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 TypeMethodDescriptionvoidaddAmbiguousTriple(Node x, Node y, Node z) addAmbiguousTriple.voidaddAttribute(String key, Object value) addAttribute.booleanaddBidirectedEdge(Node nodeA, Node nodeB) Adds a bidirected edges <-> to the graph.booleanaddDirectedEdge(Node nodeA, Node nodeB) Adds a directed edge --> to the graph.voidaddDottedUnderlineTriple(Node x, Node y, Node z) addDottedUnderlineTriple.booleanAdds the specified edge to the graph, provided it is not already in the graph.booleanAdds a node to the graph.booleanaddNondirectedEdge(Node nodeA, Node nodeB) Adds a nondirected edges o-o to the graph.booleanaddPartiallyOrientedEdge(Node nodeA, Node nodeB) Adds a partially oriented edge o-> to the graph.voidAdds a PropertyChangeListener to the graph.voidaddUnderlineTriple(Node x, Node y, Node z) addUnderlineTriple.booleanaddUndirectedEdge(Node nodeA, Node nodeB) Adds an undirected edge --- to the graph.voidclear()clear.booleancontainsEdge(Edge edge) Determines whether this graph contains the given edge.booleancontainsNode(Node node) Determines whether this graph contains the given node.booleanDetermines 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.voidfullyConnect(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.intgetDegree.intgetDegree.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.intgetIndegree(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.intgetNumEdges.intgetNumEdges(Node node) getNumEdges.intgetNumNodes.intgetOutdegree(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.booleanisAdjacentTo(Node nodeX, Node nodeY) isAdjacentTo.booleanisAmbiguousTriple(Node x, Node y, Node z) States whether r-s-r is an underline triple or not.booleanisChildOf.booleanisDefCollider(Node node1, Node node2, Node node3) Added by ekorber, 2004/6/9.booleanisDefNoncollider(Node node1, Node node2, Node node3) Added by ekorber, 2004/6/9.static booleanisErrorEdge(Edge edge) isErrorEdge.booleanisExogenous(Node node) isExogenous.booleanisParameterizable(Node node) isParameterizable.booleanisParentOf(Node node1, Node node2) Determines whether node1 is a parent of node2.booleanisShowErrorTerms.booleanisTimeLagModel.booleanisUnderlineTriple(Node x, Node y, Node z) States whether r-s-r is an underline triple or not.paths()paths.voidremoveAmbiguousTriple(Node x, Node y, Node z) removeAmbiguousTriple.voidremoveAttribute(String key) removeAttribute.voidremoveDottedUnderlineTriple(Node x, Node y, Node z) removeDottedUnderlineTriple.booleanremoveEdge(Edge edge) Removes the given edge from the graph.booleanremoveEdge(Node node1, Node node2) Removes an edge between two given nodes.booleanremoveEdges(Node node1, Node node2) Removes all edges connecting node A to node B.booleanremoveEdges(Collection<Edge> edges) Iterates through the list and removes any permissible edges found.booleanremoveNode(Node node) Removes a node from the graph.booleanremoveNodes(List<Node> nodes) Iterates through the list and removes any permissible nodes found.voidremoveTriplesNotInGraph.voidremoveUnderlineTriple(Node x, Node y, Node z) removeUnderlineTriple.voidreorientAllWith(Endpoint endpoint) Reorients all edges in the graph with the given endpoint.voidresetErrorPositions.static SemGraphGenerates a simple exemplar of this class to test serialization.voidsetAmbiguousTriples(Set<Triple> triples) setAmbiguousTriples.voidsetDottedUnderLineTriples(Set<Triple> triples) setDottedUnderLineTriples.booleansetEndpoint(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.voidsetNodes.voidsetShowErrorTerms(boolean showErrorTerms) Setter for the fieldshowErrorTerms.voidsetUnderLineTriples(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.voidtransferAttributes(Graph graph) transferAttributes.voidtransferNodesAndEdges(Graph graph) Transfers nodes and edges from one graph to another.Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, waitMethods 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:
isParameterizablein interfaceGraph- Parameters:
node- aNodeobject- 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:
transferNodesAndEdgesin 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:
transferAttributesin interfaceGraph- Parameters:
graph- aGraphobject- Throws:
IllegalArgumentException- if any.
