/**
* Run the randomization test
*
* @param baseline
* @param target
* @return
*/
public double test(HashMap<String, Double> target, HashMap<String, Double> baseline) {
double[] b = new double[baseline.keySet().size()]; // baseline
double[] t = new double[target.keySet().size()]; // target
int c = 0;
for (String key : baseline.keySet()) {
b[c] = baseline.get(key).doubleValue();
t[c] = target.get(key).doubleValue();
c++;
}
double trueDiff = Math.abs(BasicStats.mean(b) - BasicStats.mean(t));
double pvalue = 0.0;
double[] pb = new double[baseline.keySet().size()]; // permutation of baseline
double[] pt = new double[target.keySet().size()]; // permutation of target
for (int i = 0; i < nPermutation; i++) {
char[] bits = randomBitVector(b.length).toCharArray();
for (int j = 0; j < b.length; j++) {
if (bits[j] == '0') {
pb[j] = b[j];
pt[j] = t[j];
} else {
pb[j] = t[j];
pt[j] = b[j];
}
}
double pDiff = Math.abs(BasicStats.mean(pb) - BasicStats.mean(pt));
if (pDiff >= trueDiff) pvalue += 1.0;
}
return pvalue / nPermutation;
}
