Package edu.cmu.tetrad.search

Class SvarFciOrient

java.lang.Object
edu.cmu.tetrad.search.SvarFciOrient
public final class SvarFciOrient extends Object
Extends Erin Korber's implementation of the Fast Causal Inference algorithm (found in FCI.java) with Jiji Zhang's Augmented FCI rules (found in sec. 4.1 of Zhang's 2006 PhD dissertation, "Causal Inference and Reasoning in Causally Insufficient Systems").

This class is based off a copy of FCI.java taken from the repository on 2008/12/16, revision 7306. The extension is done by extending doFinalOrientation() with methods for Zhang's rules R5-R10 which implements the augmented search. (By a remark of Zhang's, the rule applications can be staged in this way.)

Author:
Erin Korber, June 2004, Alex Smith, December 2008, Joseph Ramsey, Choh-Man Teng, Daniel Malinsky

This is a copy of FciOrient.java for the SvarFCI algorithm. The main difference is that if an edge is orient, it will also orient all homologous edges to preserve the time-repeating structure assumed by SvarFCI. Based on (but not identicial to) code by Entner and Hoyer for their 2010 paper. Modified by DMalinsky 4/20/2016.

  • Constructor Details

    • SvarFciOrient

      public SvarFciOrient(SepsetProducer sepsets, IndependenceTest independenceTest)
      Constructs a new FCI search for the given independence test and background knowledge.

  • Method Details

    • orient

      public Graph orient(Graph graph)

    • getSepsets

      public SepsetProducer getSepsets()

    • getKnowledge

      public Knowledge getKnowledge()
      The background knowledge.

    • setKnowledge

      public void setKnowledge(Knowledge knowledge)

    • isCompleteRuleSetUsed

      public boolean isCompleteRuleSetUsed()
      Returns:
      true if Zhang's complete rule set should be used, false if only R1-R4 (the rule set of the original FCI) should be used. False by default.

    • setCompleteRuleSetUsed

      public void setCompleteRuleSetUsed(boolean completeRuleSetUsed)
      Parameters:
      completeRuleSetUsed - set to true if Zhang's complete rule set should be used, false if only R1-R4 (the rule set of the original FCI) should be used. False by default.

    • ruleR0

      public void ruleR0(Graph graph)
      Orients colliders in the graph. (FCI Step C)

      Zhang's step F3, rule R0.

    • doFinalOrientation

      public void doFinalOrientation(Graph graph)
      Orients the graph according to rules in the graph (FCI step D).

      Zhang's step F4, rules R1-R10.

    • rulesR1R2cycle

      public void rulesR1R2cycle(Graph graph)

    • ruleR3

      public void ruleR3(Graph graph)
      Implements the double-triangle orientation rule, which states that if D*-oB, A*->B<-*C and A*-oDo-*C, then D*->B.

      This is Zhang's rule R3.

    • ruleR4B

      public void ruleR4B(Graph graph)
      The triangles that must be oriented this way (won't be done by another rule) all look like the ones below, where the dots are a collider path from L to A with each node on the path (except L) a parent of C. 
                B
         xo           x is either an arrowhead or a circle
        /  \
       v    v
 L....A --> C

      This is Zhang's rule R4, discriminating undirectedPaths.

    • ddpOrient

      public void ddpOrient(Node a, Node b, Node c, Graph graph)
      a method to search "back from a" to find a DDP. It is called with a reachability list (first consisting only of a). This is breadth-first, utilizing "reachability" concept from Geiger, Verma, and Pearl 1990. The body of a DDP consists of colliders that are parents of c.

    • ruleR5

      public void ruleR5(Graph graph)
      Implements Zhang's rule R5, orient circle undirectedPaths: for any Ao-oB, if there is an uncovered circle path u = [A,C,...,D,B] such that A,D nonadjacent and B,C nonadjacent, then A---B and orient every edge on u undirected.

    • ruleR6R7

      public void ruleR6R7(Graph graph)
      Implements Zhang's rules R6 and R7, applies them over the graph once. Orient single tails. R6: If A---Bo-*C then A---B--*C. R7: If A--oBo-*C and A,C nonadjacent, then A--oB--*C

    • rulesR8R9R10

      public void rulesR8R9R10(Graph graph)
      Implements Zhang's rules R8, R9, R10, applies them over the graph once. Orient arrow tails. I.e., tries R8, R9, and R10 in that sequence on each Ao->C in the graph.

    • isPossibleDsepSearchDone

      public boolean isPossibleDsepSearchDone()

    • setPossibleDsepSearchDone

      public void setPossibleDsepSearchDone(boolean possibleDsepSearchDone)

    • getMaxPathLength

      public int getMaxPathLength()
      Returns:
      the maximum length of any discriminating path, or -1 of unlimited.

    • setMaxPathLength

      public void setMaxPathLength(int maxPathLength)
      Parameters:
      maxPathLength - the maximum length of any discriminating path, or -1 if unlimited.

    • isVerbose

      public boolean isVerbose()
      True iff verbose output should be printed.

    • setVerbose

      public void setVerbose(boolean verbose)

    • setTruePag

      public void setTruePag(Graph truePag)

    • getTruePag

      public Graph getTruePag()
      The true PAG if available. Can be null.

    • setChangeFlag

      public void setChangeFlag(boolean changeFlag)

    • isChangeFlag

      public boolean isChangeFlag()
      change flag for repeat rules

    • getNameNoLag

      public String getNameNoLag(Object obj)