Examples with ContinuousVariable edu.cmu.tetrad.data.ContinuousVariable used on opensource projects

Example 86 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable 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 87 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable 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();
    }
}

Example 88 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestDagInPatternIterator method test5.

@Test
public void test5() {
    RandomUtil.getInstance().setSeed(34828384L);
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 3; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag dag1 = new Dag(GraphUtils.randomGraph(nodes1, 0, 3, 30, 15, 15, false));
    Graph pattern = SearchGraphUtils.patternForDag(dag1);
    List<Node> nodes = pattern.getNodes();
    // Make random knowedge.
    int numTiers = 6;
    IKnowledge knowledge = new Knowledge2();
    for (Node node : nodes) {
        int tier = RandomUtil.getInstance().nextInt(numTiers);
        if (tier < 2)
            continue;
        knowledge.addToTier(tier, node.getName());
    }
    if (!knowledge.isViolatedBy(pattern)) {
        DagInPatternIterator iterator1 = new DagInPatternIterator(pattern);
        Graph dag0 = null;
        while (iterator1.hasNext()) {
            Graph dag = iterator1.next();
            if (!knowledge.isViolatedBy(dag)) {
                dag0 = dag;
            }
        }
        if (dag0 == null) {
            fail("Inconsistent knowledge.");
        }
    }
    if (!knowledge.isViolatedBy(pattern)) {
        DagInPatternIterator iterator2 = new DagInPatternIterator(pattern, knowledge);
        while (iterator2.hasNext()) {
            Graph dag = iterator2.next();
            if (knowledge.isViolatedBy(dag)) {
                throw new IllegalArgumentException("Knowledge violated");
            }
        }
    }
    DagInPatternIterator iterator3 = new DagInPatternIterator(pattern);
    int count = 0;
    while (iterator3.hasNext()) {
        iterator3.next();
        count++;
    }
    assertEquals(6, count);
}

Example 89 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestColtDataSet method testRemoveColumn.

@Test
public void testRemoveColumn() {
    int rows = 10;
    int cols = 5;
    List<Node> variables = new LinkedList<>();
    for (int i = 0; i < cols; i++) {
        variables.add(new ContinuousVariable("X" + i));
    }
    DataSet dataSet = new ColtDataSet(rows, variables);
    RandomUtil randomUtil = RandomUtil.getInstance();
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < cols; j++) {
            dataSet.setDouble(i, j, randomUtil.nextDouble());
        }
    }
    int[] _cols = new int[2];
    _cols[0] = 1;
    _cols[1] = 2;
    dataSet.removeCols(_cols);
    List<Node> _variables = new LinkedList<>(variables);
    _variables.remove(2);
    _variables.remove(1);
    assertEquals(dataSet.getVariables(), _variables);
}

Example 90 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestColtDataSet method testRowSubset.

@Test
public void testRowSubset() {
    int rows = 10;
    int cols = 5;
    List<Node> variables = new LinkedList<>();
    for (int i = 0; i < cols; i++) {
        variables.add(new ContinuousVariable("X" + i));
    }
    DataSet dataSet = new ColtDataSet(rows, variables);
    RandomUtil randomUtil = RandomUtil.getInstance();
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < cols; j++) {
            dataSet.setDouble(i, j, randomUtil.nextDouble());
        }
    }
    double d = dataSet.getDouble(2, 0);
    DataSet _dataSet = dataSet.subsetRows(new int[] { 2, 3, 4 });
    assertEquals(3, _dataSet.getNumRows());
    assertEquals(d, _dataSet.getDouble(0, 0), 0.001);
}