{"action":"created","issue":{"url":"https://api.github.com/repos/grunwaldlab/poppr/issues/16","labels_url":"https://api.github.com/repos/grunwaldlab/poppr/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/grunwaldlab/poppr/issues/16/comments","events_url":"https://api.github.com/repos/grunwaldlab/poppr/issues/16/events","html_url":"https://github.com/grunwaldlab/poppr/issues/16","id":63817955,"number":16,"title":"Fix poppr for upcoming release of adegenet/pegas/hierfstat","user":{"login":"zkamvar","id":3639446,"avatar_url":"https://avatars.githubusercontent.com/u/3639446?v=3","gravatar_id":"","url":"https://api.github.com/users/zkamvar","html_url":"https://github.com/zkamvar","followers_url":"https://api.github.com/users/zkamvar/followers","following_url":"https://api.github.com/users/zkamvar/following{/other_user}","gists_url":"https://api.github.com/users/zkamvar/gists{/gist_id}","starred_url":"https://api.github.com/users/zkamvar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zkamvar/subscriptions","organizations_url":"https://api.github.com/users/zkamvar/orgs","repos_url":"https://api.github.com/users/zkamvar/repos","events_url":"https://api.github.com/users/zkamvar/events{/privacy}","received_events_url":"https://api.github.com/users/zkamvar/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-23T19:56:15Z","updated_at":"2015-03-26T16:52:57Z","closed_at":null,"body":"The adegenet package is going through major changes on github and many functions in poppr will break due to these changes.\r\n\r\nThree main things will change:\r\n\r\n1. the tab slot of genind objects will store data as integers as opposed to floats\r\n2. the ploidy slot will contain the ploidy for all samples\r\n3. genind and genlight objects will gain genclone's hierarchy slot\r\n\r\nChanges that need to be implemented in poppr:\r\n\r\n- [ ] remove hierarchy slots from genclone objects as they will be inherited\r\n- [ ] remove hierarchy methods \r\n- [ ] change all references to `$tab` and `@tab` to `tab()`.\r\n- [ ] change `na.replace(object)` in `missingno` to `tab(object)` and deprecate.\r\n- [ ] ensure that distance methods are compatible.\r\n- [ ] change `SEXP pairdiffs` to take integer input.\r\n- [ ] change `SEXP permute_shuff` to take integer input.\r\n- [ ] add tab method to bootgen objects.\r\n\r\nThis is not an exhaustive list as I know bugs will crop up as I encounter them, so I'm putting this here:\r\n\r\n- [ ] **WRITE A TEST FOR EVERY BUG ENCOUNTERED**"},"comment":{"url":"https://api.github.com/repos/grunwaldlab/poppr/issues/comments/86621364","html_url":"https://github.com/grunwaldlab/poppr/issues/16#issuecomment-86621364","issue_url":"https://api.github.com/repos/grunwaldlab/poppr/issues/16","id":86621364,"user":{"login":"zkamvar","id":3639446,"avatar_url":"https://avatars.githubusercontent.com/u/3639446?v=3","gravatar_id":"","url":"https://api.github.com/users/zkamvar","html_url":"https://github.com/zkamvar","followers_url":"https://api.github.com/users/zkamvar/followers","following_url":"https://api.github.com/users/zkamvar/following{/other_user}","gists_url":"https://api.github.com/users/zkamvar/gists{/gist_id}","starred_url":"https://api.github.com/users/zkamvar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zkamvar/subscriptions","organizations_url":"https://api.github.com/users/zkamvar/orgs","repos_url":"https://api.github.com/users/zkamvar/repos","events_url":"https://api.github.com/users/zkamvar/events{/privacy}","received_events_url":"https://api.github.com/users/zkamvar/received_events","type":"User","site_admin":false},"created_at":"2015-03-26T16:52:57Z","updated_at":"2015-03-26T16:52:57Z","body":"- [ ] update vignette documentation\r\n- [ ] fix \"initialize\" method for class `bruvomat`\r\n- [ ] fix `recode_polyploids`"}}