Package edu.cmu.tetrad.graph
Class SemGraph
java.lang.Object
edu.cmu.tetrad.graph.SemGraph
- All Implemented Interfaces:
Graph
,TetradSerializable
,Serializable
Represents the graphical structure of a structural equation model. The linear structure of the structural equation
model is constructed by adding non-error nodes to the graph and connecting them with directed edges. As this is done,
the graph automatically maintains the invariant that endogenous non-error nodes are associated with explicit error
nodes in the graph and exogenous non-error nodes are not. An associated error node for a node N is an error node that
has N as its only child, E-->N. Error nodes for exogenous nodes are always implicit in the graph. So as nodes
become endogenous, error nodes are added for them, and as they become exogenous, error nodes are removed for them.
Correlated errors are represented using directed edges among exogenous nodes. Directed edges may therefore be added
among any exogenous nodes in the graph, though the easiest way to add (or remove) exogenous nodes is to determine
which non-exogenous nodes N1, N2 they are representing correlated errors for and then to use this formulation:
addBidirectedEdge(getExogenous(node1), getExogenous(node2)); removeEdge(getExogenous(node1), getExogenous(node2));This avoids the problem of not knowing whether the exogenous node for a node is itself or its associated error node.
- Version:
- $Id: $Id
- Author:
- josephramsey
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAmbiguousTriple
(Node x, Node y, Node z) addAmbiguousTriple.void
addAttribute
(String key, Object value) addAttribute.boolean
addBidirectedEdge
(Node nodeA, Node nodeB) Adds a bidirected edges <-> to the graph.boolean
addDirectedEdge
(Node nodeA, Node nodeB) Adds a directed edge --> to the graph.void
addDottedUnderlineTriple
(Node x, Node y, Node z) addDottedUnderlineTriple.boolean
Adds the specified edge to the graph, provided it is not already in the graph.boolean
Adds a node to the graph.boolean
addNondirectedEdge
(Node nodeA, Node nodeB) Adds a nondirected edges o-o to the graph.boolean
addPartiallyOrientedEdge
(Node nodeA, Node nodeB) Adds a partially oriented edge o-> to the graph.void
Adds a PropertyChangeListener to the graph.void
addUnderlineTriple
(Node x, Node y, Node z) addUnderlineTriple.boolean
addUndirectedEdge
(Node nodeA, Node nodeB) Adds an undirected edge --- to the graph.void
clear()
clear.boolean
containsEdge
(Edge edge) Determines whether this graph contains the given edge.boolean
containsNode
(Node node) Determines whether this graph contains the given node.boolean
Determines whether this graph is equal to some other graph, in the sense that they contain the same nodes and the sets of edges defined over these nodes in the two graphs are isomorphic typewise.void
fullyConnect
(Endpoint endpoint) Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.getAdjacentNodes
(Node node) getAdjacentNodes.getAllAttributes.Getter for the fieldambiguousTriples
.getAttribute
(String key) getAttribute.getChildren
(Node node) getChildren.int
getDegree.int
getDegree.getDirectedEdge
(Node node1, Node node2) getDirectedEdge.getDottedUnderlines.getEdge.getEdges()
getEdges.getEdges.getEdges.getEndpoint
(Node node1, Node node2) getEndpoint.getErrorNode
(Node node) getErrorNode.getExogenous
(Node node) getExogenous.getFullTierOrdering.int
getIndegree
(Node node) getIndegree.getNode.getNodeNames.getNodes()
getNodes.getNodesInTo
(Node node, Endpoint endpoint) Nodes adjacent to the given node with the given proximal endpoint.getNodesOutTo
(Node node, Endpoint n) Nodes adjacent to the given node with the given distal endpoint.int
getNumEdges.int
getNumEdges
(Node node) getNumEdges.int
getNumNodes.int
getOutdegree
(Node node) getOutdegree.getParents
(Node node) getParents.getSepset
(Node n1, Node n2, IndependenceTest test) Returns the set of nodes that form the separating set between two given nodes.getTimeLagGraph.getUnderLines.getVarNode
(Node node) getVarNode.boolean
isAdjacentTo
(Node nodeX, Node nodeY) isAdjacentTo.boolean
isAmbiguousTriple
(Node x, Node y, Node z) States whether r-s-r is an underline triple or not.boolean
isChildOf.boolean
isDefCollider
(Node node1, Node node2, Node node3) Added by ekorber, 2004/6/9.boolean
isDefNoncollider
(Node node1, Node node2, Node node3) Added by ekorber, 2004/6/9.static boolean
isErrorEdge
(Edge edge) isErrorEdge.boolean
isExogenous
(Node node) isExogenous.boolean
isParameterizable
(Node node) isParameterizable.boolean
isParentOf
(Node node1, Node node2) Determines whether node1 is a parent of node2.boolean
isShowErrorTerms.boolean
isTimeLagModel.boolean
isUnderlineTriple
(Node x, Node y, Node z) States whether r-s-r is an underline triple or not.paths()
paths.void
removeAmbiguousTriple
(Node x, Node y, Node z) removeAmbiguousTriple.void
removeAttribute
(String key) removeAttribute.void
removeDottedUnderlineTriple
(Node x, Node y, Node z) removeDottedUnderlineTriple.boolean
removeEdge
(Edge edge) Removes the given edge from the graph.boolean
removeEdge
(Node node1, Node node2) Removes an edge between two given nodes.boolean
removeEdges
(Node node1, Node node2) Removes all edges connecting node A to node B.boolean
removeEdges
(Collection<Edge> edges) Iterates through the list and removes any permissible edges found.boolean
removeNode
(Node node) Removes a node from the graph.boolean
removeNodes
(List<Node> nodes) Iterates through the list and removes any permissible nodes found.void
removeTriplesNotInGraph.void
removeUnderlineTriple
(Node x, Node y, Node z) removeUnderlineTriple.void
reorientAllWith
(Endpoint endpoint) Reorients all edges in the graph with the given endpoint.void
resetErrorPositions.static SemGraph
Generates a simple exemplar of this class to test serialization.void
setAmbiguousTriples
(Set<Triple> triples) setAmbiguousTriples.void
setDottedUnderLineTriples
(Set<Triple> triples) setDottedUnderLineTriples.boolean
setEndpoint
(Node node1, Node node2, Endpoint endpoint) Sets the endpoint type at the 'to' end of the edge from 'from' to 'to' to the given endpoint.void
setNodes.void
