public static Graph erdosRenyiGraph(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 = RandomUtil.getInstance().nextInt(n);
int i2 = RandomUtil.getInstance().nextInt(n);
if (i1 == i2) {
e0--;
continue;
}
Edge edge = Edges.undirectedEdge(nodes.get(i1), nodes.get(i2));
if (graph.containsEdge(edge)) {
e0--;
continue;
}
graph.addEdge(edge);
}
return graph;
}
public GraphIndex(Graph graph) {
LOG.info("Indexing graph...");
for (String feedId : graph.getFeedIds()) {
for (Agency agency : graph.getAgencies(feedId)) {
Map<String, Agency> agencyForId = agenciesForFeedId.getOrDefault(feedId, new HashMap<>());
agencyForId.put(agency.getId(), agency);
this.agenciesForFeedId.put(feedId, agencyForId);
}
}
Collection<Edge> edges = graph.getEdges();
/* We will keep a separate set of all vertices in case some have the same label.
* Maybe we should just guarantee unique labels. */
Set<Vertex> vertices = Sets.newHashSet();
for (Edge edge : edges) {
vertices.add(edge.getFromVertex());
vertices.add(edge.getToVertex());
if (edge instanceof TablePatternEdge) {
TablePatternEdge patternEdge = (TablePatternEdge) edge;
TripPattern pattern = patternEdge.getPattern();
patternForId.put(pattern.code, pattern);
}
}
for (Vertex vertex : vertices) {
vertexForId.put(vertex.getLabel(), vertex);
if (vertex instanceof TransitStop) {
TransitStop transitStop = (TransitStop) vertex;
Stop stop = transitStop.getStop();
stopForId.put(stop.getId(), stop);
stopVertexForStop.put(stop, transitStop);
stopsForParentStation.put(stop.getParentStation(), stop);
}
}
for (TransitStop stopVertex : stopVertexForStop.values()) {
Envelope envelope = new Envelope(stopVertex.getCoordinate());
stopSpatialIndex.insert(envelope, stopVertex);
}
for (TripPattern pattern : patternForId.values()) {
patternsForFeedId.put(pattern.getFeedId(), pattern);
patternsForRoute.put(pattern.route, pattern);
for (Trip trip : pattern.getTrips()) {
patternForTrip.put(trip, pattern);
tripForId.put(trip.getId(), trip);
}
for (Stop stop : pattern.getStops()) {
patternsForStop.put(stop, pattern);
}
}
for (Route route : patternsForRoute.asMap().keySet()) {
routeForId.put(route.getId(), route);
}
// Copy these two service indexes from the graph until we have better ones.
calendarService = graph.getCalendarService();
serviceCodes = graph.serviceCodes;
this.graph = graph;
LOG.info("Done indexing graph.");
}
protected Graph<String, DefaultWeightedEdge> createWithBias(boolean negate) {
Graph<String, DefaultWeightedEdge> g;
double bias = 1;
if (negate) {
// negative-weight edges are being tested, so only a directed graph
// makes sense
g = new SimpleDirectedWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
bias = -1;
} else {
// by default, use an undirected graph
g = new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
}
g.addVertex(V1);
g.addVertex(V2);
g.addVertex(V3);
g.addVertex(V4);
g.addVertex(V5);
e12 = Graphs.addEdge(g, V1, V2, bias * 2);
e13 = Graphs.addEdge(g, V1, V3, bias * 3);
e24 = Graphs.addEdge(g, V2, V4, bias * 5);
e34 = Graphs.addEdge(g, V3, V4, bias * 20);
e45 = Graphs.addEdge(g, V4, V5, bias * 5);
e15 = Graphs.addEdge(g, V1, V5, bias * 100);
return g;
}
private boolean existsUnblockedSemiDirectedPath(Node from, Node to, List<Node> cond, Graph G) {
Queue<Node> Q = new LinkedList<Node>();
Set<Node> V = new HashSet<Node>();
Q.offer(from);
V.add(from);
while (!Q.isEmpty()) {
Node t = Q.remove();
if (t == to) return true;
for (Node u : G.getAdjacentNodes(t)) {
Edge edge = G.getEdge(t, u);
Node c = Edges.traverseSemiDirected(t, edge);
if (c == null) continue;
if (cond.contains(c)) continue;
if (c == to) return true;
if (!V.contains(c)) {
V.add(c);
Q.offer(c);
}
}
}
return false;
}
/**
* Generates AdjacencyListGraph based on the values in the input file.