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paths
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getNodeNames
getNodeNames.
- Specified by:
getNodeNamesin interfaceGraph- Returns:
- a
Listobject
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fullyConnect
Removes all edges from the graph and fully connects it using #-# edges, where # is the given endpoint.- Specified by:
fullyConnectin interfaceGraph- Parameters:
endpoint- aEndpointobject
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reorientAllWith
Reorients all edges in the graph with the given endpoint.- Specified by:
reorientAllWithin interfaceGraph- Parameters:
endpoint- aEndpointobject
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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:
removeEdgein 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:
removeEdgesin interfaceGraph- Parameters:
node1- aNodeobjectnode2- aNodeobject- 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:
setEndpointin interfaceGraph- Parameters:
node1- aNodeobjectnode2- aNodeobjectendpoint- aEndpointobject- 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:
addPropertyChangeListenerin interfaceGraph- Parameters:
l- aPropertyChangeListenerobject
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containsEdge
Determines whether this graph contains the given edge.- Specified by:
containsEdgein interfaceGraph- Parameters:
edge- aEdgeobject- Returns:
- true iff the graph contain 'edge'.
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containsNode
Determines whether this graph contains the given node.- Specified by:
containsNodein interfaceGraph- Parameters:
node- aNodeobject- 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:
getNumEdgesin interfaceGraph- Parameters:
node- aNodeobject- 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:
removeEdgein interfaceGraph- Parameters:
edge- aEdgeobject- 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:
removeEdgesin interfaceGraph- Parameters:
edges- aCollectionobject- Returns:
- true if edges were added, false if not.
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removeNode
Removes a node from the graph.- Specified by:
removeNodein interfaceGraph- Parameters:
node- aNodeobject- 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:
removeNodesin interfaceGraph- Parameters:
nodes- aListobject- 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:
getIndegreein interfaceGraph- Parameters:
node- aNodeobject- Returns:
- the number of arrow endpoints adjacent to a node.
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getDegree
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getOutdegree
getOutdegree.
- Specified by:
getOutdegreein interfaceGraph- Parameters:
node- aNodeobject- 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:
isExogenousin interfaceGraph- Parameters:
node- aNodeobject- 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:
isTimeLagModelin interfaceGraph- Returns:
- a boolean
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getTimeLagGraph
getTimeLagGraph.
- Specified by:
getTimeLagGraphin interfaceGraph- Returns:
- a
TimeLagGraphobject
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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:
removeAttributein interfaceGraph- Parameters:
key- aStringobject
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addAttribute
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getAmbiguousTriples
Getter for the field
ambiguousTriples.- Specified by:
getAmbiguousTriplesin interfaceGraph- Returns:
- a
Setobject
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setAmbiguousTriples
setAmbiguousTriples.
- Specified by:
setAmbiguousTriplesin interfaceGraph- Parameters:
triples- aSetobject
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getUnderLines
getUnderLines.
- Specified by:
getUnderLinesin interfaceGraph- Returns:
- a
Setobject
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getDottedUnderlines
getDottedUnderlines.
- Specified by:
getDottedUnderlinesin interfaceGraph- Returns:
- a
Setobject
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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:
setUnderLineTriplesin interfaceGraph- Parameters:
triples- aSetobject
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setDottedUnderLineTriples
setDottedUnderLineTriples.
- Specified by:
setDottedUnderLineTriplesin interfaceGraph- Parameters:
triples- aSetobject
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removeTriplesNotInGraph
public void removeTriplesNotInGraph()removeTriplesNotInGraph.
- Specified by:
removeTriplesNotInGraphin interfaceGraph
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