Package edu.cmu.tetrad.graph

Class GraphTransforms

java.lang.Object

edu.cmu.tetrad.graph.GraphTransforms

public class GraphTransforms
extends Object

Transformations that transform one graph into another.

Version:

$Id: $Id

Author:

josephramsey

Method Summary

Modifier and Type	Method	Description
static Graph	dagFromCpdag(Graph graph)	Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG).
static Graph	dagFromCpdag(Graph graph, boolean verbose)	Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG).
static Graph	dagFromCpdag(Graph graph, boolean meekPreventCycles, boolean verbose)	Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG).
static Graph	dagFromCpdag(Graph graph, Knowledge knowledge)	dagFromCpdag.
static Graph	dagFromCpdag(Graph cpdag, Knowledge knowledge, boolean meekPreventCycles, boolean verbose)	Returns a random DAG from the given CPDAG.
static Graph	dagToCpdag(Graph dag)	Returns the completed partially directed acyclic graph (CPDAG) for a given directed acyclic graph (DAG).
static @NotNull Graph	dagToMag(Graph dag)	Converts a Directed Acyclic Graph (DAG) to a Maximal Ancestral Graph (MAG) by adding arrows to the edges.
static @NotNull Graph	dagToPag(Graph trueGraph)	Converts a Directed Acyclic Graph (DAG) to a Partial Ancestral Graph (PAG) using the DagToPag algorithm.
static List<Graph>	generateCpdagDags(Graph cpdag, boolean orientBidirectedEdges)	Generates the list of DAGs in the given cpdag.
static List<Graph>	getAllGraphsByDirectingUndirectedEdges(Graph skeleton)	Returns a list of all possible graphs obtained by directing undirected edges in the given graph.
static List<Graph>	getDagsInCpdagMeek(Graph cpdag, Knowledge knowledge)	Retrieves a list of directed acyclic graphs (DAGs) within the given completed partially directed acyclic graph (CPDAG) using the Meek rules.
static Graph	magFromPag(Graph pag)	Picks a random Maximal Ancestral Graph (MAG) from the given Partial Ancestral Graph (PAG) by randomly orienting the circle endpoints as either tail or arrow and then applying the final FCI orient algorithm after each change.
static void	transformCpdagIntoRandomDag(Graph graph, Knowledge knowledge, boolean meekPreventCycles, boolean verbose)	Transforms a completed partially directed acyclic graph (CPDAG) into a random directed acyclic graph (DAG) by randomly orienting the undirected edges in the CPDAG in shuffled order.
static void	transormPagIntoRandomMag(Graph pag)	Transforms a partially ancestral graph (PAG) into a maximally ancestral graph (MAG) by randomly orienting the circle endpoints as either tail or arrow and then applying the final FCI orient algorithm after each change.
static Graph	zhangMagFromPag(Graph pag)	Transforms a partial ancestral graph (PAG) into a maximal ancestral graph (MAG) using Zhang's 2008 Theorem 2.

Methods inherited from class java.lang.Object

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

Method Details

dagFromCpdag

public static Graph dagFromCpdag(Graph graph)

Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG). If the given CPDAG is not a PDAG (Partially Directed Acyclic Graph), returns null.

Parameters:

graph - the CPDAG to be converted into a DAG

Returns:

a directed acyclic graph (DAG) obtained from the given CPDAG. If the given CPDAG is not a PDAG, returns null.

dagFromCpdag

public static Graph dagFromCpdag(Graph graph,
 boolean verbose)

Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG). If the given CPDAG is not a PDAG (Partially Directed Acyclic Graph), returns null.

Parameters:

graph - the CPDAG to be converted into a DAG

verbose - whether to print verbose output

Returns:

a directed acyclic graph (DAG) obtained from the given CPDAG. If the given CPDAG is not a PDAG, returns null.

dagFromCpdag

public static Graph dagFromCpdag(Graph graph,
 boolean meekPreventCycles,
 boolean verbose)

Converts a completed partially directed acyclic graph (CPDAG) into a directed acyclic graph (DAG). If the given CPDAG is not a PDAG (Partially Directed Acyclic Graph), returns null.

Parameters:

graph - the CPDAG to be converted into a DAG

meekPreventCycles - whether to prevent cycles using the Meek rules by orienting additional arbitrary unshielded colliders in the graph

verbose - whether to print verbose output

Returns:

a directed acyclic graph (DAG) obtained from the given CPDAG. If the given CPDAG is not a PDAG, returns null.

dagFromCpdag

public static Graph dagFromCpdag(Graph graph,
 Knowledge knowledge)

dagFromCpdag.