setShowErrorTerms
(boolean showErrorTerms) Setter for the fieldshowErrorTerms
.void
setUnderLineTriples
(Set<Triple> triples) setUnderLineTriples.Constructs and returns a subgraph consisting of a given subset of the nodes of this graph together with the edges between them.toString()
toString.void
transferAttributes
(Graph graph) transferAttributes.void
transferNodesAndEdges
(Graph graph) Transfers nodes and edges from one graph to another.Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface edu.cmu.tetrad.graph.Graph
existsSemidirectedPath, isAncestorOf
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Constructor Details
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SemGraph
public SemGraph()Constructs a new, empty SemGraph. -
SemGraph
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SemGraph
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Method Details
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serializableInstance
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isErrorEdge
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getErrorNode
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isParameterizable
isParameterizable.
- Specified by:
isParameterizable
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- true if the given node is parameterizable.
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getFullTierOrdering
getFullTierOrdering.
- Returns:
- a tier order, including error terms, if they are shown.
- Throws:
IllegalStateException
- if the graph is cyclic.
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getVarNode
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getExogenous
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transferNodesAndEdges
Transfers nodes and edges from one graph to another. One way this is used is to change graph types. One constructs a new graph based on the old graph, and this method is called to transfer the nodes and edges of the old graph to the new graph.- Specified by:
transferNodesAndEdges
in interfaceGraph
- Parameters:
graph
- the graph from which nodes and edges are to be pilfered.- Throws:
IllegalArgumentException
- This exception is thrown if adding some node.
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transferAttributes
transferAttributes.
- Specified by:
transferAttributes
in interfaceGraph
- Parameters:
graph
- aGraph
object- Throws:
IllegalArgumentException
- if any.
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paths
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getNodeNames
getNodeNames.
- Specified by:
getNodeNames
in interfaceGraph
- Returns:
- a
List
object
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fullyConnect
Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.- Specified by:
fullyConnect
in interfaceGraph
- Parameters:
endpoint
- aEndpoint
object
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reorientAllWith
Reorients all edges in the graph with the given endpoint.- Specified by:
reorientAllWith
in interfaceGraph
- Parameters:
endpoint
- aEndpoint
object
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getAdjacentNodes
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getNodesInTo
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getNodesOutTo
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getNodes
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setNodes
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removeEdge
Removes an edge between two given nodes.- Specified by:
removeEdge
in interfaceGraph
- Parameters:
node1
- The first node.node2
- The second node.- Returns:
- true if the edge between node1 and node2 was successfully removed, false otherwise.
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removeEdges
Removes all edges connecting node A to node B. In most cases, this will remove at most one edge, but since multiple edges are permitted in some graph implementations, the number will in some cases be greater than one.- Specified by:
removeEdges
in interfaceGraph
- Parameters:
node1
- aNode
objectnode2
- aNode
object- Returns:
- true if edges were removed, false if not.
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isAdjacentTo
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setEndpoint
Sets the endpoint type at the 'to' end of the edge from 'from' to 'to' to the given endpoint. Note: NOT CONSTRAINT SAFE- Specified by:
setEndpoint
in interfaceGraph
- Parameters:
node1
- aNode
objectnode2
- aNode
objectendpoint
- aEndpoint
object- Returns:
- a boolean
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getEndpoint
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equals
Determines whether this graph is equal to some other graph, in the sense that they contain the same nodes and the sets of edges defined over these nodes in the two graphs are isomorphic typewise. That is, if node A and B exist in both graphs, and if there are, e.g., three edges between A and B in the first graph, two of which are directed edges and one of which is an undirected edge, then in the second graph there must also be two directed edges and one undirected edge between nodes A and B. -
subgraph
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addDirectedEdge
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addUndirectedEdge
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addNondirectedEdge
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addPartiallyOrientedEdge
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addBidirectedEdge
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addEdge
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addNode
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addPropertyChangeListener
Adds a PropertyChangeListener to the graph.- Specified by:
addPropertyChangeListener
in interfaceGraph
- Parameters:
l
- aPropertyChangeListener
object
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containsEdge
Determines whether this graph contains the given edge.- Specified by:
containsEdge
in interfaceGraph
- Parameters:
edge
- aEdge
object- Returns:
- true iff the graph contain 'edge'.
