Fixing initial graph / bound graph problem for FGES throughout code.

cmu-phil · Feb 14, 2023 · 0bc6a1e · 0bc6a1e
1 parent 075e2da
commit 0bc6a1e
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Showing 5 changed files with 4 additions and 45 deletions.
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java
@@ -200,7 +200,7 @@ public void execute() {
             }
         }
 
-        this.fges.setExternalGraph(this.externalGraph);
+        this.fges.setBoundGraph(this.externalGraph);
         this.fges.setKnowledge((Knowledge) getParams().get("knowledge", new Knowledge()));
         this.fges.setVerbose(true);
         Graph graph = this.fges.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java
@@ -75,7 +75,7 @@ public Graph search(List<DataModel> dataModels, Parameters parameters) {
             }
 
             if (initial != null) {
-                search.setExternalGraph(initial);
+                search.setBoundGraph(initial);
             }
 
             return search.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Bridges2.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Bridges2.java
@@ -138,7 +138,7 @@ public Graph search() {
                     g.removeEdge(edge);
                     g.addEdge(reversed);
 
-                    fges.setExternalGraph(g);
+                    fges.setInitialGraph(g);
                     Graph g1 = fges.search();
                     double s1 = fges.getModelScore();
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BridgesOld.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BridgesOld.java
@@ -66,7 +66,7 @@ public Graph search() {
 
                     meeks.orientImplied(g);
 
-                    ges.setExternalGraph(g);
+                    ges.setInitialGraph(g);
                     Graph g1 = ges.search();
                     double s1 = ges.getModelScore();
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java
@@ -1964,47 +1964,6 @@ public static int[][] graphComparison(Graph trueCpdag, Graph estCpdag, PrintStre
         return counts;
     }
 
-    public static Graph reorient(Graph graph, DataModel dataModel, Knowledge knowledge) {
-        if (dataModel instanceof DataModelList) {
-            DataModelList list = (DataModelList) dataModel;
-            List<DataModel> dataSets = new ArrayList<>(list);
-            Fges images = new Fges(new SemBicScoreImages(dataSets));
-
-            images.setBoundGraph(graph);
-            images.setKnowledge(knowledge);
-            return images.search();
-        } else if (dataModel instanceof DataSet) {
-            DataSet dataSet = (DataSet) dataModel;
-
-            Score score;
-
-            if (dataModel.isContinuous()) {
-                score = new SemBicScore(new CovarianceMatrix(dataSet));
-            } else if (dataSet.isDiscrete()) {
-                score = new BDeuScore(dataSet);
-            } else {
-                throw new NullPointerException();
-            }
-
-            Fges ges = new Fges(score);
-
-            ges.setBoundGraph(graph);
-            ges.setKnowledge(knowledge);
-            return ges.search();
-        } else if (dataModel instanceof CovarianceMatrix) {
-            ICovarianceMatrix cov = (CovarianceMatrix) dataModel;
-            Score score = new SemBicScore(cov);
-
-            Fges ges = new Fges(score);
-
-            ges.setBoundGraph(graph);
-            ges.setKnowledge(knowledge);
-            return ges.search();
-        }
-
-        throw new IllegalStateException("Can do that that reorientation.");
-    }
-
     @NotNull
     public static Graph dagToPag(Graph trueGraph) {
         return new DagToPag(trueGraph).convert();