Package edu.cmu.tetrad.sem

Class GeneralizedSemPm

java.lang.Object

edu.cmu.tetrad.sem.GeneralizedSemPm

All Implemented Interfaces:

Pm, TetradSerializable, Serializable

public final class GeneralizedSemPm
extends Object
implements Pm, TetradSerializable

Parametric model for a Generalized SEM model. This contains all the equations of the model with parameters represented symbolically (i.e., no values for parameters).

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
GeneralizedSemPm(Graph graph)	Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.
GeneralizedSemPm(SemGraph graph)	Constructs a new SemPm from the given SemGraph.
GeneralizedSemPm(GeneralizedSemPm semPm)	Initializes a new instance of the GeneralizedSemPm class by copying the properties of the provided GeneralizedSemPm object.
GeneralizedSemPm(SemPm semPm)	Constructs a new GeneralizedSemPm object based on the given SemPm object.

Method Summary

Modifier and Type	Method	Description
Node	getErrorNode(Node node)	Retrieves the error node associated with the given node.
List<Node>	getErrorNodes()	Returns the list of exogenous variableNodes.
String	getErrorsTemplate()	Returns the error template string.
SemGraph	getGraph()	Returns the structural model graph this SEM PM is using.
List<Node>	getMeasuredNodes()	Returns a list of measured nodes.
Node	getNode(String name)	Returns the Node with the given name.
Expression	getNodeExpression(Node node)	getNodeExpression.
String	getNodeExpressionString(Node node)	getNodeExpressionString.
List<Node>	getNodes()	Retrieves a list of nodes.
Expression	getParameterEstimationInitializationExpression(String parameter)	Retrieves the initialization expression for a given parameter used in parameter estimation.
String	getParameterEstimationInitializationExpressionString(String parameter)	Returns the initialization expression string for the given parameter.
Expression	getParameterExpression(String parameter)	Retrieves the expression associated with the given parameter.
String	getParameterExpressionString(String parameter)	Returns the expression string associated with the given parameter.
static List<String>	getParameterNames()	Retrieves the names of the parameters required for a certain operation.
Set<String>	getParameters()	Retrieves the set of parameters.
String	getParametersEstimationInitializationTemplate()	Retrieves the parameter estimation initialization template.
String	getParametersTemplate()	Retrieves the template for the parameters.
List<Node>	getParents(Node node)	Retrieves the list of parent nodes for the given node.
Set<Node>	getReferencedNodes(Node node)	Retrieves a set of referenced nodes for the given node.
Set<String>	getReferencedParameters(Node node)	Retrieves the set of referenced parameters from a given node.
Set<Node>	getReferencingNodes(Node node)	Retrieves the set of referencing nodes for a given node.
Set<Node>	getReferencingNodes(String parameter)	Returns a set of nodes that reference the given parameter.
String	getStartsWithParameterEstimationInitializationTemplate(String startsWith)	Retrieves the initialization template for parameter estimation based on the provided starting string.
String	getStartsWithParameterTemplate(String startsWith)	getStartsWithParameterTemplate.
List<Node>	getVariableNodes()	Returns the list of variable nodes--that is, node that is not error nodes.
String	getVariablesTemplate()	Retrieves the variable template.
String	nextParameterName(String base)	Given base b (a String), returns the first name in the sequence "b1", "b2", "b3", etc., which is not already the name of a node in the workbench.
static GeneralizedSemPm	serializableInstance()	Generates a simple exemplar of this class to test serialization.
void	setErrorsTemplate(String errorsTemplate)	Sets the error template for the software.
void	setNodeExpression(Node node, String expressionString)	Sets the expression for a given node.
void	setParameterEstimationInitializationExpression(String parameter, String expressionString)	Sets the parameter estimation initialization expression for the given parameter.
void	setParameterEstimationInitializationExpression(String startsWith, String parameter, String expressionString)	Sets the expression which should be evaluated when calculating new values for the given parameter.
void	setParameterExpression(String parameter, String expressionString)	Sets the expression which should be evaluated when calculating new values for the given parameter.
void	setParameterExpression(String startsWith, String parameter, String expressionString)	Sets the expression which should be evaluated when calculating new values for the given parameter.
void	setParametersEstimationInitializationTemplate(String parametersTemplate)	Sets the template for parameter estimation initialization.
void	setParametersTemplate(String parametersTemplate)	Sets the parameter template for the object.
void	setStartsWithParametersEstimationInitializationTemplate(String startsWith, String parametersEstimationInitializationTemplate)	Sets the parameter estimation initialization template for a given startsWith string.
void	setStartsWithParametersTemplate(String startsWith, String parametersTemplate)	Sets the parameter template for expressions that start with the specified string.
void	setVariablesTemplate(String variablesTemplate)	Sets the variable template.
Set<String>	startsWithPrefixes()	startsWithPrefixes.
String	toString()	Returns a relatively brief String representation of this SEM PM--the equations and distributions of the model.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

