    The number of restarts to use.
    
    scoreType
    
    ScoreType scoreType
    
    The score type used to optimize the SEM.
    
    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.
- Class edu.cmu.tetrad.sem.SemEstimatorGibbsParams
  
  class SemEstimatorGibbsParams extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    flatPrior
    
    boolean flatPrior
    
    Whether to use a flat prior.
    
    numIterations
    
    int numIterations
    
    The number of iterations to run.
    
    startIm
    
    SemIm startIm
    
    The initial SEM.
    
    stretch
    
    double stretch
    
    The stretch factor.
    
    tolerance
    
    double tolerance
    
    The tolerance for convergence.
- Class edu.cmu.tetrad.sem.SemEvidence
  
  class SemEvidence extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
    
    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.
    
    errorParam1
    
    double errorParam1
    
    Error distribution parameters.
    
    errorParam2
    
    double errorParam2
    
    Error distribution parameters.
    
    estimated
    
    boolean estimated
    
    True iff this SemIm is estimated.
    
    fixedMappings
    
    List<Mapping> fixedMappings
    
    The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedParameters.
    
    fixedParameters
    
    List<Parameter> fixedParameters
    
    The list of fixed freeParameters (Unmodifiable). This must be in the same order as this.fixedMappings.
    
    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.
    
    freeParameters
    
    List<Parameter> freeParameters
    
    The list of free freeParameters (Unmodifiable). This must be in the same order as this.freeMappings.
    
    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.)
    
    numRandomCalls
    
    int numRandomCalls
    
    Number of random calls.
    
    parameterBoundsEnforced
    
    boolean parameterBoundsEnforced
    
    True iff setting freeParameters to out-of-bound values throws exceptions.
    
    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
    
    The type of score to use for estimation.
    
    sampleSize
    
    int sampleSize
    
    The sample size.
    
    scoreType
    
    ScoreType scoreType
    
    Types of scores that yield a chi square value when minimized.
    
    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.
    
    standardErrors
    
    double[] standardErrors
    
    Stores the standard errors for the freeParameters. May 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.
    
    variableMeansStdDev
    
    double[] variableMeansStdDev
    
    Standard Deviations of means. Needed to calculate standard errors.
    
    variableNodes
    
    List<Node> variableNodes
    
    The list of measured and latent variableNodes for the semPm. (Unmodifiable.)
    
    variablesHash
    
    Map<Node,Integer> variablesHash
    
    The type of score to use for estimation.
- Class edu.cmu.tetrad.sem.SemManipulation
  
  class SemManipulation extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    Error parent of each node.
    
    expectedCov
    
    Matrix expectedCov
    
    Expected covariance matrix.
    
    graph
    
    SemGraph graph
    
    The SEM graph.
    
    idxLatent
    
    int[] idxLatent
    
    Indices of the latent variables.
    
    idxObserved
    
    int[] idxObserved
    
    Indices of the latent variables.
    
    nodeParentsCov
    
    double[][] nodeParentsCov
    
    Covariance of each node with its parents.
    
    numLatent
    
    int numLatent
    
    Number of observed and latent variables.
    
    numObserved
    
    int numObserved
    
    Number of observed and latent variables.
    
    numRestarts
    
    int numRestarts
    
    Number of restarts.
    
    parents
    
    int[][] parents
    
    Indices of the parents of each node.
    
    parentsCov
    
    double[][][] parentsCov
    
    Parents covariance matrix.
    
    semIm
    
    SemIm semIm
    
    The SEM to optimize.
    
    yCov
    
    Matrix yCov
    
    The sample covariance matrix.
    
    yCovModel
    
    Matrix yCovModel
    
    Partitions of the modeled cov.
    
    yzCovModel
    
    Matrix yzCovModel
    
    Partitions of the modeled cov.
    
    zCovModel
    
    Matrix zCovModel
    
    Partitions of the modeled cov.
- Class edu.cmu.tetrad.sem.SemOptimizerPowell
  
  class SemOptimizerPowell extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    numRestarts
    
    int numRestarts
    
    The number of restarts.
- Class edu.cmu.tetrad.sem.SemOptimizerRegression
  
  class SemOptimizerRegression extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    numRestarts
    
    int numRestarts
    
    The number of restarts.
- Class edu.cmu.tetrad.sem.SemOptimizerRicf
  
  class SemOptimizerRicf extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    numRestarts
    
    int numRestarts
    
    The number of restarts to use.
- Class edu.cmu.tetrad.sem.SemOptimizerScattershot
  
  class SemOptimizerScattershot extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    numRestarts
    
    int numRestarts
    
    The number of restarts to use.
- Class edu.cmu.tetrad.sem.SemPm
  
  class SemPm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    semIm
    
    SemIm semIm
    
    Represents a final variable semIm.
    
