Examples with IndTestDSep edu.cmu.tetrad.search.IndTestDSep used on opensource projects

Example 1 with IndTestDSep

use of edu.cmu.tetrad.search.IndTestDSep in project tetrad by cmu-phil.

the class IndependenceFactsAction method actionPerformed.

// ========================PUBLIC METHODS==========================//
/**
 * Performs the action of opening a session from a file.
 */
public void actionPerformed(ActionEvent e) {
    this.independenceTest = getIndTestProducer().getIndependenceTest();
    final List<String> varNames = new ArrayList<>();
    varNames.add("VAR");
    varNames.addAll(getDataVars());
    varNames.add("?");
    varNames.add("+");
    final JComboBox variableBox = new JComboBox();
    DefaultComboBoxModel aModel1 = new DefaultComboBoxModel(varNames.toArray(new String[varNames.size()]));
    aModel1.setSelectedItem("VAR");
    variableBox.setModel(aModel1);
    // variableBox.addMouseListener(new MouseAdapter() {
    // public void mouseClicked(MouseEvent e) {
    // System.out.println(e);
    // }
    // });
    variableBox.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            JComboBox box = (JComboBox) e.getSource();
            String var = (String) box.getSelectedItem();
            LinkedList<String> vars = getVars();
            int size = vars.size();
            if ("VAR".equals(var)) {
                return;
            }
            for (int i = 2; i < getVars().size() - 1; i++) {
                if (wildcard(i)) {
                    if (!("?".equals(var) || "+".equals(var))) {
                        JOptionPane.showMessageDialog(centeringComp, "Please specify wildcards after other variables (e.g. X _||_ ? | Y, +)");
                        return;
                    }
                }
            }
            if ("?".equals(var)) {
                if (size >= 0 && !vars.contains("+")) {
                    vars.addLast(var);
                }
            } else if ("+".equals(var)) {
                if (size >= 2) {
                    vars.addLast(var);
                }
            } else if ((vars.indexOf("?") < 2) && !(vars.contains("+")) && !(vars.contains(var))) {
                vars.add(var);
            }
            if (wildcard(0) && vars.size() >= 2 && !wildcard(1)) {
                JOptionPane.showMessageDialog(centeringComp, "Please specify wildcards after other variables (e.g. X _||_ ? | Y, +)");
                return;
            }
            resetText();
            // This is a workaround to an introduced bug in the JDK whereby
            // repeated selections of the same item send out just one
            // action event.
            DefaultComboBoxModel aModel = new DefaultComboBoxModel(varNames.toArray(new String[varNames.size()]));
            aModel.setSelectedItem("VAR");
            variableBox.setModel(aModel);
        }
    });
    final JButton delete = new JButton("Delete");
    delete.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            if (!getVars().isEmpty()) {
                getVars().removeLast();
                resetText();
            }
        }
    });
    textField.addKeyListener(new KeyAdapter() {

        public void keyTyped(KeyEvent e) {
            if ('?' == e.getKeyChar()) {
                variableBox.setSelectedItem("?");
            } else if ('+' == e.getKeyChar()) {
                variableBox.setSelectedItem("+");
            } else if ('\b' == e.getKeyChar()) {
                vars.removeLast();
                resetText();
            }
            e.consume();
        }
    });
    delete.addKeyListener(new KeyAdapter() {

        public void keyTyped(KeyEvent e) {
            if ('?' == e.getKeyChar()) {
                variableBox.setSelectedItem("?");
            } else if ('+' == e.getKeyChar()) {
                variableBox.setSelectedItem("+");
            } else if ('\b' == e.getKeyChar()) {
                vars.removeLast();
                resetText();
            }
        }
    });
    variableBox.addKeyListener(new KeyAdapter() {