GeneralizedSemPm

public GeneralizedSemPm(Graph graph)

Constructs a BayesPm from the given Graph, which must be convertible first into a ProtoSemGraph and then into a SemGraph.

Parameters:

graph - a Graph object

GeneralizedSemPm

public GeneralizedSemPm(SemGraph graph)

Constructs a new SemPm from the given SemGraph.

Parameters:

graph - a SemGraph object

GeneralizedSemPm

public GeneralizedSemPm(SemPm semPm)

Constructs a new GeneralizedSemPm object based on the given SemPm object.

Parameters:

semPm - the SemPm object used to construct the GeneralizedSemPm

Throws:

IllegalStateException - if there is a parse error in constructing the initial model

GeneralizedSemPm

public GeneralizedSemPm(GeneralizedSemPm semPm)

Initializes a new instance of the GeneralizedSemPm class by copying the properties of the provided GeneralizedSemPm object.

Parameters:

semPm - The GeneralizedSemPm object to copy.

Method Details

serializableInstance

public static GeneralizedSemPm serializableInstance()

Generates a simple exemplar of this class to test serialization.

Returns:

a GeneralizedSemPm object

getParameterNames

public static List<String> getParameterNames()

Retrieves the names of the parameters required for a certain operation.

Returns:

a list containing the names of the parameters

getNodeExpression

public Expression getNodeExpression(Node node)

getNodeExpression.

Parameters:

node - a Node object

Returns:

a Expression object

getNodeExpressionString

public String getNodeExpressionString(Node node)

getNodeExpressionString.

Parameters:

node - a Node object

Returns:

a String object

setNodeExpression

public void setNodeExpression(Node node,
 String expressionString)
                       throws ParseException

Sets the expression for a given node.

Parameters:

node - the node for which to set the expression

expressionString - the expression string to set

Throws:

ParseException - if the expression string cannot be parsed

NullPointerException - if node is null or expressionString is null

setParameterExpression

public void setParameterExpression(String parameter,
 String expressionString)
                            throws ParseException

Sets the expression which should be evaluated when calculating new values for the given parameter. These values are used to initialize the freeParameters.

Parameters:

parameter - The parameter whose initial value needs to be computed.

expressionString - The formula for picking initial values.

Throws:

ParseException - If the formula cannot be parsed or contains variable names.

setParameterEstimationInitializationExpression

public void setParameterEstimationInitializationExpression(String parameter,
 String expressionString)
                                                    throws ParseException

Sets the parameter estimation initialization expression for the given parameter.

Parameters:

parameter - The parameter to set the initialization expression for.

expressionString - The expression string to be parsed and stored.

Throws:

NullPointerException - If either parameter or expressionString is null.

ParseException - If the expressionString is not valid and cannot be parsed.

IllegalArgumentException - If the expressionString contains parameters.

setParameterExpression

public void setParameterExpression(String startsWith,
 String parameter,
 String expressionString)
                            throws ParseException

Sets the expression which should be evaluated when calculating new values for the given parameter. These values are used to initialize the freeParameters.

Parameters:

startsWith - a String object

parameter - The parameter whose initial value needs to be computed.

expressionString - The formula for picking initial values.

