{"action":"closed","issue":{"url":"https://api.github.com/repos/chr1swallace/GUESSFM/issues/8","repository_url":"https://api.github.com/repos/chr1swallace/GUESSFM","labels_url":"https://api.github.com/repos/chr1swallace/GUESSFM/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/chr1swallace/GUESSFM/issues/8/comments","events_url":"https://api.github.com/repos/chr1swallace/GUESSFM/issues/8/events","html_url":"https://github.com/chr1swallace/GUESSFM/issues/8","id":144823896,"number":8,"title":"No prior plot with pp.nsnp","user":{"login":"jinshaw16","id":14347839,"avatar_url":"https://avatars.githubusercontent.com/u/14347839?v=3","gravatar_id":"","url":"https://api.github.com/users/jinshaw16","html_url":"https://github.com/jinshaw16","followers_url":"https://api.github.com/users/jinshaw16/followers","following_url":"https://api.github.com/users/jinshaw16/following{/other_user}","gists_url":"https://api.github.com/users/jinshaw16/gists{/gist_id}","starred_url":"https://api.github.com/users/jinshaw16/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jinshaw16/subscriptions","organizations_url":"https://api.github.com/users/jinshaw16/orgs","repos_url":"https://api.github.com/users/jinshaw16/repos","events_url":"https://api.github.com/users/jinshaw16/events{/privacy}","received_events_url":"https://api.github.com/users/jinshaw16/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-03-31T08:21:14Z","updated_at":"2016-04-11T20:30:49Z","closed_at":"2016-04-11T20:30:49Z","body":"As I understand it, a prior distribution line should appear in the graph if I use the option \"expected=\" in the  pp.nsnp command.  I have attempted this on a few different datasets and the prior line does not appear (but the y axis is labelled \"Prior/Posterior probability\", and the \"Prior\" label appears in the legend).\r\n\r\nHaving inspected the issue, it seems to be that, due to specifying no over-dispersion parameter, it defaults to 1, which defaults the \"rho\" parameter in the dbetabinom command to 0 as part of the pp.snp command.  Under the help for dbetabinom, it states that the rho parameter should be in the range (0,1), but that \"the value 0 is sometimes supported\".  \r\n\r\nIn my system, the 0 value appears not to be supported, as NaN is produced for the prior results.  When I manually change the rho parameter to a very small value, the prior appears.\r\n\r\nI thought I would flag with you so you were aware."}}