New FGES, EBIC, revised SEM BIC, related files.

tetrad-gui/src/main/java/edu/cmu/tetradapp/FciTemp.java

@@ -0,0 +1,85 @@
+///////////////////////////////////////////////////////////////////////////////
+// For information as to what this class does, see the Javadoc, below.       //
+// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
+// 2007, 2008, 2009, 2010, 2014, 2015 by Peter Spirtes, Richard Scheines, Joseph   //
+// Ramsey, and Clark Glymour.                                                //
+//                                                                           //
+// This program is free software; you can redistribute it and/or modify      //
+// it under the terms of the GNU General Public License as published by      //
+// the Free Software Foundation; either version 2 of the License, or         //
+// (at your option) any later version.                                       //
+//                                                                           //
+// This program is distributed in the hope that it will be useful,           //
+// but WITHOUT ANY WARRANTY; without even the implied warranty of            //
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
+// GNU General Public License for more details.                              //
+//                                                                           //
+// You should have received a copy of the GNU General Public License         //
+// along with this program; if not, write to the Free Software               //
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
+///////////////////////////////////////////////////////////////////////////////
+package edu.cmu.tetradapp;
+
+import edu.cmu.tetrad.data.DataReader;
+import edu.cmu.tetrad.data.DataSet;
+import edu.cmu.tetrad.data.IKnowledge;
+import edu.cmu.tetrad.graph.Graph;
+import edu.cmu.tetrad.graph.GraphUtils;
+import edu.cmu.tetrad.search.Fci;
+import edu.cmu.tetrad.search.IndTestFisherZ;
+import edu.cmu.tetrad.util.DataConvertUtils;
+import edu.pitt.dbmi.data.reader.Data;
+import edu.pitt.dbmi.data.reader.Delimiter;
+import edu.pitt.dbmi.data.reader.tabular.ContinuousTabularDatasetFileReader;
+import edu.pitt.dbmi.data.reader.tabular.ContinuousTabularDatasetReader;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+
+public final class FciTemp {
+
+    public static void main(String... args) {
+        if (args.length != 3) {
+            throw new RuntimeException("java -jar edu.cmu.edu.tetrad.FciTemp [data] [knowledge] [alpha]");
+        }
+
+        Path dataFile = new File(args[0]).toPath();
+        Delimiter delimiter = Delimiter.TAB;
+
+        ContinuousTabularDatasetReader dataReader = new ContinuousTabularDatasetFileReader(dataFile, delimiter);
+        dataReader.setHasHeader(true);
+        DataSet dataSet;
+
+        try {
+            Data data = dataReader.readInData();
+            dataSet = (DataSet) DataConvertUtils.toDataModel(data);
+        } catch (IOException e) {
+            e.printStackTrace();
+            throw new RuntimeException("Expecting a properly formatted data file: " + args[0]);
+        }
+
+        IKnowledge knowledge;
+
+        try {
+            knowledge = new DataReader().parseKnowledge(new File(args[1]));
+        } catch (IOException e) {
+            throw new RuntimeException("Expecting properly formatted knowledge file: " + args[1]);
+        }
+
+        double alpha = 0;
+        try {
+            alpha = Double.parseDouble(args[2]);
+        } catch (NumberFormatException e) {
+            throw new RuntimeException("Expecting a number for alpha");
+        }
+
+        Fci fci = new Fci(new IndTestFisherZ(dataSet, alpha));
+        fci.setKnowledge(knowledge);
+        fci.setHeuristic(1); // lexicographic order.
+
+        Graph graph = fci.search();
+
+        System.out.println(GraphUtils.graphToText(graph));
+    }
+}