コード例 #1
0
ファイル: TestSearchGraph.java プロジェクト: jdramsey/tetrad
  public static Graph weightedRandomGraph(int n, int e) {
    List<Node> nodes = new ArrayList<Node>();
    for (int i = 0; i < n; i++) nodes.add(new GraphNode("X" + i));

    Graph graph = new EdgeListGraph(nodes);

    for (int e0 = 0; e0 < e; e0++) {
      int i1 = weightedRandom(nodes, graph);
      //            int i2 = RandomUtil.getInstance().nextInt(n);
      int i2 = weightedRandom(nodes, graph);

      if (!(shortestPath(nodes.get(i1), nodes.get(i2), graph) < 9)) {
        e0--;
        continue;
      }

      if (i1 == i2) {
        e0--;
        continue;
      }

      Edge edge = Edges.undirectedEdge(nodes.get(i1), nodes.get(i2));

      if (graph.containsEdge(edge)) {
        e0--;
        continue;
      }

      graph.addEdge(edge);
    }

    for (Edge edge : graph.getEdges()) {
      Node n1 = edge.getNode1();
      Node n2 = edge.getNode2();

      if (!graph.isAncestorOf(n2, n1)) {
        graph.removeEdge(edge);
        graph.addDirectedEdge(n1, n2);
      } else {
        graph.removeEdge(edge);
        graph.addDirectedEdge(n2, n1);
      }
    }

    return graph;
  }
コード例 #2
0
ファイル: TestMimbuild3.java プロジェクト: jdramsey/tetrad
  public void rtest3() {
    Node x = new GraphNode("X");
    Node y = new GraphNode("Y");
    Node z = new GraphNode("Z");
    Node w = new GraphNode("W");

    List<Node> nodes = new ArrayList<Node>();
    nodes.add(x);
    nodes.add(y);
    nodes.add(z);
    nodes.add(w);

    Graph g = new EdgeListGraph(nodes);
    g.addDirectedEdge(x, y);
    g.addDirectedEdge(x, z);
    g.addDirectedEdge(y, w);
    g.addDirectedEdge(z, w);

    Graph maxGraph = null;
    double maxPValue = -1.0;
    ICovarianceMatrix maxLatentCov = null;

    Graph mim = DataGraphUtils.randomMim(g, 8, 0, 0, 0, true);
    //        Graph mim = DataGraphUtils.randomSingleFactorModel(5, 5, 8, 0, 0, 0);
    Graph mimStructure = structure(mim);
    SemPm pm = new SemPm(mim);

    System.out.println("\n\nTrue graph:");
    System.out.println(mimStructure);

    SemImInitializationParams params = new SemImInitializationParams();
    params.setCoefRange(0.5, 1.5);

    SemIm im = new SemIm(pm, params);

    int N = 1000;

    DataSet data = im.simulateData(N, false);

    CovarianceMatrix cov = new CovarianceMatrix(data);

    for (int i = 0; i < 1; i++) {

      ICovarianceMatrix _cov = DataUtils.reorderColumns(cov);
      List<List<Node>> partition;

      FindOneFactorClusters fofc = new FindOneFactorClusters(_cov, TestType.TETRAD_WISHART, .001);
      fofc.search();
      partition = fofc.getClusters();
      System.out.println(partition);

      List<String> latentVarList = reidentifyVariables(mim, data, partition, 2);

      Mimbuild2 mimbuild = new Mimbuild2();

      mimbuild.setAlpha(0.001);
      //            mimbuild.setMinimumSize(5);

      // To test knowledge.
      //            Knowledge knowledge = new Knowledge2();
      //            knowledge.setEdgeForbidden("L.Y", "L.W", true);
      //            knowledge.setEdgeRequired("L.Y", "L.Z", true);
      //            mimbuild.setKnowledge(knowledge);

      Graph mimbuildStructure = mimbuild.search(partition, latentVarList, _cov);

      double pValue = mimbuild.getpValue();
      System.out.println(mimbuildStructure);
      System.out.println("P = " + pValue);
      System.out.println("Latent Cov = " + mimbuild.getLatentsCov());

      if (pValue > maxPValue) {
        maxPValue = pValue;
        maxGraph = new EdgeListGraph(mimbuildStructure);
        maxLatentCov = mimbuild.getLatentsCov();
      }
    }

    System.out.println("\n\nTrue graph:");
    System.out.println(mimStructure);
    System.out.println("\nBest graph:");
    System.out.println(maxGraph);
    System.out.println("P = " + maxPValue);
    System.out.println("Latent Cov = " + maxLatentCov);
    System.out.println();
  }
コード例 #3
0
ファイル: GesConcurrent.java プロジェクト: renjiey/tetrad
  private void addRequiredEdges(Graph graph) {
    if (true) return;
    if (knowledgeEmpty()) return;

    for (Iterator<KnowledgeEdge> it = getKnowledge().requiredEdgesIterator(); it.hasNext(); ) {
      KnowledgeEdge next = it.next();

