{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/American-Gut/issues/127","labels_url":"https://api.github.com/repos/biocore/American-Gut/issues/127/labels{/name}","comments_url":"https://api.github.com/repos/biocore/American-Gut/issues/127/comments","events_url":"https://api.github.com/repos/biocore/American-Gut/issues/127/events","html_url":"https://github.com/biocore/American-Gut/pull/127","id":58163006,"number":127,"title":"Statistical power","user":{"login":"JWDebelius","id":5534846,"avatar_url":"https://avatars.githubusercontent.com/u/5534846?v=3","gravatar_id":"","url":"https://api.github.com/users/JWDebelius","html_url":"https://github.com/JWDebelius","followers_url":"https://api.github.com/users/JWDebelius/followers","following_url":"https://api.github.com/users/JWDebelius/following{/other_user}","gists_url":"https://api.github.com/users/JWDebelius/gists{/gist_id}","starred_url":"https://api.github.com/users/JWDebelius/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JWDebelius/subscriptions","organizations_url":"https://api.github.com/users/JWDebelius/orgs","repos_url":"https://api.github.com/users/JWDebelius/repos","events_url":"https://api.github.com/users/JWDebelius/events{/privacy}","received_events_url":"https://api.github.com/users/JWDebelius/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-02-19T03:15:31Z","updated_at":"2015-03-03T07:03:22Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biocore/American-Gut/pulls/127","html_url":"https://github.com/biocore/American-Gut/pull/127","diff_url":"https://github.com/biocore/American-Gut/pull/127.diff","patch_url":"https://github.com/biocore/American-Gut/pull/127.patch"},"body":"This is a cleaned up power notebook, loosely related to what was presented in #121 \r\n\r\nThe rendered notebook can be found [here](http://nbviewer.ipython.org/github/JWDebelius/American-Gut/blob/statistical_power/ipynb/Power.ipynb).\r\n\r\nThe text is in [Google docs](https://docs.google.com/document/d/1DOEFP4SwqiJuLrMqgGitQwhss4ayREVQ4WWueltHiRM/edit?usp=sharing), which may be a better place for text editing.\r\n\r\nThis notebook relies on code generated in #125 and on the data files generated when #126 is run."},"comment":{"url":"https://api.github.com/repos/biocore/American-Gut/issues/comments/76896935","html_url":"https://github.com/biocore/American-Gut/pull/127#issuecomment-76896935","issue_url":"https://api.github.com/repos/biocore/American-Gut/issues/127","id":76896935,"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},"created_at":"2015-03-03T07:03:22Z","updated_at":"2015-03-03T07:03:22Z","body":"I can't link directly into the notebook, so below are the initial pass comments on the notebook itself. Note, it does not appear that the `power_plots` code or the `diversity_analysis` code is included in this PR, and which appear to be necessary for this code to work.\r\n\r\nhttps://github.com/JWDebelius/American-Gut/blob/statistical_power/ipynb/Power.ipynb#L16\r\n\t- copyright 2015\r\n\t\r\nhttps://github.com/JWDebelius/American-Gut/blob/statistical_power/ipynb/Power.ipynb#L27\r\n\t- css file doesn't appear to be in the repo\r\n\t\r\nhttps://github.com/JWDebelius/American-Gut/blob/statistical_power/ipynb/Power.ipynb#L113\r\n\t- The return to the table of contents link is confusing as it advances you in the document. Shouldn't the TOC be early or first thing in the notebook if there is one?\r\n\r\nfunction imports, american_gut.power_plots does not appear to exist nor does americangut.diversity_analysis. \r\n\r\ngeneral: it is QIIME\r\n\r\nalpha diversity parameters section, the beta diversity link is 404\r\n\r\nIn parameters for fecal samples, the ANTIBIOTIC_SELECT values are \"In the past month\" and \"Not in the past year\". Earlier in the document it indicates that \"in the past week\" will also included?\r\n\r\nIn the files and directories section, the download links to dropbox. Are these data not in the repo? Ah, or these precomputed distance matrices? \r\n\r\nIn data download, we should not source from what look like random dropbox accounts. If the volume is such that it doesn't make sense to host on github, we can drop the data on ftp.microbio.me. \r\n\r\nIn power calculation for fecal samples, the first two lines are not preallocating a list but creating an empty list. \r\n\r\nIn power calculation for fecal samples,\r\n\r\n\t# Removes the category from the control cats, if necessary\r\n    if cat in fecal_control_cats:        \r\n        ctrl_cats = copy.deepcopy(fecal_control_cats)\r\n        ctrl_cats.remove(cat)\r\n\r\n\tcan be replaced with\r\n\t\r\n\t# Removes the category from the control cats, if necessary\r\n    if cat in fecal_control_cats:        \r\n        ctrl_cats = fecal_control_cats[:]\r\n        ctrl_cats.remove(cat)\r\n\r\n\tbut since order does not appear to matter, it would be more efficient if fecal_control_cats was a set. This is likely in a block of code that is not a bottleneck, so just a minor comment.\r\n\t\r\neffect size estimation, the capitalization of a lot of items in the table is wrong (e.g., Ibd)\r\n\r\nBeta diversity section has a \"[beta diversity discussion]\", is that a place holder?\r\n\r\nUnweighted unifrac is quite powerful? The text previously mentioned weighted unifrac as well, should there be a plot for that too?\r\n"}}