        public void keyTyped(KeyEvent e) {
            super.keyTyped(e);
            if ('\b' == e.getKeyChar()) {
                vars.removeLast();
                resetText();
            }
        }
    });
    JButton list = new JButton("LIST");
    list.setFont(new Font("Dialog", Font.BOLD, 14));
    list.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            generateResults();
        }
    });
    Box b1 = Box.createVerticalBox();
    Box b2 = Box.createHorizontalBox();
    b2.add(new JLabel("Test: "));
    b2.add(new JLabel(getIndependenceTest().toString()));
    b2.add(Box.createHorizontalGlue());
    b1.add(b2);
    b1.add(Box.createVerticalStrut(10));
    Box b3 = Box.createHorizontalBox();
    b3.add(getTextField());
    b3.add(variableBox);
    b3.add(delete);
    b1.add(b3);
    b1.add(Box.createVerticalStrut(10));
    tableModel = new AbstractTableModel() {

        public String getColumnName(int column) {
            if (column == 0) {
                return "Index";
            }
            if (column == 1) {
                if (independenceTest instanceof IndTestDSep) {
                    return "D-Separation Relation";
                } else {
                    return "Independence Relation";
                }
            } else if (column == 2) {
                return "Judgment";
            } else if (column == 3) {
                return "P Value";
            }
            return null;
        }

        public int getColumnCount() {
            if (usesDSeparation()) {
                return 3;
            } else {
                return 4;
            }
        }

        public int getRowCount() {
            return getResults().size();
        }

        public Object getValueAt(int rowIndex, int columnIndex) {
            Result result = getResults().get(rowIndex);
            if (columnIndex == 0) {
                return result.getIndex() + 1;
            }
            if (columnIndex == 1) {
                return result.getFact();
            } else if (columnIndex == 2) {
                if (independenceTest instanceof IndTestDSep) {
                    if (result.getType() == Result.Type.INDEPENDENT) {
                        return "D-Separated";
                    } else if (result.getType() == Result.Type.DEPENDENT) {
                        return "D-Connected";
                    } else if (result.getType() == Result.Type.UNDETERMINED) {
                        return "*";
                    }
                // return result.getType() ? "D-Separated" : "D-Connected";
                } else {
                    if (result.getType() == Result.Type.INDEPENDENT) {
                        return "Independent";
                    } else if (result.getType() == Result.Type.DEPENDENT) {
                        return "Dependent";
                    } else if (result.getType() == Result.Type.UNDETERMINED) {
                        return "*";
                    }
                // return result.getType() ? "Independent" : "Dependent";
                }
            } else if (columnIndex == 3) {
                return nf.format(result.getpValue());
            }
            return null;
        }

        public Class getColumnClass(int columnIndex) {
            if (columnIndex == 0) {
                return Number.class;
            }
            if (columnIndex == 1) {
                return String.class;
            } else if (columnIndex == 2) {
                return Number.class;
            } else if (columnIndex == 3) {
                return Number.class;
            }
            return null;
        }
    };
    JTable table = new JTable(tableModel);
    table.getColumnModel().getColumn(0).setMinWidth(40);
    table.getColumnModel().getColumn(0).setMaxWidth(40);
    table.getColumnModel().getColumn(1).setMinWidth(200);
    table.getColumnModel().getColumn(2).setMinWidth(100);
    table.getColumnModel().getColumn(2).setMaxWidth(100);
    if (!(usesDSeparation())) {
        table.getColumnModel().getColumn(3).setMinWidth(80);
        table.getColumnModel().getColumn(3).setMaxWidth(80);
    }
    JTableHeader header = table.getTableHeader();
    header.addMouseListener(new MouseAdapter() {

        public void mouseClicked(MouseEvent e) {
            JTableHeader header = (JTableHeader) e.getSource();
            Point point = e.getPoint();
            int col = header.columnAtPoint(point);
            int sortCol = header.getTable().convertColumnIndexToModel(col);
            sortByColumn(sortCol, true);
        }
    });
    JScrollPane scroll = new JScrollPane(table);
    scroll.setPreferredSize(new Dimension(400, 400));
    b1.add(scroll);
    Box b4 = Box.createHorizontalBox();
    b4.add(new JLabel("Limit list to "));
    IntTextField field = new IntTextField(getListLimit(), 7);
    field.setFilter(new IntTextField.Filter() {