    values
    
    double[] values
    
    Represents a private final array of double values.
    This variable is part of the SemProposition class in the Tetrad API. SemProposition is a class that represents a Proposition for a Bayes IM (Bayesian Inference Model). It allows for semantic checks when deserializing.
    The values array contains the double values associated with the Proposition.
- Class edu.cmu.tetrad.sem.SemUpdater
  
  class SemUpdater extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    evidence
    
    SemEvidence evidence
    
    The evidence to be used in the update.
    
    semIm
    
    SemIm semIm
    
    The SEM to be updated.
- Class edu.cmu.tetrad.sem.StandardizedSemIm
  
  class StandardizedSemIm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    edgeCoef
    
    Matrix edgeCoef
    
    The edge coefficient matrix of the model, a la SemIm. Note that this will normally need to be transposed, since [a][b] is the edge coefficient for a-->b, not b-->a. Sorry. History. THESE ARE PARAMETERS OF THE MODEL--THE ONLY PARAMETERS.
    
    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
    
    The edge being edited.
    
    errorCovar
    
    Matrix errorCovar
    
    The error covariance matrix of the model. i.e. [a][b] is the covariance of E_a and E_b, with [a][a] of course being the variance of E_a. THESE ARE NOT PARAMETERS OF THE MODEL; THEY ARE CALCULATED. Note that elements of this matrix may be Double.NaN; this indicates that these elements cannot be calculated.
    
    errorVariances
    
    Map<Node,Double> errorVariances
    
    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.
    
    implCovar
    
    Matrix implCovar
    
    The implied covariance matrix over all the variables.
    
    implCovarMeas
    
    Matrix implCovarMeas
    
    The implied covariance matrix over the measured variables only.
    
    range
    
    StandardizedSemIm.ParameterRange range
    
    The range of the parameter being edited.
    
    sampleSize
    
    int sampleSize
    
    The sample size for the model.
    
    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
    
    The coefficient value for which the range is needed.
    
    edge
    
    Edge edge
    
    The edge for which the range is needed.
    
    high
    
    double high
    
    The high end of the range to which the coefficient value may be adjusted.
    
    low
    
    double low
    
    The low end of the range to which the coefficient value may be adjusted.
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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    lagGraph
    
    LagGraph lagGraph
    
    Underlying graph representing the update graph.
- 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - Serialized Fields
    
    lagGraph
    
    BasicLagGraph lagGraph
    
    The lag graph.
- 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - if any.
    
    ClassNotFoundException - if any.
  - 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.StoredLagGraphParams
  
  class StoredLagGraphParams extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    factor
    
    String factor
    
    The name of the factor.
    
    laggedFactor
    
    LaggedFactor laggedFactor
    
    The lagged factor.
- 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - if any.
    
    ClassNotFoundException - if any.
  - 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.
    
    Parameters:
    
    s - an ObjectInputStream object
    
    Throws:
    
    IOException - if any.
    
    ClassNotFoundException - if any.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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.
    
    Parameters:
    
    s - The input stream from which this object is being deserialized.
    
    Throws:
    
    IOException - If any.
    
    ClassNotFoundException - If any.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    cellNumber
    
    int cellNumber
    
    The cellNumber variable represents the number of a cell. It is a private integer variable with an initial value of -1.
    
    dishNumber
    
    int dishNumber
    
    The dishNumber variable stores the number of a dish. It is an integer value and is initially set to -1.
    
    history
    
    GeneHistory history
    
    The history that will be used to simulate the data.
    
    measuredData
    
    double[][][] measuredData
    
    Array variable to store measured data.
    This variable is a 3-dimensional array of type double to store measured data. It is used to store data collected from various measures or experiments. The first dimension represents the measure index, the second dimension represents the sample index within the measure, and the third dimension represents the data value.
    
    The structure of the array is as follows:
    
    The first dimension represents the measure index, ranging from 0 to n-1.
    
    The second dimension represents the sample index within the measure, ranging from 0 to m-1.
    
    The third dimension represents the data value, ranging from 0 to k-1.
    
    The data values in the array are of type double, allowing for the storage of decimal values. The array dimensions and size may vary based on the specific application and requirements.
    
    Access to this variable is restricted to the private scope to ensure encapsulation and proper data management.
    