Throws:

ParseException - If the formula cannot be parsed or contains variable names.

setParameterEstimationInitializationExpression

public void setParameterEstimationInitializationExpression(String startsWith,
 String parameter,
 String expressionString)
                                                    throws ParseException

Sets the expression which should be evaluated when calculating new values for the given parameter. These values are used to initialize the freeParameters.

Parameters:

startsWith - a String object

parameter - The parameter whose initial value needs to be computed.

expressionString - The formula for picking initial values.

Throws:

ParseException - If the formula cannot be parsed or contains variable names.

getParameters

public Set<String> getParameters()

Retrieves the set of parameters.

Returns:

a Set of String representing the parameters.

getParameterExpression

public Expression getParameterExpression(String parameter)

Retrieves the expression associated with the given parameter.

Parameters:

parameter - the name of the parameter

Returns:

the expression associated with the given parameter, or null if not found

getParameterEstimationInitializationExpression

public Expression getParameterEstimationInitializationExpression(String parameter)

Retrieves the initialization expression for a given parameter used in parameter estimation.

Parameters:

parameter - the parameter for which to retrieve the initialization expression

Returns:

the initialization expression for the specified parameter, or null if not found

getParameterExpressionString

public String getParameterExpressionString(String parameter)

Returns the expression string associated with the given parameter.

Parameters:

parameter - the parameter name

Returns:

the expression string associated with the parameter

getParameterEstimationInitializationExpressionString

public String getParameterEstimationInitializationExpressionString(String parameter)

Returns the initialization expression string for the given parameter.

Parameters:

parameter - the parameter for which the initialization expression string is needed

Returns:

the initialization expression string for the given parameter, or null if not found

getGraph

public SemGraph getGraph()

Returns the structural model graph this SEM PM is using.

Returns:

a SemGraph object

getNodes

public List<Node> getNodes()

Retrieves a list of nodes.

Returns:

A list of nodes.

getVariableNodes

public List<Node> getVariableNodes()

Returns the list of variable nodes--that is, node that is not error nodes.

Returns:

a List object

getMeasuredNodes

public List<Node> getMeasuredNodes()

Returns a list of measured nodes.

Returns:

a list of measured nodes.

getErrorNodes

public List<Node> getErrorNodes()

Returns the list of exogenous variableNodes.

Returns:

a List object

getErrorNode

public Node getErrorNode(Node node)

Retrieves the error node associated with the given node.

Parameters:

node - The node to check for error association.

Returns:

The error node associated with the given node, or null if no error node is found.

getNode

public Node getNode(String name)

Returns the Node with the given name.

Parameters:

name - the name of the Node to retrieve

Returns:

the Node with the given name, or null if no Node exists with the specified name

getReferencingNodes

public Set<Node> getReferencingNodes(String parameter)

Returns a set of nodes that reference the given parameter.

Parameters:

parameter - the parameter to search for referencing nodes

Returns:

a set of nodes that reference the given parameter, or an empty set if no nodes are found

getReferencedParameters

public Set<String> getReferencedParameters(Node node)

Retrieves the set of referenced parameters from a given node.

Parameters:

node - The node for which to retrieve referenced parameters.

Returns:

The set of referenced parameters found in the given node.

getReferencingNodes

public Set<Node> getReferencingNodes(Node node)

Retrieves the set of referencing nodes for a given node.

Parameters:

node - the node for which to retrieve the referencing nodes

Returns:

a set of referencing nodes

getReferencedNodes

public Set<Node> getReferencedNodes(Node node)

Retrieves a set of referenced nodes for the given node.

Parameters:

node - the node for which to retrieve the referenced nodes

Returns:

a set of referenced nodes

nextParameterName

public String nextParameterName(String base)

Given base b (a String), returns the first name in the sequence "b1", "b2", "b3", etc., which is not already the name of a node in the workbench.

Parameters:

base - the base string.

Returns:

the first string in the sequence not already being used.

getParents

public List<Node> getParents(Node node)

Retrieves the list of parent nodes for the given node.