        public int filter(int value, int oldValue) {
            try {
                setListLimit(value);
                return value;
            } catch (Exception e) {
                return oldValue;
            }
        }
    });
    b4.add(field);
    b4.add(new JLabel(" items."));
    b4.add(Box.createHorizontalGlue());
    b4.add(list);
    b1.add(b4);
    b1.add(Box.createVerticalStrut(10));
    JPanel panel = new JPanel();
    panel.setLayout(new BorderLayout());
    panel.add(b1, BorderLayout.CENTER);
    panel.setBorder(new EmptyBorder(10, 10, 10, 10));
    EditorWindow editorWindow = new EditorWindow(panel, "Independence Facts", "Save", false, centeringComp);
    DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
    editorWindow.setVisible(true);
    // Set the ok button so that pressing enter activates it.
    // jdramsey 5/5/02
    JRootPane root = SwingUtilities.getRootPane(editorWindow);
    if (root != null) {
        root.setDefaultButton(list);
    }
}

Example 2 with IndTestDSep

use of edu.cmu.tetrad.search.IndTestDSep in project tetrad by cmu-phil.

the class TestIndTestWaldLR method testIsIndependent.

@Test
public void testIsIndependent() {
    RandomUtil.getInstance().setSeed(1450705713157L);
    int numPassed = 0;
    for (int i = 0; i < 10; i++) {
        List<Node> nodes = new ArrayList<>();
        for (int i1 = 0; i1 < 10; i1++) {
            nodes.add(new ContinuousVariable("X" + (i1 + 1)));
        }
        Graph graph = GraphUtils.randomGraph(nodes, 0, 10, 3, 3, 3, false);
        SemPm pm = new SemPm(graph);
        SemIm im = new SemIm(pm);
        DataSet data = im.simulateData(1000, false);
        Discretizer discretizer = new Discretizer(data);
        discretizer.setVariablesCopied(true);
        discretizer.equalCounts(data.getVariable(0), 2);
        discretizer.equalCounts(data.getVariable(3), 2);
        data = discretizer.discretize();
        Node x1 = data.getVariable("X1");
        Node x2 = data.getVariable("X2");
        Node x3 = data.getVariable("X3");
        Node x4 = data.getVariable("X4");
        Node x5 = data.getVariable("X5");
        List<Node> cond = new ArrayList<>();
        cond.add(x3);
        cond.add(x4);
        cond.add(x5);
        Node x1Graph = graph.getNode(x1.getName());
        Node x2Graph = graph.getNode(x2.getName());
        List<Node> condGraph = new ArrayList<>();
        for (Node node : cond) {
            condGraph.add(graph.getNode(node.getName()));
        }
        // Using the Wald LR test since it's most up to date.
        IndependenceTest test = new IndTestMultinomialLogisticRegressionWald(data, 0.05, false);
        IndTestDSep dsep = new IndTestDSep(graph);
        boolean correct = test.isIndependent(x2, x1, cond) == dsep.isIndependent(x2Graph, x1Graph, condGraph);
        if (correct) {
            numPassed++;
        }
    }
    // System.out.println(RandomUtil.getInstance().getSeed());
    // Do not always get all 10.
    assertEquals(10, numPassed);
}

Example 3 with IndTestDSep

use of edu.cmu.tetrad.search.IndTestDSep in project tetrad by cmu-phil.

the class TestMbfs method testGenerateDaglist.

