Minor Description
For large array size (say, over 5,000), numPairs > 10 million.
in line 258, (numPairs - tiedXPairs) * (numPairs - tiedYPairs) possibly > 100 billion, which will cause an integer overflow, resulting in a negative number, which will result in the end result in a NaN since the square-root of that number is calculated.
This can easily be solved by changing line 163 to
final long numPairs = ((long)n) * (n - 1) / 2; // to avoid overflow