Parameters:

graph - a Graph

knowledge - a Knowledge

Returns:

a Graph object

dagFromCpdag

public static Graph dagFromCpdag(Graph cpdag,
 Knowledge knowledge,
 boolean meekPreventCycles,
 boolean verbose)

Returns a random DAG from the given CPDAG. If the given CPDAG is not a PDAG, returns null.

Parameters:

cpdag - the CPDAG

knowledge - the knowledge

meekPreventCycles - whether to prevent cycles using the Meek rules by orienting additional arbitrary unshielded colliders in the graph.

verbose - whether to print verbose output.

Returns:

a DAG from the given CPDAG. If the given CPDAG is not a PDAG, returns null.

transformCpdagIntoRandomDag

public static void transformCpdagIntoRandomDag(Graph graph,
 Knowledge knowledge,
 boolean meekPreventCycles,
 boolean verbose)

Transforms a completed partially directed acyclic graph (CPDAG) into a random directed acyclic graph (DAG) by randomly orienting the undirected edges in the CPDAG in shuffled order.

Parameters:

graph - The original graph from which the CPDAG was derived.

knowledge - The knowledge available to check if a potential DAG violates any constraints.

meekPreventCycles - Whether to prevent cycles using the Meek rules by orienting additional arbitrary unshielded colliders in the graph.

verbose - Whether to print verbose output.

magFromPag

public static Graph magFromPag(Graph pag)

Picks a random Maximal Ancestral Graph (MAG) from the given Partial Ancestral Graph (PAG) by randomly orienting the circle endpoints as either tail or arrow and then applying the final FCI orient algorithm after each change. The PAG graph type is not checked.

Parameters:

pag - The partially ancestral pag to transform.

Returns:

The maximally ancestral pag obtained from the PAG.

transormPagIntoRandomMag

public static void transormPagIntoRandomMag(Graph pag)

Transforms a partially ancestral graph (PAG) into a maximally ancestral graph (MAG) by randomly orienting the circle endpoints as either tail or arrow and then applying the final FCI orient algorithm after each change.

Parameters:

pag - The partially ancestral graph to transform.

zhangMagFromPag

public static Graph zhangMagFromPag(Graph pag)

Transforms a partial ancestral graph (PAG) into a maximal ancestral graph (MAG) using Zhang's 2008 Theorem 2.

Parameters:

pag - The partially ancestral graph to transform.

Returns:

The maximally ancestral graph obtained from the PAG.

generateCpdagDags

public static List<Graph> generateCpdagDags(Graph cpdag,
 boolean orientBidirectedEdges)

Generates the list of DAGs in the given cpdag.

Parameters:

cpdag - a Graph object

orientBidirectedEdges - a boolean

Returns:

a List object

getDagsInCpdagMeek

public static List<Graph> getDagsInCpdagMeek(Graph cpdag,
 Knowledge knowledge)

Retrieves a list of directed acyclic graphs (DAGs) within the given completed partially directed acyclic graph (CPDAG) using the Meek rules.

Parameters:

cpdag - The completed partially directed acyclic graph (CPDAG) from which to retrieve the DAGs.

knowledge - The knowledge available to check if a potential DAG violates any constraints.

Returns:

A List of Graph objects representing the DAGs within the CPDAG.

getAllGraphsByDirectingUndirectedEdges

public static List<Graph> getAllGraphsByDirectingUndirectedEdges(Graph skeleton)

Returns a list of all possible graphs obtained by directing undirected edges in the given graph.

Parameters:

skeleton - the graph to transform

Returns:

a list of all possible graphs obtained by directing undirected edges

dagToCpdag

public static Graph dagToCpdag(Graph dag)

Returns the completed partially directed acyclic graph (CPDAG) for a given directed acyclic graph (DAG).

Parameters:

dag - The input DAG.

Returns:

The CPDAG resulting from applying Meek Rules to the input DAG.

dagToPag

@NotNull
public static @NotNull Graph dagToPag(Graph trueGraph)

Converts a Directed Acyclic Graph (DAG) to a Partial Ancestral Graph (PAG) using the DagToPag algorithm.

Parameters:

trueGraph - The input DAG to be converted.

Returns:

The resulting PAG obtained from the input DAG.

dagToMag

@NotNull
public static @NotNull Graph dagToMag(Graph dag)

Converts a Directed Acyclic Graph (DAG) to a Maximal Ancestral Graph (MAG) by adding arrows to the edges.

Parameters:

dag - The input DAG to be converted.

Returns:

The resulting MAG obtained from the input DAG.