public Graph search(IFas fas, List<Node> nodes) {
this.logger.log("info", "Starting PC algorithm");
this.logger.log("info", "Independence test = " + getIndependenceTest() + ".");
// this.logger.log("info", "Variables " + independenceTest.getVariables());
long startTime = System.currentTimeMillis();
if (getIndependenceTest() == null) {
throw new NullPointerException();
}
List<Node> allNodes = getIndependenceTest().getVariables();
if (!allNodes.containsAll(nodes)) {
throw new IllegalArgumentException(
"All of the given nodes must " + "be in the domain of the independence test provided.");
}
fas.setKnowledge(getKnowledge());
fas.setDepth(getDepth());
fas.setVerbose(verbose);
graph = fas.search();
sepsets = fas.getSepsets();
this.numIndependenceTests = fas.getNumIndependenceTests();
this.numFalseDependenceJudgements = fas.getNumFalseDependenceJudgments();
this.numDependenceJudgements = fas.getNumDependenceJudgments();
// enumerateTriples();
SearchGraphUtils.pcOrientbk(knowledge, graph, nodes);
SearchGraphUtils.orientCollidersUsingSepsets(this.sepsets, knowledge, graph, verbose);
MeekRules rules = new MeekRules();
rules.setAggressivelyPreventCycles(this.aggressivelyPreventCycles);
rules.setKnowledge(knowledge);
rules.setUndirectUnforcedEdges(false);
rules.orientImplied(graph);
this.logger.log("graph", "\nReturning this graph: " + graph);
this.elapsedTime = System.currentTimeMillis() - startTime;
this.logger.log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s");
this.logger.log("info", "Finishing PC Algorithm.");
this.logger.flush();
return graph;
}
public Graph search(IFas fas, List<Node> nodes) {
long beginTime = System.currentTimeMillis();
logger.log("info", "Starting FCI algorithm.");
logger.log("info", "Independence test = " + getIndependenceTest() + ".");
setMaxPathLength(maxPathLength);
this.graph = new EdgeListGraph(nodes);
long start1 = System.currentTimeMillis();
fas.setKnowledge(getKnowledge());
fas.setDepth(depth);
fas.setVerbose(verbose);
// fas.setFci(true);
graph = fas.search();
graph.reorientAllWith(Endpoint.CIRCLE);
this.sepsets = fas.getSepsets();
long stop1 = System.currentTimeMillis();
long start2 = System.currentTimeMillis();
// The original FCI, with or without JiJi Zhang's orientation rules
fciOrientbk(getKnowledge(), graph, variables);
ruleR0_RFCI(getRTuples()); // RFCI Algorithm 4.4
doFinalOrientation();
long endTime = System.currentTimeMillis();
this.elapsedTime = endTime - beginTime;
logger.log("graph", "Returning graph: " + graph);
long stop2 = System.currentTimeMillis();
logger.log("info", "Elapsed time adjacency search = " + (stop1 - start1) / 1000L + "s");
logger.log("info", "Elapsed time orientation search = " + (stop2 - start2) / 1000L + "s");
return graph;
}