Sample independent paired permutations using the paired statistic - #238
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Sample independent paired permutations using the paired statistic#238lllleolin-max wants to merge 1 commit into
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Paired permutation tests currently swap a uniformly chosen number of pairs on top of the previous permutation, then evaluate the unpaired statistic. This introduces dependent draws and, for paired median differences, samples an incorrect null statistic.
Independently swap each original pair with probability 1/2 and evaluate the paired effect. Use the paired sign-permutation count for the existing optional bias adjustment. Tests compare the median null distribution with exact SciPy enumeration, check independence of successive sign patterns, and retain seeded reproducibility.
Reference: SciPy paired permutation tests (
permutation_type="samples"). The existing tail comparison and the opt-in nature ofps_adjustare preserved.Validation: regression tests fail on the pinned
vnbdevsource and pass with this change; regression tests plus the existing load-error suite pass on Windows / Python 3.12 with NumPy 2.1.3 and SciPy 1.15.3. Notebook sources were edited and their Python modules regenerated with nbdev.AI assistance: Codex with GPT-6 Astra was used to develop and test this patch.