/**
* Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model.
*/
private double localSemScore(int i, int[] parents) {
try {
ICovarianceMatrix cov = getCovMatrix();
double varianceY = cov.getValue(i, i);
double residualVariance = varianceY;
int n = sampleSize();
int p = parents.length;
int k = (p * (p + 1)) / 2 + p;
// int k = (p + 1) * (p + 1);
// int k = p + 1;
TetradMatrix covxx = cov.getSelection(parents, parents);
TetradMatrix covxxInv = covxx.inverse();
TetradVector covxy = cov.getSelection(parents, new int[] {i}).getColumn(0);
TetradVector b = covxxInv.times(covxy);
residualVariance -= covxy.dotProduct(b);
if (residualVariance <= 0 && verbose) {
out.println(
"Nonpositive residual varianceY: resVar / varianceY = "
+ (residualVariance / varianceY));
return Double.NaN;
}
double c = getPenaltyDiscount();
// return -n * log(residualVariance) - 2 * k; //AIC
return -n * Math.log(residualVariance) - c * k * Math.log(n);
// return -n * log(residualVariance) - c * k * (log(n) - log(2 * PI));
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException(e);
// throwMinimalLinearDependentSet(parents, cov);
}
}
/** Adds the given componet to the given layer. */
public void addEditorWindow(EditorWindowIndirectRef windowRef) {
final JInternalFrame window = (JInternalFrame) windowRef;
Dimension desktopSize = desktopPane.getSize();
Dimension preferredSize = window.getPreferredSize();
int x = desktopSize.width / 2 - preferredSize.width / 2;
int y = desktopSize.height / 2 - preferredSize.height / 2;
window.setBounds(x, y, preferredSize.width, preferredSize.height);
// This line sometimes hangs, so I'm putting it in a watch process
// so it can be stopped by the user. Not ideal.
// Window owner = (Window) getTopLevelAncestor();
//
// new WatchedProcess(owner) {
// public void watch() {
getDesktopPane().add(window);
window.setLayer(100);
window.moveToFront();
try {
window.setVisible(true);
} catch (Exception e) {
if (e instanceof ClassCastException || e instanceof NullPointerException) {
// skip. These is being caused apparently the workbench
// having labeled nodes and edges. Can't find a
// workaround--probably a Java bug. jdramsey
} else {
e.printStackTrace();
}
}
// prevents the component from being hidden.
// window.addComponentListener(new PositionListener());
// }
// };
}