The EmpiricalDistribution class in the random package is designed to support large samples. It does not store all of data points in memory, but instead bins the data and uses smoothing kernels within the bins. I have recently had the need for a discrete empirical distribution - i.e., an implementation that stores the full dataset in memory and creates the empirical distribution exactly from it. If there are no objections, I would like to open a JIRA and commit o.a.c.m.distribution.DiscreteEmpiricalDistribution implementing this. I will document the approach and design decisions in the JIRA if others are OK with this addition.
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