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containsNode
Determines whether this graph contains the given node.- Specified by:
containsNode
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- true iff the graph contains 'node'.
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getEdges
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getEdges
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getEdges
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getNode
getNode.
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getNumEdges
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getNumNodes
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getNumEdges
getNumEdges.
- Specified by:
getNumEdges
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- the number of edges in the graph which are connected to a particular node.
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removeEdge
Removes the given edge from the graph.- Specified by:
removeEdge
in interfaceGraph
- Parameters:
edge
- aEdge
object- Returns:
- true if the edge was removed, false if not.
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removeEdges
Iterates through the list and removes any permissible edges found. The order in which edges are added is the order in which they are presented in the iterator.- Specified by:
removeEdges
in interfaceGraph
- Parameters:
edges
- aCollection
object- Returns:
- true if edges were added, false if not.
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removeNode
Removes a node from the graph.- Specified by:
removeNode
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- true if the node was removed, false if not.
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clear
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removeNodes
Iterates through the list and removes any permissible nodes found. The order in which nodes are removed is the order in which they are presented in the iterator.- Specified by:
removeNodes
in interfaceGraph
- Parameters:
nodes
- aList
object- Returns:
- true if nodes were added, false if not.
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isDefNoncollider
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isDefCollider
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getChildren
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getDegree
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getEdge
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getDirectedEdge
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getParents
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getIndegree
getIndegree.
- Specified by:
getIndegree
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- the number of arrow endpoints adjacent to a node.
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getDegree
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getOutdegree
getOutdegree.
- Specified by:
getOutdegree
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- the number of null endpoints adjacent to an edge.
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isChildOf
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isParentOf
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isExogenous
isExogenous.
- Specified by:
isExogenous
in interfaceGraph
- Parameters:
node
- aNode
object- Returns:
- true iff the given node is exogenous in the graph.
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toString
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isShowErrorTerms
public boolean isShowErrorTerms()isShowErrorTerms.
- Returns:
- a boolean
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setShowErrorTerms
public void setShowErrorTerms(boolean showErrorTerms) Setter for the field
showErrorTerms
.- Parameters:
showErrorTerms
- a boolean
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isTimeLagModel
public boolean isTimeLagModel()isTimeLagModel.
- Specified by:
isTimeLagModel
in interfaceGraph
- Returns:
- a boolean
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getTimeLagGraph
getTimeLagGraph.
- Specified by:
getTimeLagGraph
in interfaceGraph
- Returns:
- a
TimeLagGraph
object
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getSepset
Returns the set of nodes that form the separating set between two given nodes. A separating set is a set of nodes that, when conditioned on, renders the given nodes d-separated. -
resetErrorPositions
public void resetErrorPositions()resetErrorPositions.
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getAllAttributes
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getAttribute
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removeAttribute
removeAttribute.
- Specified by:
removeAttribute
in interfaceGraph
- Parameters:
key
- aString
object
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addAttribute
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getAmbiguousTriples
Getter for the field
ambiguousTriples
.- Specified by:
getAmbiguousTriples
in interfaceGraph
- Returns:
- a
Set
object
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setAmbiguousTriples
setAmbiguousTriples.
- Specified by:
setAmbiguousTriples
in interfaceGraph
- Parameters:
triples
- aSet
object
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getUnderLines
getUnderLines.
- Specified by:
getUnderLines
in interfaceGraph
- Returns:
- a
Set
object
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getDottedUnderlines
getDottedUnderlines.
- Specified by:
getDottedUnderlines
in interfaceGraph
- Returns:
- a
Set
object
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isAmbiguousTriple
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isUnderlineTriple
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addAmbiguousTriple
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addUnderlineTriple
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addDottedUnderlineTriple
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removeAmbiguousTriple
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removeUnderlineTriple
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removeDottedUnderlineTriple
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setUnderLineTriples
setUnderLineTriples.
- Specified by:
setUnderLineTriples
in interfaceGraph
- Parameters:
triples
- aSet
object
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setDottedUnderLineTriples
setDottedUnderLineTriples.
- Specified by:
setDottedUnderLineTriples
in interfaceGraph
- Parameters:
triples
- aSet
object
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removeTriplesNotInGraph
public void removeTriplesNotInGraph()removeTriplesNotInGraph.
- Specified by:
removeTriplesNotInGraph
in interfaceGraph
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