{"action":"created","issue":{"url":"https://api.github.com/repos/bomeara/BMhyb/issues/2","repository_url":"https://api.github.com/repos/bomeara/BMhyb","labels_url":"https://api.github.com/repos/bomeara/BMhyb/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/bomeara/BMhyb/issues/2/comments","events_url":"https://api.github.com/repos/bomeara/BMhyb/issues/2/events","html_url":"https://github.com/bomeara/BMhyb/issues/2","id":169681646,"number":2,"title":"bad numerical issues","user":{"login":"bomeara","id":1612612,"avatar_url":"https://avatars.githubusercontent.com/u/1612612?v=3","gravatar_id":"","url":"https://api.github.com/users/bomeara","html_url":"https://github.com/bomeara","followers_url":"https://api.github.com/users/bomeara/followers","following_url":"https://api.github.com/users/bomeara/following{/other_user}","gists_url":"https://api.github.com/users/bomeara/gists{/gist_id}","starred_url":"https://api.github.com/users/bomeara/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bomeara/subscriptions","organizations_url":"https://api.github.com/users/bomeara/orgs","repos_url":"https://api.github.com/users/bomeara/repos","events_url":"https://api.github.com/users/bomeara/events{/privacy}","received_events_url":"https://api.github.com/users/bomeara/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-05T19:41:24Z","updated_at":"2016-08-21T00:37:43Z","closed_at":null,"body":"If the final VCV has any eigen values < 0 (or just tiny), it is not positive definite. Calculation of the likelihoods may have no relation to the truth. And this can happen for realistic values of our parameters. The spline smoothing is supposed to deal with this, but doesn't do it well. We can see if matrices are ultrametric (this does not mean the same as trees being ultrametric) but how do you get likelihood in a region that is biologically realistic but which isn't appropriate?\r\n\r\nWe've tried simulating, estimating a var() on the simulated tips to get the VCV, and then use that, but that often has issues as well. We implemented a pseudo-determinant: that also failed. We might do ABC, but it's embarrassing. "},"comment":{"url":"https://api.github.com/repos/bomeara/BMhyb/issues/comments/241231974","html_url":"https://github.com/bomeara/BMhyb/issues/2#issuecomment-241231974","issue_url":"https://api.github.com/repos/bomeara/BMhyb/issues/2","id":241231974,"user":{"login":"djhwueng","id":20727189,"avatar_url":"https://avatars.githubusercontent.com/u/20727189?v=3","gravatar_id":"","url":"https://api.github.com/users/djhwueng","html_url":"https://github.com/djhwueng","followers_url":"https://api.github.com/users/djhwueng/followers","following_url":"https://api.github.com/users/djhwueng/following{/other_user}","gists_url":"https://api.github.com/users/djhwueng/gists{/gist_id}","starred_url":"https://api.github.com/users/djhwueng/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djhwueng/subscriptions","organizations_url":"https://api.github.com/users/djhwueng/orgs","repos_url":"https://api.github.com/users/djhwueng/repos","events_url":"https://api.github.com/users/djhwueng/events{/privacy}","received_events_url":"https://api.github.com/users/djhwueng/received_events","type":"User","site_admin":false},"created_at":"2016-08-21T00:37:43Z","updated_at":"2016-08-21T00:37:43Z","body":"The log likelihood shall have range on R. We will rerun our analysis and check if there is still any numerical issue described here."}}
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