{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/42772125","id":42772125,"diff_hunk":"@@ -608,10 +612,274 @@ def centralize(mat):\n \n     \"\"\"\n     mat = closure(mat)\n-    cen = ss.gmean(mat, axis=0)\n+    cen = scipy.stats.gmean(mat, axis=0)\n     return perturb_inv(mat, cen)\n \n \n+@experimental(as_of=\"0.4.0-dev\")\n+def ancom(matrix, categories,\n+          alpha=0.05,\n+          tau=0.02,\n+          theta=0.1,\n+          multiple_comparisons_correction=None,\n+          significance_test=scipy.stats.ttest_ind):\n+    r\"\"\"\n+    Calculates pairwise log ratios between all otus\n+    and performs a signficance test to determine if there is a\n+    significant difference in feature ratios with respect to the\n+    variable of interest\n+\n+    In an experiment with only two treatments, this test tests the\n+    following hypothesis for feature :math:`i`\n+    :math:`H_{0i}:\\E[\\ln(u_i^{(1)})] = \\E[\\ln(u_i^{(2)})]`\n+\n+    where :math:`u_i^{(1)}` is the mean abundance for feature\n+    :math:`i` in the first group and :math:`u_i^{(2)}` is the\n+    mean abundance for feature :math:`i` in the second group.\n+\n+    This method can be extended two an arbitrary number of classes\n+    by passing in a different statistical function.\n+\n+","path":"skbio/stats/composition.py","position":67,"original_position":67,"commit_id":"10fc9a60aeae7fdbe3b31b9cd076e38855cbbee0","original_commit_id":"10fc9a60aeae7fdbe3b31b9cd076e38855cbbee0","user":{"login":"wasade","id":474290,"avatar_url":"https://avatars.githubusercontent.com/u/474290?v=3","gravatar_id":"","url":"https://api.github.com/users/wasade","html_url":"https://github.com/wasade","followers_url":"https://api.github.com/users/wasade/followers","following_url":"https://api.github.com/users/wasade/following{/other_user}","gists_url":"https://api.github.com/users/wasade/gists{/gist_id}","starred_url":"https://api.github.com/users/wasade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wasade/subscriptions","organizations_url":"https://api.github.com/users/wasade/orgs","repos_url":"https://api.github.com/users/wasade/repos","events_url":"https://api.github.com/users/wasade/events{/privacy}","received_events_url":"https://api.github.com/users/wasade/received_events","type":"User","site_admin":false},"body":"extra space","created_at":"2015-10-22T16:35:11Z","updated_at":"2015-10-22T16:35:11Z","html_url":"https://github.com/biocore/scikit-bio/pull/1114#discussion_r42772125","pull_request_url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1114","_links":{"self":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/42772125"},"html":{"href":"https://github.com/biocore/scikit-bio/pull/1114#discussion_r42772125"},"pull_request":{"href":"https://api.github.com/repos/biocore/scikit-bio/pulls/1114"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1114","id":44265665,"html_url":"https://github.com/biocore/scikit-bio/pull/1114","diff_url":"https://github.com/biocore/scikit-bio/pull/1114.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/1114.patch","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1114","number":1114,"state":"open","locked":false,"title":"Ancom","user":{"login":"mortonjt","id":4184797,"avatar_url":"https://avatars.githubusercontent.com/u/4184797?v=3","gravatar_id":"","url":"https://api.github.com/users/mortonjt","html_url":"https://github.com/mortonjt","followers_url":"https://api.github.com/users/mortonjt/followers","following_url":"https://api.github.com/users/mortonjt/following{/other_user}","gists_url":"https://api.github.com/users/mortonjt/gists{/gist_id}","starred_url":"https://api.github.com/users/mortonjt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mortonjt/subscriptions","organizations_url":"https://api.github.com/users/mortonjt/orgs","repos_url":"https://api.github.com/users/mortonjt/repos","events_url":"https://api.github.com/users/mortonjt/events{/privacy}","received_events_url":"https://api.github.com/users/mortonjt/received_events","type":"User","site_admin":false},"body":"Here is the a PR for integrating ANCOM  this addresses #1054\r\n\r\nTo address @ebolyen 's concern, it is only a single function with a couple of helper functions.  If you guys think it is too beefy, let me know.\r\n\r\nAlso, there were some parameters in the most up to date version of ANCOM that didn't make complete sense to me.  @wdwvt1 , do you think you could address some of these parameters?  I highlighted them in the code.\r\n\r\nTodo:\r\n- [ ] squash 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