Examples with EdgeListGraph edu.cmu.tetrad.graph.EdgeListGraph used on opensource projects

Example 41 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method test4.

// Three latent fork case
@Test
public void test4() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(6);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X5"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2 });
    search.setOutputs(new int[] { 3, 4, 5 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Three Latent Fork Case");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X5"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 42 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method test6.

// Four latent case.
@Test
public void test6() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(8);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X3"), new ContinuousVariable("X7"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(1000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3 });
    search.setOutputs(new int[] { 4, 5, 6, 7 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Four Latent Case");
    print("search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure())");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("X6"));
    trueGraph.addNode(new ContinuousVariable("X7"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addNode(new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X5"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X6"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X3"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L3"), new ContinuousVariable("X7"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 43 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method test1.

@Test
public void test1() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    NodeEqualityMode.setEqualityMode(NodeEqualityMode.Type.NAME);
    Graph graph = emptyGraph(4);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1 });
    search.setOutputs(new int[] { 2, 3 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Test Case 1");
    // System.out.println(search.getDmStructure());
    // System.out.println(foundGraph);
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    assertEquals(trueGraph, foundGraph);
}

Example 44 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method test3.

@Test
public void test3() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(12);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X11"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X11"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X11"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X11"));
    graph.addDirectedEdge(new ContinuousVariable("X8"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X8"), new ContinuousVariable("X11"));
    graph.addDirectedEdge(new ContinuousVariable("X9"), new ContinuousVariable("X10"));
    graph.addDirectedEdge(new ContinuousVariable("X9"), new ContinuousVariable("X11"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 4, 5, 8, 9 });
    search.setOutputs(new int[] { 2, 3, 6, 7, 10, 11 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Test Case 3");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("X6"));
    trueGraph.addNode(new ContinuousVariable("X7"));
    trueGraph.addNode(new ContinuousVariable("X8"));
    trueGraph.addNode(new ContinuousVariable("X9"));
    trueGraph.addNode(new ContinuousVariable("X10"));
    trueGraph.addNode(new ContinuousVariable("X11"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X6"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X7"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X8"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X9"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X10"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X11"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 45 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method finishRenaming.

public void finishRenaming(int penalty) {
    String currentLine;
    try {
        FileReader file = new FileReader("src/edu/cmu/tetradproj/amurrayw/final_run/renamed_graph_penalty" + penalty + ".r.txt");
        BufferedReader br = new BufferedReader(file);
        String[] varNames = null;
        int nVar = 0;
        int lineNumber = 0;
        Graph graph = new EdgeListGraph();
        while ((currentLine = br.readLine()) != null) {
            // finds/gets variable names and adds to graph. Note that it assumes no whitespace in variable names.
            if (lineNumber == 0) {
                varNames = currentLine.split("\\s+");
                nVar = varNames.length;
                for (String nodeName : varNames) {
                    graph.addNode(new ContinuousVariable(nodeName));
                }
            } else {
                // splits line to single
                String[] adjInfoString = currentLine.split("\\s+");
                for (int i = 0; i < nVar; i++) {
                    ;
                    if (Integer.parseInt(adjInfoString[i]) > 1) {
                        print(adjInfoString[i]);
                    } else if (Integer.parseInt(adjInfoString[i]) < 0) {
                        print(adjInfoString[i]);
                    }
                    // System.out.println(adjInfoString[i]);
                    if (Integer.parseInt(adjInfoString[i]) == 1) {
                        // System.out.println("i");
                        // System.out.println(i);
                        // 
                        // System.out.println("varNames[i]");
                        // System.out.println(varNames[i]);
                        // 
                        // 
                        // System.out.println("lineNumber");
                        // System.out.println(lineNumber);
                        // 
                        // System.out.println("varNames.length");
                        // System.out.println(varNames.length);
                        // 
                        // 
                        // System.out.println("varNames[lineNumber]");
                        // System.out.println(varNames[lineNumber]);
                        graph.addDirectedEdge(graph.getNode(varNames[lineNumber - 1]), graph.getNode(varNames[i]));
                    // graph.addDirectedEdge(graph.getNode(varNames[i]), graph.getNode(varNames[lineNumber]));
                    }
                }
            }
            lineNumber++;
        // System.out.println(currentLine);
        }
        File outfile = new File("src/edu/cmu/tetradproj/amurrayw/final_run/renamed_final_output_" + penalty + "_.txt");
        try {
            FileOutputStream out = new FileOutputStream(outfile);
            PrintStream outStream = new PrintStream(out);
            outStream.println(graph);
        // outStream.println();
        } catch (java.io.FileNotFoundException e) {
            String x = "Can't write to file.";
            print(x);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}