where myDoubleArray contains 2.0, 4.0, 6.0, 8.0, 10.0, 12.0
then sigma is 14.0.
So I would conclude that the variance calculated by Commons Math is a sample variance not a population variance.

How would I calculate a sample variance using Commons Math?

just apply the formulas above...
if VAR is sum of squares divided by n-1, then multiply by n-1 and then divide by n to get VARP
variance.evaluate(myDoubleArray) * ( myDoubleArray.length - 1) /

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