{"comment":{"url":"https://api.github.com/repos/jairideout/scikit-bio/comments/10289663","html_url":"https://github.com/jairideout/scikit-bio/commit/789676424d9767a82de32b02bb0db474ab06e972#commitcomment-10289663","id":10289663,"user":{"login":"tanaes","id":8292608,"avatar_url":"https://avatars.githubusercontent.com/u/8292608?v=3","gravatar_id":"","url":"https://api.github.com/users/tanaes","html_url":"https://github.com/tanaes","followers_url":"https://api.github.com/users/tanaes/followers","following_url":"https://api.github.com/users/tanaes/following{/other_user}","gists_url":"https://api.github.com/users/tanaes/gists{/gist_id}","starred_url":"https://api.github.com/users/tanaes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tanaes/subscriptions","organizations_url":"https://api.github.com/users/tanaes/orgs","repos_url":"https://api.github.com/users/tanaes/repos","events_url":"https://api.github.com/users/tanaes/events{/privacy}","received_events_url":"https://api.github.com/users/tanaes/received_events","type":"User","site_admin":false},"position":186,"line":179,"path":"skbio/stats/evolve/_hommola.py","commit_id":"789676424d9767a82de32b02bb0db474ab06e972","created_at":"2015-03-19T16:43:52Z","updated_at":"2015-03-19T16:43:52Z","body":"From my testing, the ultimate reason for a difference in the returned p-value is simply that different ordering of the value pairs going into the `pearsonr` calculation return slightly different correlation coefficients (even though the correlations should be identical regardless of ordering). Thus the equality test between `corr_coeff`from two identical sets of array pairs can fail if they are ordered differently. From my understanding, the proximate differences in permutation in the two tests really only matters in that it leads to more or less regular ordering of the arrays going into `pearsonr`.\r\n\r\nIf this pathological behavior of pearsonr is accounted for, the p-values returned by the two tests are statistically indistinguishable. \r\n\r\nNot sure that this matters at all if we're happy about the tests...\r\n"}}