*
* @requires twitterStream is properly initialized
* @param twitterStream initialized input stream for reading twitter file
* @return generated graph based on input file
*/
private static Graph readTwitterFile(FileInputStream twitterStream) {
final int U1_INDEX = 0;
final int U2_INDEX = 1;
try {
Graph g = new AdjacencyListGraph();
BufferedReader twitterReader = new BufferedReader(new InputStreamReader(twitterStream));
String line;
while ((line = twitterReader.readLine()) != null) {
// eliminate any unnecessary whitespace
String[] columns = line.trim().replaceAll("\\s+", "").split("->");
// first column is user 1
// second column is user 2
Vertex u1 = new Vertex(columns[U1_INDEX]);
Vertex u2 = new Vertex(columns[U2_INDEX]);
// System.out.println(columns[0]+","+columns[1]);
g.addVertex(u1);
g.addVertex(u2);
g.addEdge(u1, u2);
// System.out.println(line);
}
twitterReader.close();
return g;
} catch (Exception e) { // if something somehow goes wrong
throw new RuntimeException(e);
}
}
Graph create(Collection<? extends Deployer> deployers) {
// S ← Set of all nodes with no incoming edges
List<Deployer> s = new ArrayList<Deployer>();
Map<String, Collection<Deployer>> inputCache = new HashMap<String, Collection<Deployer>>();
// Map<Deployer, Set<Edge>> edgeCache = new IdentityHashMap<Deployer, Set<Edge>>();
Map edgeCache = new IdentityHashMap<Deployer, Set<?>>();
Set<String> outputs = new HashSet<String>();
Map<String, Collection<Deployer>> outputCache = new HashMap<String, Collection<Deployer>>();
for (Deployer deployer : deployers) {
process(deployer, s, inputCache, edgeCache, outputs, outputCache);
}
processTransientDeployers(s, inputCache, outputCache, edgeCache);
Graph graph = new Graph();
for (Deployer d : deployers) {
graph.addNode(d.toString());
}
for (Map.Entry entry : (Set<Map.Entry>) edgeCache.entrySet()) {
System.out.println(entry);
Set<Object> edges = (Set<Object>) entry.getValue();
for (Object edge : edges) {
String fromNode = fromNode(edge);
String edgeLabel = edgeLabel(edge);
String toNode = toNode(edge);
graph.addEdge(fromNode, toNode, edgeLabel);
}
}
System.out.println(graph.edges.size());
return graph;
}
/** Get a graph and direct only the unshielded colliders. */
public static void basicPattern(Graph graph) {
Set<Edge> undirectedEdges = new HashSet<Edge>();
NEXT_EDGE:
for (Edge edge : graph.getEdges()) {
Node head = null, tail = null;
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.TAIL) {
head = edge.getNode1();
tail = edge.getNode2();
} else if (edge.getEndpoint2() == Endpoint.ARROW && edge.getEndpoint1() == Endpoint.TAIL) {
head = edge.getNode2();
tail = edge.getNode1();
}
if (head != null) {
for (Node node : graph.getParents(head)) {
if (node != tail && !graph.isAdjacentTo(tail, node)) {
continue NEXT_EDGE;
}
}
undirectedEdges.add(edge);
}
}
for (Edge nextUndirected : undirectedEdges) {
Node node1 = nextUndirected.getNode1(), node2 = nextUndirected.getNode2();
graph.removeEdge(nextUndirected);
graph.addUndirectedEdge(node1, node2);
}
}
/**
* Creates a new iterator for the specified graph. Iteration will start at the specified start
* vertex. If the specified start vertex is <code>
* null</code>, Iteration will start at an arbitrary graph vertex.
