Updating version to 7.3.4 and fixing knowledge problem for PcMax. Als…

…o fixing a null pointer problem for PcMb.
cmu-phil · Apr 13, 2023 · e46656b · e46656b
1 parent c94c7f2
commit e46656b
Show file tree

Hide file tree

Showing 6 changed files with 26 additions and 14 deletions.
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Pc.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Pc.java
@@ -23,7 +23,7 @@
 import java.util.List;
 
 /**
- * CPC.
+ * PC.
  *
  * @author jdramsey
  */

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/PcMax.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/PcMax.java
@@ -23,13 +23,13 @@
 import java.util.List;
 
 /**
- * CPC.
+ * PC-Max.
  *
  * @author jdramsey
  */
 @edu.cmu.tetrad.annotation.Algorithm(
         name = "PC-Max",
-        command = "pcmax",
+        command = "pc-max",
         algoType = AlgType.forbid_latent_common_causes
 )
 @Bootstrapping
@@ -68,9 +68,9 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             search.setDepth(parameters.getInt(Params.DEPTH));
             search.setAggressivelyPreventCycles(true);
             search.setVerbose(parameters.getBoolean(Params.VERBOSE));
-            dataModel.setKnowledge(this.knowledge);
+            search.setKnowledge(this.knowledge);
 //            search.setConcurrent(parameters.getBoolean(Params.CONCURRENT_FAS));
-            search.setUseHeuristic(parameters.getBoolean(Params.USE_MAX_P_ORIENTATION_HEURISTIC));
+            search.setUseMaxP(parameters.getBoolean(Params.USE_MAX_P_ORIENTATION_HEURISTIC));
             search.setMaxPPathLength(parameters.getInt(Params.MAX_P_ORIENTATION_MAX_PATH_LENGTH));
             return search.search();
         } else {
@@ -95,7 +95,7 @@ public Graph getComparisonGraph(Graph graph) {
 
     @Override
     public String getDescription() {
-        return "PCMAX using " + this.test.getDescription();
+        return "PC-Max using " + this.test.getDescription();
     }
 
     @Override
@@ -127,7 +127,7 @@ public Knowledge getKnowledge() {
 
     @Override
     public void setKnowledge(Knowledge knowledge) {
-        this.knowledge = new Knowledge((Knowledge) knowledge);
+        this.knowledge = new Knowledge(knowledge);
     }
 
     @Override

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/OrientCollidersMaxP.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/OrientCollidersMaxP.java
@@ -143,6 +143,11 @@ private void testColliderMaxP(Graph graph, Map<Triple, Double> scores, Node a, N
         adja.remove(c);
         adjc.remove(a);
 
+        if (!(PcAll.isArrowpointAllowed(a, b, knowledge)
+                && (PcAll.isArrowpointAllowed(c, b, knowledge)))) {
+            return;
+        }
+
         double p = 0;
         List<Node> S = null;
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcAll.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcAll.java
@@ -360,6 +360,7 @@ public Graph search(List<Node> nodes) {
             orientCollidersMaxP.setUseHeuristic(this.useHeuristic);
             orientCollidersMaxP.setMaxPathLength(this.maxPathLength);
             orientCollidersMaxP.setDepth(this.depth);
+            orientCollidersMaxP.setKnowledge(this.knowledge);
             orientCollidersMaxP.orient(this.graph);
         } else if (this.colliderDiscovery == ColliderDiscovery.CONSERVATIVE) {
             if (this.verbose) {

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcMax.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcMax.java
@@ -91,8 +91,8 @@ public class PcMax implements GraphSearch {
 
     private boolean verbose;
     private boolean stable;
-    private boolean concurrent;
-    private boolean useHeuristic = false;
+    //    private boolean concurrent;
+    private boolean useMaxP = false;
     private int maxPPathLength = -1;
     private PcAll.ConflictRule conflictRule = PcAll.ConflictRule.OVERWRITE;
 
@@ -233,7 +233,7 @@ public Graph search(IFas fas, List<Node> nodes) {
                     "be in the domain of the independence test provided.");
         }
 
-        PcAll search = new PcAll(independenceTest);
+        edu.cmu.tetrad.search.PcAll search = new edu.cmu.tetrad.search.PcAll(independenceTest);
         search.setDepth(depth);
         search.setHeuristic(1);
         search.setKnowledge(this.knowledge);
@@ -249,14 +249,18 @@ public Graph search(IFas fas, List<Node> nodes) {
 //        } else {
 //            search.setConcurrent(PcAll.Concurrent.NO);
 //        }
-//
+
         search.setColliderDiscovery(PcAll.ColliderDiscovery.MAX_P);
         search.setConflictRule(conflictRule);
-        search.setUseHeuristic(useHeuristic);
+        search.setUseHeuristic(useMaxP);
         search.setMaxPathLength(maxPPathLength);
 //        search.setExternalGraph(externalGraph);
         search.setVerbose(verbose);
 
+//        fas.setKnowledge(getKnowledge());
+//        fas.setDepth(getDepth());
+//        fas.setVerbose(this.verbose);
+
         this.graph = search.search();
         this.sepsets = fas.getSepsets();
 
@@ -315,8 +319,8 @@ public void setStable(boolean stable) {
 //        this.concurrent = concurrent;
 //    }
 
-    public void setUseHeuristic(boolean useHeuristic) {
-        this.useHeuristic = useHeuristic;
+    public void setUseMaxP(boolean useMaxP) {
+        this.useMaxP = useMaxP;
     }
 
     public void setMaxPPathLength(int maxPPathLength) {

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcMb.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/PcMb.java
@@ -204,6 +204,8 @@ public Graph search(List<Node> targets) {
         this.logger.log("info", "BEGINNING step 1 (prune targets).");
 
         for (Node target : getTargets()) {
+            if (target == null) throw new NullPointerException("Target not specified");
+
             graph.addNode(target);
             constructFan(target, graph);