{"action":"created","issue":{"url":"https://api.github.com/repos/xfim/ggmcmc/issues/40","labels_url":"https://api.github.com/repos/xfim/ggmcmc/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/xfim/ggmcmc/issues/40/comments","events_url":"https://api.github.com/repos/xfim/ggmcmc/issues/40/events","html_url":"https://github.com/xfim/ggmcmc/issues/40","id":91215585,"number":40,"title":"Cannot include the warmup using ggs for a stanfit object","user":{"login":"perkaer","id":1407740,"avatar_url":"https://avatars.githubusercontent.com/u/1407740?v=3","gravatar_id":"","url":"https://api.github.com/users/perkaer","html_url":"https://github.com/perkaer","followers_url":"https://api.github.com/users/perkaer/followers","following_url":"https://api.github.com/users/perkaer/following{/other_user}","gists_url":"https://api.github.com/users/perkaer/gists{/gist_id}","starred_url":"https://api.github.com/users/perkaer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/perkaer/subscriptions","organizations_url":"https://api.github.com/users/perkaer/orgs","repos_url":"https://api.github.com/users/perkaer/repos","events_url":"https://api.github.com/users/perkaer/events{/privacy}","received_events_url":"https://api.github.com/users/perkaer/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-26T10:20:25Z","updated_at":"2015-07-27T06:51:18Z","closed_at":null,"body":"Hi there\r\n\r\nWhen I run the following command, I cant seem to get out the warmup samples..\r\n\r\nBut I guess this is the idea with inc_warmup = T?\r\n\r\n```R\r\n> ggs(STAN_fit, family = 'sigma', inc_warmup = T)\r\nSource: local data frame [1,000 x 4]\r\n\r\n   Iteration Chain          Parameter    value\r\n1          1     1 transactions_sigma 208765.6\r\n2          2     1 transactions_sigma 206573.2\r\n3          3     1 transactions_sigma 198310.6\r\n4          4     1 transactions_sigma 214327.9\r\n5          5     1 transactions_sigma 209830.3\r\n6          6     1 transactions_sigma 205860.9\r\n7          7     1 transactions_sigma 199150.3\r\n8          8     1 transactions_sigma 209000.2\r\n9          9     1 transactions_sigma 200834.9\r\n10        10     1 transactions_sigma 217648.9\r\n..       ...   ...                ...      ...\r\nWarning message:\r\nIn ggs(STAN_fit, family = \"sigma\", inc_warmup = T) :\r\n  inc_warmup must be 'FALSE', so it is ignored.\r\n```"},"comment":{"url":"https://api.github.com/repos/xfim/ggmcmc/issues/comments/125105780","html_url":"https://github.com/xfim/ggmcmc/issues/40#issuecomment-125105780","issue_url":"https://api.github.com/repos/xfim/ggmcmc/issues/40","id":125105780,"user":{"login":"perkaer","id":1407740,"avatar_url":"https://avatars.githubusercontent.com/u/1407740?v=3","gravatar_id":"","url":"https://api.github.com/users/perkaer","html_url":"https://github.com/perkaer","followers_url":"https://api.github.com/users/perkaer/followers","following_url":"https://api.github.com/users/perkaer/following{/other_user}","gists_url":"https://api.github.com/users/perkaer/gists{/gist_id}","starred_url":"https://api.github.com/users/perkaer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/perkaer/subscriptions","organizations_url":"https://api.github.com/users/perkaer/orgs","repos_url":"https://api.github.com/users/perkaer/repos","events_url":"https://api.github.com/users/perkaer/events{/privacy}","received_events_url":"https://api.github.com/users/perkaer/received_events","type":"User","site_admin":false},"created_at":"2015-07-27T06:51:18Z","updated_at":"2015-07-27T06:51:18Z","body":"Thx for your answer.\r\n\r\nI am pretty sure `stan` returns all samples, both warmup and real samples, and you cannot disable it afaik. Both `rstan::extract` and `rstan::traceplot` have `inc_warmup` arguments, which include warmup samples in their output.\r\n\r\nWhen setting `inc_warmup=TRUE`, I simply expected to be able to do all the nice things `ggmcmc` does, but including warmup sample :) But more specifically I just want traceplots including warmup samples, to see how many warmup samples I typically need.\r\n\r\nThx for a great piece of software.\r\n\r\n\r\n"}}