    Usage example: measuredData[1][2][3]
    
    parameters
    
    Parameters parameters
    
    The parameters for this simulation.
    
    rawData
    
    double[][][] rawData
    
    This variable stores raw data in a three-dimensional array.
    The first dimension represents the rows in the data.
    The second dimension represents the columns in the data.
    The third dimension represents additional dimensions for the data, which can be used for organizing multidimensional data.
    The values stored in this array are of type double.
    Access to this variable is private, meaning it can only be accessed from within the class it is declared in.
    Modifying this variable should be done with caution, as it contains sensitive raw data.
    
    timeSteps
    
    int[] timeSteps
    
    Represents an array of time steps.
    This variable is used to store an array of integers representing different time steps.
Package edu.cmu.tetrad.study.gene.tetradapp.model
- Class edu.cmu.tetrad.study.gene.tetradapp.model.GenePm
  
  class GenePm extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    lagGraph
    
    LagGraph lagGraph
    
    The wrapped lag workbench.
- Class edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams
  
  class MeasurementSimulatorParams extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    includeDishAndChipVariables
    
    boolean includeDishAndChipVariables
    
    Whether to include dish and chip variables in the simulation.
    
    simulator
    
    MeasurementSimulator simulator
    
    The wrapped measurement simulator.
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
    
    The description of the event.
    
    id
    
    String id
    
    The id of the event.
- Class edu.cmu.tetrad.util.Matrix
  
  class Matrix extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    data
    
    org.ejml.simple.SimpleMatrix data
    
    The `data` variable represents a matrix structure used for numerical computations and data representation. It is an immutable instance of the `SimpleMatrix` class that supports various matrix operations.
    
    m
    
    int m
    
    The number of rows.
    
    matrixView
    
    MView matrixView
    
    The view of the matrix. This is used to allow a subset of the matrix to be viewed and set.
    
    n
    
    int n
    
    The number of columns.
- Class edu.cmu.tetrad.util.MView
  
  class MView extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    matrix
    
    Matrix matrix
    
    Represents the underlying Matrix object associated with this MatrixView. This field stores the original matrix or a reference to it, which serves as the basis for any operations or sub-views created by this MatrixView instance. It can be null if the MatrixView is not initialized with a specific matrix.
    
    matrixView
    
    MView matrixView
    
    Represents a view of a matrix, typically used to access or modify a subset of the rows and columns of an original matrix or another matrix view. This variable holds a reference to an immutable object of type MView. The matrixView object can include functionalities such as retrieving specific elements, updating values, or creating further sub-views of its data.
    
    viewCols
    
    int[] viewCols
    
    Represents the columns of the associated matrix view. Each element in this array corresponds to an index of a column in the original matrix that is part of the view. This array defines the mapping of columns from the original matrix to the matrix view. It is immutable.
    
    viewRows
    
    int[] viewRows
    
    Represents an array of row indices included in the matrix view. This array determines which rows from the original matrix are part of the current view. Immutable and specific to the representation of rows in a submatrix.
- Class edu.cmu.tetrad.util.Parameters
  
  class Parameters extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    overriddenParameters
    
    Map<String,Object> overriddenParameters
    
    The overridden parameters.
    
    parameters
    
    Map<String,Object[]> parameters
    
    The parameters.
    
    usedParameters
    
    Set<String> usedParameters
    
    The used parameters.
- 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
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    Represents the activation status of an event in the logger configuration.
- Class edu.cmu.tetrad.util.TetradLoggerEvent
  
  class TetradLoggerEvent extends EventObject implements Serializable
  - Serialized Fields
    
    config
    
    TetradLoggerConfig config
    
    The config associated with the event, may be null.
- Class edu.cmu.tetrad.util.Vector
  
  class Vector extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    data
    
    org.ejml.simple.SimpleMatrix data
    
    The data.
- Class edu.cmu.tetrad.util.Version
  
  class Version extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    df
    
    double df
    
    The stored degrees 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
    
    The probabilities of the different values.
- Class edu.cmu.tetrad.util.dist.Exponential
  
  class Exponential extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    lambda
    
    double lambda
    
    The rate parameter.
- Class edu.cmu.tetrad.util.dist.Gamma
  
  class Gamma extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    alpha
    
    double alpha
    
    The shape parameter.
    
    lambda
    
    double lambda
    
    The rate parameter.
- Class edu.cmu.tetrad.util.dist.GaussianPower
  
  class GaussianPower extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    name
    
    String name
    
    The name.
    
    power
    
    double power
    
    The power.
    
