{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/1063","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1063/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1063/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1063/events","html_url":"https://github.com/biocore/scikit-bio/issues/1063","id":101758155,"number":1063,"title":"improvements to phylogenetic diversity metrics","user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-08-18T21:55:16Z","updated_at":"2015-08-19T03:51:45Z","closed_at":null,"body":"These issues came up in the context of #1027. These are also related to #1040. \r\n\r\n- [ ] port original UniFrac web docs\r\n- [ ] explore alternative weighting schemes (see @rob-knight's comment [here](https://github.com/biocore/scikit-bio/pull/1027/files#r36536782))\r\n- [ ] phylogenetic metrics should be generalized to DAGs (we had some offline discussion on this, and @wasade did some prototyping [here](https://github.com/wasade/yummy-octo-duck)).\r\n- [ ] phylogenetic metrics should support sparse vectors as input (will depend on the contingency table API)\r\n- [ ] Should we use *OTU* (may be the most easily understandable to our users) versus *observation* (for consistency with BIOM) versus *feature* (for consistency with sklearn) in docs? This should probably be an RFC. \r\n- [ ] add formulas for metrics (including normalization of weighted unifrac)"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/132438067","html_url":"https://github.com/biocore/scikit-bio/issues/1063#issuecomment-132438067","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1063","id":132438067,"user":{"login":"rob-knight","id":2014505,"avatar_url":"https://avatars.githubusercontent.com/u/2014505?v=3","gravatar_id":"","url":"https://api.github.com/users/rob-knight","html_url":"https://github.com/rob-knight","followers_url":"https://api.github.com/users/rob-knight/followers","following_url":"https://api.github.com/users/rob-knight/following{/other_user}","gists_url":"https://api.github.com/users/rob-knight/gists{/gist_id}","starred_url":"https://api.github.com/users/rob-knight/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rob-knight/subscriptions","organizations_url":"https://api.github.com/users/rob-knight/orgs","repos_url":"https://api.github.com/users/rob-knight/repos","events_url":"https://api.github.com/users/rob-knight/events{/privacy}","received_events_url":"https://api.github.com/users/rob-knight/received_events","type":"User","site_admin":false},"created_at":"2015-08-19T03:51:44Z","updated_at":"2015-08-19T03:51:44Z","body":"Not OTU, can use with raw seqs, genomes etc.\n\nOn Aug 18, 2015, at 2:55 PM, Greg Caporaso <notifications@github.com> wrote:\n\nThese issues came up in the context of #1027\n<https://github.com/biocore/scikit-bio/pull/1027>:\n\n   - port original UniFrac web docs\n   - explore alternative weighting schemes (see @rob-knight\n   <https://github.com/rob-knight>'s comment here\n   <https://github.com/biocore/scikit-bio/pull/1027/files#r36536782>)\n   - phylogenetic metrics should be generalized to DAGs (we had some\n   offline discussion on this, and @wasade <https://github.com/wasade> did\n   some prototyping here <https://github.com/wasade/yummy-octo-duck>).\n   - phylogenetic metrics should support sparse vectors as input (will\n   depend on the contingency table API)\n   - Should we use *OTU* (may be the most easily understandable to our\n   users) versus *observation* (for consistency with BIOM) versus *feature*\n   (for consistency with sklearn) in docs? This should probably be an RFC.\n   - add formulas for metrics (including normalization of weighted unifrac)\n\n—\nReply to this email directly or view it on GitHub\n<https://github.com/biocore/scikit-bio/issues/1063>.\n"}}