*
* @param g the graph to be iterated.
* @param startVertex the vertex iteration to be started.
* @throws IllegalArgumentException if <code>g==null</code> or does not contain <code>startVertex
* </code>
*/
public CrossComponentIterator(Graph<V, E> g, V startVertex) {
super();
if (g == null) {
throw new IllegalArgumentException("graph must not be null");
}
graph = g;
specifics = createGraphSpecifics(g);
vertexIterator = g.vertexSet().iterator();
setCrossComponentTraversal(startVertex == null);
reusableEdgeEvent = new FlyweightEdgeEvent<V, E>(this, null);
reusableVertexEvent = new FlyweightVertexEvent<V>(this, null);
if (startVertex == null) {
// pick a start vertex if graph not empty
if (vertexIterator.hasNext()) {
this.startVertex = vertexIterator.next();
} else {
this.startVertex = null;
}
} else if (g.containsVertex(startVertex)) {
this.startVertex = startVertex;
} else {
throw new IllegalArgumentException("graph must contain the start vertex");
}
}
private void init(Graph<V, E> g, Set<V> vertexSet, Set<E> edgeSet) {
// create a map between vertex value to its order(1st,2nd,etc)
// "CAT"=1 "DOG"=2 "RHINO"=3
this.mapVertexToOrder = new HashMap<V, Integer>(vertexSet.size());
int counter = 0;
for (V vertex : vertexSet) {
mapVertexToOrder.put(vertex, new Integer(counter));
counter++;
}
// create a friendlier representation of an edge
// by order, like 2nd->3rd instead of B->A
// use the map to convert vertex to order
// on directed graph, edge A->B must be (A,B)
// on undirected graph, edge A-B can be (A,B) or (B,A)
this.labelsEdgesSet = new HashSet<LabelsEdge>(edgeSet.size());
for (E edge : edgeSet) {
V sourceVertex = g.getEdgeSource(edge);
Integer sourceOrder = mapVertexToOrder.get(sourceVertex);
int sourceLabel = sourceOrder.intValue();
int targetLabel = (mapVertexToOrder.get(g.getEdgeTarget(edge))).intValue();
LabelsEdge lablesEdge = new LabelsEdge(sourceLabel, targetLabel);
this.labelsEdgesSet.add(lablesEdge);
if (g instanceof UndirectedGraph<?, ?>) {
LabelsEdge oppositeEdge = new LabelsEdge(targetLabel, sourceLabel);
this.labelsEdgesSet.add(oppositeEdge);
}
}
}
private Graph changeLatentNames(Graph full, Clusters measurements, List<String> latentVarList) {
Graph g2 = null;
try {
g2 = (Graph) new MarshalledObject(full).get();
} catch (IOException e) {
e.printStackTrace();
} catch (ClassNotFoundException e) {
e.printStackTrace();
}
for (int i = 0; i < measurements.getNumClusters(); i++) {
List<String> d = measurements.getCluster(i);
String latentName = latentVarList.get(i);
for (Node node : full.getNodes()) {
if (!(node.getNodeType() == NodeType.LATENT)) {
continue;
}
List<Node> _children = full.getChildren(node);
_children.removeAll(ReidentifyVariables.getLatents(full));
List<String> childNames = getNames(_children);
if (new HashSet<String>(childNames).equals(new HashSet<String>(d))) {
g2.getNode(node.getName()).setName(latentName);
}
}
}
return g2;
}
/**
* @param vertexNumber the number which identifies the vertex v in this order.
* @return the identifying numbers of all vertices which are connected to v by an edge incoming to
* v.
