public boolean isIndependent(Node x, Node y, List<Node> z) {
int[] all = new int[z.size() + 2];
all[0] = variablesMap.get(x);
all[1] = variablesMap.get(y);
for (int i = 0; i < z.size(); i++) {
all[i + 2] = variablesMap.get(z.get(i));
}
int sampleSize = data.get(0).rows();
List<Double> pValues = new ArrayList<Double>();
for (int m = 0; m < ncov.size(); m++) {
TetradMatrix _ncov = ncov.get(m).getSelection(all, all);
TetradMatrix inv = _ncov.inverse();
double r = -inv.get(0, 1) / sqrt(inv.get(0, 0) * inv.get(1, 1));
double fisherZ =
sqrt(sampleSize - z.size() - 3.0) * 0.5 * (Math.log(1.0 + r) - Math.log(1.0 - r));
double pValue;
if (Double.isInfinite(fisherZ)) {
pValue = 0;
} else {
pValue = 2.0 * (1.0 - RandomUtil.getInstance().normalCdf(0, 1, abs(fisherZ)));
}
pValues.add(pValue);
}
double _cutoff = alpha;
if (fdr) {
_cutoff = StatUtils.fdrCutoff(alpha, pValues, false);
}
Collections.sort(pValues);
int index = (int) round((1.0 - percent) * pValues.size());
this.pValue = pValues.get(index);
// if (this.pValue == 0) {
// System.out.println("Zero pvalue "+ SearchLogUtils.independenceFactMsg(x, y, z,
// getPValue()));
// }
boolean independent = this.pValue > _cutoff;
if (verbose) {
if (independent) {
TetradLogger.getInstance()
.log("independencies", SearchLogUtils.independenceFactMsg(x, y, z, getPValue()));
// System.out.println(SearchLogUtils.independenceFactMsg(x, y, z, getPValue()));
} else {
TetradLogger.getInstance()
.log("dependencies", SearchLogUtils.dependenceFactMsg(x, y, z, getPValue()));
}
}
return independent;
}
/*Generates a random exponential distribution random time difference vs. timeIn based on the frequency lambda */
private double nextRandomTime(double lambda) {
double timeLag = 0;
/*System.out.println("I am computing nextRandomTime");
System.out.println("When I am getting timeIn of " +timeIn+" and lambda of "+lambda);*/
double random = Math.random();
timeLag = -Math.log(random) / (lambda / (LENGTHOFADAY * 1000));
/*System.out.println("I am returning a time difference of "+timeLag);*/
return timeLag;
}
/**
* Calculates the binary logarithm.
*
* @param x a <code>double</code> value
* @return log2(x)
*/
private double log2(double x) {
return Math.log(x) / Math.log(2);
}
/** poprawka szerokosci dla w/h >= 1/(2ă) */
private double FDW2(double epf, double w, double h) {
DWType = "DW2"; /* slad - ktory wzor byl ostatni */
return 1.25 / pi * t * (1 + Math.log(2 * h / t));
}
/** wyliczenie Z0 dla w/h >= 1 */
private double FZ2(double epf, double we, double h) {
FZType = "FZ2"; /* slad - ktory wzor byl ostatni */
return 376.7 / (Math.sqrt(epf) * (we / h + 1.393 + 0.667 * Math.log(we / h + 1.444)));
}
/** wyliczenie Z0 dla w/h <= 1 */
private double FZ1(double epf, double we, double h) {
FZType = "FZ1"; /* slad - ktory wzor byl ostatni */
return 60 / Math.sqrt(epf) * Math.log(8 * h / we + 0.25 * we / h);
}
