{"issue":{"user":{"id":112708,"login":"matsen","url":"https://api.github.com/users/matsen","avatar_url":"https://secure.gravatar.com/avatar/4db85b793d1add116997fbfde4e83f58?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"4db85b793d1add116997fbfde4e83f58"},"milestone":{"creator":{"id":112708,"login":"matsen","url":"https://api.github.com/users/matsen","avatar_url":"https://secure.gravatar.com/avatar/4db85b793d1add116997fbfde4e83f58?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"4db85b793d1add116997fbfde4e83f58"},"open_issues":11,"created_at":"2011-12-15T00:25:18Z","title":"alpha12","state":"open","due_on":null,"closed_issues":0,"description":"","number":9,"url":"https://api.github.com/repos/matsen/pplacer/milestones/9"},"created_at":"2011-12-14T12:10:50Z","title":"pentropy-- a phylogenetic entropy measure","state":"open","updated_at":"2011-12-20T21:12:34Z","labels":[{"name":"has branch","url":"https://api.github.com/repos/matsen/pplacer/labels/has+branch","color":"C2FF8A"},{"name":"ready to merge","url":"https://api.github.com/repos/matsen/pplacer/labels/ready+to+merge","color":"DDDDDD"},{"name":"top","url":"https://api.github.com/repos/matsen/pplacer/labels/top","color":"e10c02"}],"id":2550740,"html_url":"https://github.com/matsen/pplacer/issues/189","closed_at":null,"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"body":"This one is thanks to @cmccoy, who found a [paper](http://www.people.fas.harvard.edu/~ballen/NewPhylogenetic.pdf) describing a generalization of Shannon entropy to the phylogenetic context. \r\n\r\nIt's very simple. \r\n\r\nFor any snippet e (recall that a snippet is a section of edge without any placements), let p(e) be the unitized amount of mass on the non-root side of e. Let l(e) be the length of the snippet. From there, the phylogenetic entropy is\r\n\r\n    - \\sum_e l(e) p(e) log p(e)\r\n\r\nNote that p(e) log p(e) should be defined to be zero when p(e) is zero, although the log term will give infinity.\r\n","number":189,"url":"https://api.github.com/repos/matsen/pplacer/issues/189","comments":1,"assignee":{"id":21168,"login":"habnabit","url":"https://api.github.com/users/habnabit","avatar_url":"https://secure.gravatar.com/avatar/2c2f9d59e797ad575432d1da7681ce78?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"2c2f9d59e797ad575432d1da7681ce78"}},"comment":{"user":{"id":112708,"login":"matsen","url":"https://api.github.com/users/matsen","avatar_url":"https://secure.gravatar.com/avatar/4db85b793d1add116997fbfde4e83f58?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"4db85b793d1add116997fbfde4e83f58"},"created_at":"2011-12-20T21:12:34Z","updated_at":"2011-12-20T21:12:34Z","id":3225417,"body":"Connor has now used this one. Ready to merge.","url":"https://api.github.com/repos/matsen/pplacer/issues/comments/3225417"},"action":"created"}