*/
public int[] getInEdges(int vertexNumber) {
if (cacheEdges && (incomingEdges[vertexNumber] != null)) {
return incomingEdges[vertexNumber];
}
V v = getVertex(vertexNumber);
Set<E> edgeSet;
if (graph instanceof DirectedGraph<?, ?>) {
edgeSet = ((DirectedGraph<V, E>) graph).incomingEdgesOf(v);
} else {
edgeSet = graph.edgesOf(v);
}
int[] vertexArray = new int[edgeSet.size()];
int i = 0;
for (E edge : edgeSet) {
V source = graph.getEdgeSource(edge), target = graph.getEdgeTarget(edge);
vertexArray[i++] = mapVertexToOrder.get(source.equals(v) ? target : source);
}
if (cacheEdges) {
incomingEdges[vertexNumber] = vertexArray;
}
return vertexArray;
}
public List<Triple> getUnshieldedCollidersFromGraph(Graph graph) {
List<Triple> colliders = new ArrayList<>();
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
if (graph.isDefCollider(a, b, c)) {
colliders.add(new Triple(a, b, c));
}
}
}
return colliders;
}
////////////////////////////////////////////////
// collect in rTupleList all unshielded tuples
////////////////////////////////////////////////
private List<Node[]> getRTuples() {
List<Node[]> rTuples = new ArrayList<Node[]>();
List<Node> nodes = graph.getNodes();
for (Node j : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(j);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node i = adjacentNodes.get(combination[0]);
Node k = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (!graph.isAdjacentTo(i, k)) {
Node[] newTuple = {i, j, k};
rTuples.add(newTuple);
}
}
}
return (rTuples);
}
public Set<Edge> getNonadjacencies() {
Graph complete = GraphUtils.completeGraph(graph);
Set<Edge> nonAdjacencies = complete.getEdges();
Graph undirected = GraphUtils.undirectedGraph(graph);
nonAdjacencies.removeAll(undirected.getEdges());
return new HashSet<Edge>(nonAdjacencies);
}
public Graph copy() {
WeightedArcSet list = new WeightedArcSet();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
} catch (Exception ex) {
throw new Error(ex);
}
}
Graph result = new Graph(list.toArray(new WeightedArc[0]));
result.nodes.clear();
result.nodesReverse.clear();
for (Integer n : this.nodes.keySet()) {
if (commit++ % COMMIT_SIZE == 0) {
result.commit();
}
result.nodesReverse.put(this.nodes.get(n), n);
result.nodes.put(n, this.nodes.get(n));
}
return result;
}
/**
* Random graph. Generates randomly k directed edges out of each node. The neighbors (edge
* targets) are chosen randomly without replacement from the nodes of the graph other than the
* source node (i.e. no loop edge is added). If k is larger than N-1 (where N is the number of
* nodes) then k is set to be N-1 and a complete graph is returned.