Parameters:

node - the specified node

Returns:

the list of parent nodes

toString

public String toString()

Returns a relatively brief String representation of this SEM PM--the equations and distributions of the model. Initial value distributions for freeParameters are not printed.

Overrides:

toString in class Object

Returns:

a String object

getVariablesTemplate

public String getVariablesTemplate()

Retrieves the variable template.

Returns:

the variable template

setVariablesTemplate

public void setVariablesTemplate(String variablesTemplate)
                          throws ParseException

Sets the variable template.

Parameters:

variablesTemplate - the template for variables

Throws:

ParseException - if the variable template fails to parse

NullPointerException - if the variable template is null

getErrorsTemplate

public String getErrorsTemplate()

Returns the error template string.

Returns:

the error template string

setErrorsTemplate

public void setErrorsTemplate(String errorsTemplate)
                       throws ParseException

Sets the error template for the software.

Parameters:

errorsTemplate - the string representation of the error template

Throws:

ParseException - if the error template cannot be parsed successfully

NullPointerException - if the errorsTemplate parameter is null

getParametersTemplate

public String getParametersTemplate()

Retrieves the template for the parameters.

Returns:

The template for the parameters.

setParametersTemplate

public void setParametersTemplate(String parametersTemplate)
                           throws ParseException

Sets the parameter template for the object.

Parameters:

parametersTemplate - the template string representing the parameters

Throws:

ParseException - if the given parameters template is not valid

NullPointerException - if the parameter template is null

IllegalArgumentException - if the parameter template contains parameters

See Also:

• ExpressionParser

getParametersEstimationInitializationTemplate

public String getParametersEstimationInitializationTemplate()

Retrieves the parameter estimation initialization template.

Returns:

The parameter estimation initialization template as a String.

setParametersEstimationInitializationTemplate

public void setParametersEstimationInitializationTemplate(String parametersTemplate)
                                                   throws ParseException

Sets the template for parameter estimation initialization.

Parameters:

parametersTemplate - the template string for parameter estimation initialization

Throws:

ParseException - if the provided parameters template is not parseable

NullPointerException - if the provided parameters template is null

setStartsWithParametersTemplate

public void setStartsWithParametersTemplate(String startsWith,
 String parametersTemplate)
                                     throws ParseException

Sets the parameter template for expressions that start with the specified string. If the startsWith parameter is null or empty, the method does nothing. If the parametersTemplate parameter is null, a NullPointerException is thrown. The method parses the parametersTemplate to ensure it is a valid expression. If the startsWith string contains spaces, an IllegalArgumentException is thrown.

Parameters:

startsWith - The starting string for the expressions.

parametersTemplate - The template for the parameters of the expressions.

Throws:

ParseException - If the parametersTemplate is not a valid expression.

NullPointerException - If the parametersTemplate is null.

IllegalArgumentException - If the startsWith string contains spaces.

setStartsWithParametersEstimationInitializationTemplate

public void setStartsWithParametersEstimationInitializationTemplate(String startsWith,
 String parametersEstimationInitializationTemplate)
                                                             throws ParseException

Sets the parameter estimation initialization template for a given startsWith string.

Parameters:

startsWith - the string that the template should start with

parametersEstimationInitializationTemplate - the template for initializing the parameter estimation

Throws:

ParseException - if the template is unable to be parsed

NullPointerException - if the parametersTemplate is null

IllegalArgumentException - if the startsWith string contains spaces

getStartsWithParameterTemplate

public String getStartsWithParameterTemplate(String startsWith)

getStartsWithParameterTemplate.

Parameters:

startsWith - a String object

Returns:

a String object

getStartsWithParameterEstimationInitializationTemplate

public String getStartsWithParameterEstimationInitializationTemplate(String startsWith)

Retrieves the initialization template for parameter estimation based on the provided starting string.

Parameters:

startsWith - The starting string used to find the initialization template.

Returns:

The initialization template corresponding to the starting string.

startsWithPrefixes

public Set<String> startsWithPrefixes()

startsWithPrefixes.

Returns:

a Set object