/** Constructs a new FCI search for the given independence test and background knowledge. */
public Rfci(IndependenceTest independenceTest) {
if (independenceTest == null || knowledge == null) {
throw new NullPointerException();
}
this.independenceTest = independenceTest;
this.variables.addAll(independenceTest.getVariables());
}
/**
* Constructs a new FCI search for the given independence test and background knowledge and a list
* of variables to search over.
*/
public Rfci(IndependenceTest independenceTest, List<Node> searchVars) {
if (independenceTest == null || knowledge == null) {
throw new NullPointerException();
}
this.independenceTest = independenceTest;
this.variables.addAll(independenceTest.getVariables());
Set<Node> remVars = new HashSet<Node>();
for (Node node1 : this.variables) {
boolean search = false;
for (Node node2 : searchVars) {
if (node1.getName().equals(node2.getName())) {
search = true;
}
}
if (!search) {
remVars.add(node1);
}
}
this.variables.removeAll(remVars);
}
/**
* Runs PC starting with a complete graph over all nodes of the given conditional independence
* test, using the given independence test and knowledge and returns the resultant graph. The
* returned graph will be a pattern if the independence information is consistent with the
* hypothesis that there are no latent common causes. It may, however, contain cycles or
* bidirected edges if this assumption is not born out, either due to the actual presence of
* latent common causes, or due to statistical errors in conditional independence judgments.
*/
public Graph search() {
return search(independenceTest.getVariables());
}