*
* @param g the graph to be wired
* @param k samples to be drawn for each node
* @param r source of randomness
* @return returns g for convenience
*/
public static Graph wireKOut(Graph g, int k, Random r) {
final int n = g.size();
if (n < 2) {
return g;
}
if (n <= k) {
k = n - 1;
}
int[] nodes = new int[n];
for (int i = 0; i < nodes.length; ++i) {
nodes[i] = i;
}
for (int i = 0; i < n; ++i) {
int j = 0;
while (j < k) {
int newedge = j + r.nextInt(n - j);
int tmp = nodes[j];
nodes[j] = nodes[newedge];
nodes[newedge] = tmp;
if (nodes[j] != i) {
g.setEdge(i, nodes[j]);
j++;
}
}
}
return g;
}
// ===========================SCORING METHODS===================//
public double scoreDag(Graph graph) {
Graph dag = new EdgeListGraphSingleConnections(graph);
buildIndexing(graph);
double score = 0.0;
for (Node y : dag.getNodes()) {
Set<Node> parents = new HashSet<Node>(dag.getParents(y));
int nextIndex = -1;
for (int i = 0; i < getVariables().size(); i++) {
nextIndex = hashIndices.get(variables.get(i));
}
int parentIndices[] = new int[parents.size()];
Iterator<Node> pi = parents.iterator();
int count = 0;
while (pi.hasNext()) {
Node nextParent = pi.next();
parentIndices[count++] = hashIndices.get(nextParent);
}
if (this.isDiscrete()) {
score += localDiscreteScore(nextIndex, parentIndices);
} else {
score += localSemScore(nextIndex, parentIndices);
}
}
return score;
}
/** @return dfs wenn gefunden, ansonsten NULL */
@Override
public Graph<Integer> dfs(Node<Integer> start, Node<Integer> goal) {
this.unvisitAllNodes();
Graph<Integer> dfs = new ImplGraph();
dfs.setNode(start.value());
boolean found = this.dfs(start, goal, dfs);
return found ? dfs : null;
}
private void populateLists(List<Vertex> verticies, List<Edge> edges) {
for (Vertex v : graph.getVertices()) {
verticies.add(v);
}
for (Edge e : graph.getEdges()) {
edges.add(e);
}
}
private Set<String> getDownstream(String mut) {
Set<String> tfs = new HashSet<String>();
tfs.add(mut);
if (depth > 1) tfs.addAll(travSt.getDownstream(tfs, depth - 1));
return travExp.getDownstream(tfs);
}
/**
* A sink star. Wires a sink star topology adding a link to 0 from all other nodes.
*
* @param g the graph to be wired
* @return returns g for convenience
*/
public static Graph wireStar(Graph g) {
final int n = g.size();
for (int i = 1; i < n; ++i) {
g.setEdge(i, 0);
}
return g;
}
public static void main(String[] args) {
Graph g = new Graph();
g.addEdge(0, 1);
g.addEdge(1, 2);
System.out.println(g.edges);
g.removeNode(1);
System.out.println(g.edges);
}
/**
* Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *->
* y <-* z just in case y is in Sepset({x, z}).
*/
public Map<Triple, Double> findCollidersUsingSepsets(
SepsetProducer sepsetProducer, Graph graph, boolean verbose, IKnowledge knowledge) {
TetradLogger.getInstance().log("details", "Starting Collider Orientation:");
Map<Triple, Double> colliders = new HashMap<>();
System.out.println("Looking for colliders");
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
List<Node> sepset = sepsetProducer.getSepset(a, c);
if (sepset == null) continue;
// if (sepsetProducer.getPValue() < 0.5) continue;
if (!sepset.contains(b)) {
if (verbose) {
// boolean dsep = this.dsep.isIndependent(a, c);
// System.out.println("QQQ p = " + independenceTest.getPValue() +
// " " + dsep);
System.out.println(
"\nCollider orientation <" + a + ", " + b + ", " + c + "> sepset = " + sepset);
}
colliders.put(new Triple(a, b, c), sepsetProducer.getPValue());
TetradLogger.getInstance()
.log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c, sepset));
}
}
}
TetradLogger.getInstance().log("details", "Finishing Collider Orientation.");
System.out.println("Done finding colliders");
return colliders;
}
private boolean isUndirected(Graph graph, Node x, Node y) {
List<Edge> edges = graph.getEdges(x, y);
if (edges.size() == 1) {
Edge edge = graph.getEdge(x, y);
return Edges.isUndirectedEdge(edge);
}
return false;
}
public int[] getEdgeNumbers(E e) {
V v1 = graph.getEdgeSource(e), v2 = graph.getEdgeTarget(e);
int[] edge = new int[2];
edge[0] = mapVertexToOrder.get(v1);
edge[1] = mapVertexToOrder.get(v2);
return edge;
}
/**
* Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that
* X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W
* just being *in* the sepset of (X, Y).