/**
 * Tests to make sure the algorithm for generating MB DAGs from an MB Pattern works, at least for one kind of tricky
 * case.
 */
@Test
public void testGenerateDaglist() {
    Graph graph = GraphConverter.convert("T-->X1,T-->X2,X1-->X2,T-->X3,X4-->T");
    IndTestDSep test = new IndTestDSep(graph);
    Mbfs search = new Mbfs(test, -1);
    Graph resultGraph = search.search("T");
    List mbDags = MbUtils.generateMbDags(resultGraph, true, search.getTest(), search.getDepth(), search.getTarget());
    assertTrue(mbDags.size() == 9);
    assertTrue(mbDags.contains(graph));
}

Example 4 with IndTestDSep

use of edu.cmu.tetrad.search.IndTestDSep in project tetrad by cmu-phil.

the class TestMbfs method testRandom.

@Test
public void testRandom() {
    RandomUtil.getInstance().setSeed(8388428832L);
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag dag = new Dag(GraphUtils.randomGraph(nodes1, 0, 10, 5, 5, 5, false));
    IndependenceTest test = new IndTestDSep(dag);
    Mbfs search = new Mbfs(test, -1);
    List<Node> nodes = dag.getNodes();
    for (Node node : nodes) {
        Graph resultMb = search.search(node.getName());
        Graph trueMb = GraphUtils.markovBlanketDag(node, dag);
        List<Node> resultNodes = resultMb.getNodes();
        List<Node> trueNodes = trueMb.getNodes();
        Set<String> resultNames = new HashSet<>();
        for (Node resultNode : resultNodes) {
            resultNames.add(resultNode.getName());
        }
        Set<String> trueNames = new HashSet<>();
        for (Node v : trueNodes) {
            trueNames.add(v.getName());
        }
        assertTrue(resultNames.equals(trueNames));
        Set<Edge> resultEdges = resultMb.getEdges();
        for (Edge resultEdge : resultEdges) {
            if (Edges.isDirectedEdge(resultEdge)) {
                String name1 = resultEdge.getNode1().getName();
                String name2 = resultEdge.getNode2().getName();
                Node node1 = trueMb.getNode(name1);
                Node node2 = trueMb.getNode(name2);
                // possibility that the node is actually a child.
                if (node1 == null) {
                    fail("Node " + name1 + " is not in the true graph.");
                }
                if (node2 == null) {
                    fail("Node " + name2 + " is not in the true graph.");
                }
                Edge trueEdge = trueMb.getEdge(node1, node2);
                if (trueEdge == null) {
                    Node resultNode1 = resultMb.getNode(node1.getName());
                    Node resultNode2 = resultMb.getNode(node2.getName());
                    Node resultTarget = resultMb.getNode(node.getName());
                    Edge a = resultMb.getEdge(resultNode1, resultTarget);
                    Edge b = resultMb.getEdge(resultNode2, resultTarget);
                    if (a == null || b == null) {
                        continue;
                    }
                    if ((Edges.isDirectedEdge(a) && Edges.isUndirectedEdge(b)) || (Edges.isUndirectedEdge(a) && Edges.isDirectedEdge(b))) {
                        continue;
                    }
                    fail("EXTRA EDGE: Edge in result MB but not true MB = " + resultEdge);
                }
                assertEquals(resultEdge.getEndpoint1(), trueEdge.getEndpoint1());
                assertEquals(resultEdge.getEndpoint2(), trueEdge.getEndpoint2());
            }
        }
    }
}

Example 5 with IndTestDSep

use of edu.cmu.tetrad.search.IndTestDSep in project tetrad by cmu-phil.

the class TestPcd method checkSearch.

/**
 * Presents the input graph to FCI and checks to make sure the output of FCI is equivalent to the given output
 * graph.
 */
private void checkSearch(String inputGraph, String outputGraph) {
    // Set up graph and node objects.
    Graph graph = GraphConverter.convert(inputGraph);
    // Set up search.
    IndependenceTest independence = new IndTestDSep(graph);
    Pcd pc = new Pcd(independence);
    // Run search
    Graph resultGraph = pc.search();
    // Build comparison graph.
    Graph trueGraph = GraphConverter.convert(outputGraph);
    resultGraph = GraphUtils.replaceNodes(resultGraph, trueGraph.getNodes());
    // Do test.
    assertTrue(resultGraph.equals(trueGraph));
}