      Node nodeA = graph.getNode(next.getFrom());
      Node nodeB = graph.getNode(next.getTo());

      if (!graph.isAncestorOf(nodeB, nodeA)) {
        graph.removeEdges(nodeA, nodeB);
        graph.addDirectedEdge(nodeA, nodeB);
        TetradLogger.getInstance()
            .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
      }
    }
    for (Edge edge : graph.getEdges()) {
      final String A = edge.getNode1().getName();
      final String B = edge.getNode2().getName();

      if (knowledge.isForbidden(A, B)) {
        Node nodeA = edge.getNode1();
        Node nodeB = edge.getNode2();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      } else if (knowledge.isForbidden(B, A)) {
        Node nodeA = edge.getNode2();
        Node nodeB = edge.getNode1();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      }
    }
  }
コード例 #4
0
ファイル: GesConcurrent.java プロジェクト: renjiey/tetrad
  /** Do an actual deletion (Definition 13 from Chickering, 2002). */
  private void delete(Node x, Node y, List<Node> subset, Graph graph, double bump) {

    Edge trueEdge = null;

    if (trueGraph != null) {
      Node _x = trueGraph.getNode(x.getName());
      Node _y = trueGraph.getNode(y.getName());
      trueEdge = trueGraph.getEdge(_x, _y);
    }

    if (log && verbose) {
      Edge oldEdge = graph.getEdge(x, y);

      String label = trueGraph != null && trueEdge != null ? "*" : "";
      TetradLogger.getInstance()
          .log(
              "deletedEdges",
              (graph.getNumEdges() - 1)
                  + ". DELETE "
                  + oldEdge
                  + " "
                  + subset
                  + " ("
                  + bump
                  + ") "
                  + label);
      out.println(
          (graph.getNumEdges() - 1)
              + ". DELETE "
              + oldEdge
              + " "
              + subset
              + " ("
              + bump
              + ") "
              + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (numEdges % 50 == 0) out.println(numEdges);
    }

    graph.removeEdge(x, y);

    for (Node h : subset) {
      Edge oldEdge = graph.getEdge(y, h);

      graph.removeEdge(y, h);
      graph.addDirectedEdge(y, h);

      if (log) {
        TetradLogger.getInstance()
            .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
      }

      if (verbose) {
        out.println("--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
      }

      if (Edges.isUndirectedEdge(graph.getEdge(x, h))) {
        if (!graph.isAdjacentTo(x, h))
          throw new IllegalArgumentException("Not adjacent: " + x + ", " + h);
        oldEdge = graph.getEdge(x, h);

        graph.removeEdge(x, h);
        graph.addDirectedEdge(x, h);

        if (log) {
          TetradLogger.getInstance()
              .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
        }

        if (verbose) {
          out.println("--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
        }
      }
    }
  }
コード例 #5
0
ファイル: GesConcurrent.java プロジェクト: renjiey/tetrad
  // serial.
  private void insert(Node x, Node y, List<Node> t, Graph graph, double bump) {
    if (graph.isAdjacentTo(x, y)) {
      return; // The initial graph may already have put this edge in the graph.
      //            throw new IllegalArgumentException(x + " and " + y + " are already adjacent in
      // the graph.");
    }

    Edge trueEdge = null;

    if (trueGraph != null) {
      Node _x = trueGraph.getNode(x.getName());
      Node _y = trueGraph.getNode(y.getName());
      trueEdge = trueGraph.getEdge(_x, _y);
    }

    graph.addDirectedEdge(x, y);

    if (log) {
      String label = trueGraph != null && trueEdge != null ? "*" : "";
      TetradLogger.getInstance()
          .log(
              "insertedEdges",
              graph.getNumEdges()
                  + ". INSERT "
                  + graph.getEdge(x, y)
                  + " "
                  + t
                  + " "
                  + bump
                  + " "
                  + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (verbose) {
        if (numEdges % 50 == 0) out.println(numEdges);
      }
    }

    if (verbose) {
      String label = trueGraph != null && trueEdge != null ? "*" : "";
      out.println(
          graph.getNumEdges()
              + ". INSERT "
              + graph.getEdge(x, y)
              + " "
              + t
              + " "
              + bump
              + " "
              + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (verbose) {
        if (numEdges % 50 == 0) out.println(numEdges);
      }
    }

    for (Node _t : t) {
      Edge oldEdge = graph.getEdge(_t, y);

      if (oldEdge == null) throw new IllegalArgumentException("Not adjacent: " + _t + ", " + y);

      graph.removeEdge(_t, y);
      graph.addDirectedEdge(_t, y);

      if (log && verbose) {
        TetradLogger.getInstance()
            .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
        out.println("--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
      }
    }
  }