*/
public static void pcdOrientC(
SepsetMap set, IndependenceTest test, Knowledge knowledge, Graph graph) {
TetradLogger.getInstance().log("info", "Staring Collider Orientation:");
List<Node> nodes = graph.getNodes();
for (Node y : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(y);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node x = adjacentNodes.get(combination[0]);
Node z = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(x, z)) {
continue;
}
List<Node> sepset = set.get(x, z);
if (sepset == null) {
continue;
}
List<Node> augmentedSet = new LinkedList<Node>(sepset);
augmentedSet.add(y);
if (test.determines(sepset, y)) {
continue;
}
//
if (!test.splitDetermines(sepset, x, z) && test.splitDetermines(augmentedSet, x, z)) {
continue;
}
if (!isArrowpointAllowed(x, y, knowledge) || !isArrowpointAllowed(z, y, knowledge)) {
continue;
}
graph.setEndpoint(x, y, Endpoint.ARROW);
graph.setEndpoint(z, y, Endpoint.ARROW);
TetradLogger.getInstance()
.log("colliderOriented", SearchLogUtils.colliderOrientedMsg(x, y, z));
}
}
TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}
private boolean localMarkovIndep(Node x, Node y, Graph pattern, IndependenceTest test) {
List<Node> future = pattern.getDescendants(Collections.singletonList(x));
List<Node> boundary = pattern.getAdjacentNodes(x);
boundary.removeAll(future);
List<Node> closure = new ArrayList<>(boundary);
closure.add(x);
closure.remove(y);
if (future.contains(y) || boundary.contains(y)) return false;
return test.isIndependent(x, y, boundary);
}
public Graph transpose() {
Graph g = copy();
try {
g.graph = Transform.transposeOffline(g.graph, 1000);
g.reverse = Transform.transposeOffline(g.reverse, 1000);
} catch (IOException ex) {
throw new Error(ex);
}
return g;
}
public static GraphOrder forwardGraph(Graph graph) {
GraphOrder result = new GraphOrder();
NodeBitMap visited = graph.createNodeBitMap();
for (ControlSinkNode node : graph.getNodes(ControlSinkNode.class)) {
result.visitForward(visited, node);
}
return result;
}
private double getPMulticluster(List<List<Integer>> clusters, int numRestarts) {
if (false) {
Graph g = new EdgeListGraph();
List<Node> latents = new ArrayList<Node>();
for (int i = 0; i < clusters.size(); i++) {
GraphNode latent = new GraphNode("L" + i);
latent.setNodeType(NodeType.LATENT);
latents.add(latent);
g.addNode(latent);
List<Node> cluster = variablesForIndices(clusters.get(i));
for (int j = 0; j < cluster.size(); j++) {
g.addNode(cluster.get(j));
g.addDirectedEdge(latent, cluster.get(j));
}
}
SemPm pm = new SemPm(g);
// pm.fixOneLoadingPerLatent();
SemOptimizerPowell semOptimizer = new SemOptimizerPowell();
semOptimizer.setNumRestarts(numRestarts);
SemEstimator est = new SemEstimator(cov, pm, semOptimizer);
est.setScoreType(SemIm.ScoreType.Fgls);
est.estimate();
return est.getEstimatedSem().getPValue();
} else {
double max = Double.NEGATIVE_INFINITY;
for (int i = 0; i < numRestarts; i++) {
Mimbuild2 mimbuild = new Mimbuild2();
List<List<Node>> _clusters = new ArrayList<List<Node>>();
for (List<Integer> _cluster : clusters) {
_clusters.add(variablesForIndices(_cluster));
}
List<String> names = new ArrayList<String>();
for (int j = 0; j < clusters.size(); j++) {
names.add("L" + j);
}
mimbuild.search(_clusters, names, cov);
double c = mimbuild.getpValue();
if (c > max) max = c;
}
return max;
}
}