    sd
    
    double sd
    
    The standard deviation of the Gaussian distribution.
- Class edu.cmu.tetrad.util.dist.Indicator
  
  class Indicator extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    p
    
    double p
    
    The probability of returning 1.
- Class edu.cmu.tetrad.util.dist.LogNormal
  
  class LogNormal extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    sd
    
    double sd
    
    The standard deviation.
- Class edu.cmu.tetrad.util.dist.MixtureOfGaussians
  
  class MixtureOfGaussians extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    a
    
    double a
    
    The mixing parameter.
    
    mean1
    
    double mean1
    
    The mean of the first Gaussian.
    
    mean2
    
    double mean2
    
    The mean of the second Gaussian.
    
    sd1
    
    double sd1
    
    The standard deviation of the first Gaussian.
    
    sd2
    
    double sd2
    
    The standard deviation of the second Gaussian.
- Class edu.cmu.tetrad.util.dist.Normal
  
  class Normal extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    The mean of the Poisson distribution.
- Class edu.cmu.tetrad.util.dist.SingleValue
  
  class SingleValue extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialized Fields
    
    value
    
    double value
    
    Represents a single value in a statistical distribution.
- Class edu.cmu.tetrad.util.dist.Split
  
  class Split extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - Serialized Fields
    
    a
    
    double a
    
    Represents the variable 'a' in the Split distribution.
    
    b
    
    double b
    
    A private variable representing the value of `b`.
- Class edu.cmu.tetrad.util.dist.TruncatedNormal
  
  class TruncatedNormal extends Object implements Serializable
  
  serialVersionUID:
  
  23L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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 in) throws IOException, ClassNotFoundException
    
    Reads the object from the specified ObjectInputStream. This method is used during deserialization to restore the state of the object.
    
    Parameters:
    
    in - The ObjectInputStream to read the object from.
    
    Throws:
    
    IOException - If an I/O error occurs.
    
    ClassNotFoundException - If the class of the serialized object cannot be found.
    
    writeObject
    
    private void writeObject(ObjectOutputStream out) throws IOException
    
    Writes the object to the specified ObjectOutputStream.
    
    Parameters:
    
    out - The ObjectOutputStream to write the object to.
    
    Throws:
    
    IOException - If an I/O error occurs.
  - 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
    
    The attribute lookup.
    
    attributes
    
    List<A> attributes
    
    The attributes.
    
    root
    
    edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode root
    
    The root of the tree
    
    values
    
    List<AdTree<A,V>.edu.pitt.isp.sverchkov.data.AdTree.VHelper> values
    
    The values.
- Class edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode
  
  class CountNode extends Object implements Serializable
  - Serialized Fields
    
    attr
    
    int attr
    
    The attribute of this node.
    
    count
    
    int count
    
    The number of instances in the data set.
    
    vary
    
    edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode[] vary
    
    The children of this node.
- Class edu.pitt.isp.sverchkov.data.AdTreeHelper.VaryNode
  
  class VaryNode extends Object implements Serializable
  - Serialized Fields
    
    mcv
    
    int mcv
    
    The most common value of the attribute.
    
    values
    
    edu.pitt.isp.sverchkov.data.AdTreeHelper.CountNode[] values
    
    The values of the attribute.

Serialized Form

Package edu.cmu.tetrad.algcomparison

Class edu.cmu.tetrad.algcomparison.Comparison

Serialized Fields

comparisonGraph

dataPath

graphTypeUsed

knowledge

parallelism

resultsPath

saveCPDAGs

saveData

saveGraphs

savePags

setAlgorithmKnowledge

showUtilities

sortByUtility

tabDelimitedTables

Package edu.cmu.tetrad.algcomparison.algorithm

Class edu.cmu.tetrad.algcomparison.algorithm.AbstractBootstrapAlgorithm

Serialized Fields

count

Class edu.cmu.tetrad.algcomparison.algorithm.Algorithms

Serialization Methods

readObject

writeObject

Serialized Fields

algorithms

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

Serialized Fields

path

simIndex

simulation

usedParameters

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

Serialized Fields

algorithm

high

increment

low

parameter

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

Serialized Fields

algorithm

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

Serialized Fields

algorithm

high

low

parameter

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

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

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

Serialized Fields

knowledge

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

Serialized Fields

knowledge

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

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

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

Serialized Fields

score

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

Serialized Fields

algorithm

knowledge

score

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

Serialized Fields

algorithm

externalGraph

knowledge

score

test

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

Serialized Fields

bHat

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

Serialized Fields