{"action":"created","issue":{"url":"https://api.github.com/repos/stephenslab/dsc2/issues/93","repository_url":"https://api.github.com/repos/stephenslab/dsc2","labels_url":"https://api.github.com/repos/stephenslab/dsc2/issues/93/labels{/name}","comments_url":"https://api.github.com/repos/stephenslab/dsc2/issues/93/comments","events_url":"https://api.github.com/repos/stephenslab/dsc2/issues/93/events","html_url":"https://github.com/stephenslab/dsc2/issues/93","id":301971735,"number":93,"title":"Convention to skip codes in Rmarkdown when running in DSC","user":{"login":"gaow","id":917985,"avatar_url":"https://avatars1.githubusercontent.com/u/917985?v=4","gravatar_id":"","url":"https://api.github.com/users/gaow","html_url":"https://github.com/gaow","followers_url":"https://api.github.com/users/gaow/followers","following_url":"https://api.github.com/users/gaow/following{/other_user}","gists_url":"https://api.github.com/users/gaow/gists{/gist_id}","starred_url":"https://api.github.com/users/gaow/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gaow/subscriptions","organizations_url":"https://api.github.com/users/gaow/orgs","repos_url":"https://api.github.com/users/gaow/repos","events_url":"https://api.github.com/users/gaow/events{/privacy}","received_events_url":"https://api.github.com/users/gaow/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-03-03T05:50:00Z","updated_at":"2018-03-05T19:01:46Z","closed_at":null,"author_association":"MEMBER","body":"Previously we have implemented support to RMD file as DSC executable modules. Thinking about it a bit more, I think we can make some efforts to bridge between interactive analyses and running in DSC if we invent some conventions for RMD indented to be used in DSC. Since I'm not very sure how RMD is typically used I hope you could suggest me what to do. \r\n\r\nBasically, one possibility could be something like this, eg, in DSC:\r\n\r\n```yaml\r\nnormal: normal.Rmd\r\n  n: 1000\r\n  ...\r\n```\r\n\r\nAnd the Rmd file might look like:\r\n\r\n```rmd\r\n\r\nNow let's prototype this method. First set parameters:\r\n\r\n` ` `{r}\r\nn = 1000\r\n` ` ` \r\nThen run this method\r\n\r\n` ` `{r chunck_name}\r\nx = rnorm(n)\r\n` ` `\r\n\r\nwhere (explain what everything is)\r\n\r\nNow let's make a diagnostic plot:\r\n\r\n` ` `{r}\r\nplot(x)\r\n` ` `\r\n\r\n```\r\n\r\n\r\nYou see DSC will only need the 2nd code chunk.  Does it seem to be useful to have something along the lines of:\r\n\r\n```yaml\r\nnormal: normal.Rmd:name\r\n  n:1000\r\n```\r\n\r\nOr even eg, \r\n\r\n```yaml\r\ntrunk_normal: normal.Rmd:simulate + normal.Rmd:truncate\r\n  n: 1000\r\n```\r\nThis way will in some way tie DSC with exploratory analysis. If this propose looks useful in practice, could we decide on a syntax for it?"},"comment":{"url":"https://api.github.com/repos/stephenslab/dsc2/issues/comments/370526224","html_url":"https://github.com/stephenslab/dsc2/issues/93#issuecomment-370526224","issue_url":"https://api.github.com/repos/stephenslab/dsc2/issues/93","id":370526224,"user":{"login":"gaow","id":917985,"avatar_url":"https://avatars1.githubusercontent.com/u/917985?v=4","gravatar_id":"","url":"https://api.github.com/users/gaow","html_url":"https://github.com/gaow","followers_url":"https://api.github.com/users/gaow/followers","following_url":"https://api.github.com/users/gaow/following{/other_user}","gists_url":"https://api.github.com/users/gaow/gists{/gist_id}","starred_url":"https://api.github.com/users/gaow/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gaow/subscriptions","organizations_url":"https://api.github.com/users/gaow/orgs","repos_url":"https://api.github.com/users/gaow/repos","events_url":"https://api.github.com/users/gaow/events{/privacy}","received_events_url":"https://api.github.com/users/gaow/received_events","type":"User","site_admin":false},"created_at":"2018-03-05T19:01:46Z","updated_at":"2018-03-05T19:01:46Z","author_association":"MEMBER","body":"> Also, my personal opinion is that this is Bad Practice, and I'm hesistant to provide options that would allow for Bad Practice.\r\n\r\nI acknowledge this, as have explained in the documentation, with warning messages in the runs:\r\n\r\n![2018-03-05-12-44-47_scrot](https://user-images.githubusercontent.com/917985/36993276-03a07d66-2073-11e8-99a0-cf64ef51065c.png)\r\n\r\nIt is perhaps a judgement call, but in general I'm tend to be liberal at the point where too rigorous requirement of best practice sacrifices productivity (drawing a line is tricky though). Other than what we are discussing here, I can already see ways people might abuse DSC that we may not have the energy to support. My only motivation is that it might be convenient to people who know what they are doing, eg, to lab members the most important target users of DSC. One can also make feature requests to  support `ipynb` which, given the mechanism we already have, is not hard, but I'd not spend the energy unless the request comes from the lab.\r\n\r\n> Also, do you think it is worthwhile adding more complexity to the module syntax for this special case?\r\n\r\nI agree, too. My argument is that this could be a case / syntax some people never use, if they do not like it; or decide to like and use it after 10min reading. I guess it is acceptable if it did not make existing simple case complicated. Plus we can always work on syntax (to the limit I can properly handle). The main issue I agree is perhaps still on best practice, which I shared my view above."}}
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