{"action":"created","issue":{"url":"https://api.github.com/repos/ropensci/rrrpkg/issues/8","labels_url":"https://api.github.com/repos/ropensci/rrrpkg/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/ropensci/rrrpkg/issues/8/comments","events_url":"https://api.github.com/repos/ropensci/rrrpkg/issues/8/events","html_url":"https://github.com/ropensci/rrrpkg/issues/8","id":85884737,"number":8,"title":"Where to save results/processed data? Or is that not expected to be saved because it can be reproduced?","user":{"login":"daattali","id":952340,"avatar_url":"https://avatars.githubusercontent.com/u/952340?v=3","gravatar_id":"","url":"https://api.github.com/users/daattali","html_url":"https://github.com/daattali","followers_url":"https://api.github.com/users/daattali/followers","following_url":"https://api.github.com/users/daattali/following{/other_user}","gists_url":"https://api.github.com/users/daattali/gists{/gist_id}","starred_url":"https://api.github.com/users/daattali/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daattali/subscriptions","organizations_url":"https://api.github.com/users/daattali/orgs","repos_url":"https://api.github.com/users/daattali/repos","events_url":"https://api.github.com/users/daattali/events{/privacy}","received_events_url":"https://api.github.com/users/daattali/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-06-07T09:44:54Z","updated_at":"2015-06-11T08:41:18Z","closed_at":null,"body":"(Is this the proper place to ask such questions or is there anywhere else I should be voicing my thoughts?)\r\n\r\nWhat is the suggested solution for dealing with intermediate useful output/results data?  It might be argued that results should not be included since the whole point is that you can technically reproduce them with the repository, but in many cases it can be beneficial to 1. have some results in the repo that can be easily shown, and 2. maybe save some important intermediate outputs if they can be regarded as interesting results on their own.  You might disagree, and I'm fine with that, but in either case I feel like it would be helpful to at least include a small blurb on the topic - either include them or don't include them or list the pros/cons.\r\n\r\nFrom my own personal (and limited) experience, I like having not only the raw data but also the clean version if it takes a long time to produce it and is more useful."},"comment":{"url":"https://api.github.com/repos/ropensci/rrrpkg/issues/comments/111043402","html_url":"https://github.com/ropensci/rrrpkg/issues/8#issuecomment-111043402","issue_url":"https://api.github.com/repos/ropensci/rrrpkg/issues/8","id":111043402,"user":{"login":"benmarwick","id":1262179,"avatar_url":"https://avatars.githubusercontent.com/u/1262179?v=3","gravatar_id":"","url":"https://api.github.com/users/benmarwick","html_url":"https://github.com/benmarwick","followers_url":"https://api.github.com/users/benmarwick/followers","following_url":"https://api.github.com/users/benmarwick/following{/other_user}","gists_url":"https://api.github.com/users/benmarwick/gists{/gist_id}","starred_url":"https://api.github.com/users/benmarwick/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benmarwick/subscriptions","organizations_url":"https://api.github.com/users/benmarwick/orgs","repos_url":"https://api.github.com/users/benmarwick/repos","events_url":"https://api.github.com/users/benmarwick/events{/privacy}","received_events_url":"https://api.github.com/users/benmarwick/received_events","type":"User","site_admin":false},"created_at":"2015-06-11T08:41:18Z","updated_at":"2015-06-11T08:41:18Z","body":"Hi @karthik, there are a few opinions on ProjectTemplate shared over here https://github.com/swcarpentry/site/issues/806 and @rmflight has some interesting [notes on a comparison of R packages and ProjectTemplate](http://rmflight.github.io/posts/2014/07/zpackages_vs_projectTemplate.html). For me, ProjectTemplate too complicated for my typical use cases, and lacks the ubiquity and recognition that the R package structure has. But maybe others find the ProjectTemplate approach suits their research more, I'd be interested to see examples of research compendia using ProjectTemplate (do you know of any?)\r\n\r\n@daattali, yes, I think there is an ethic that results (ie. output artefacts) should be treated as disposable or overwritable (cf. @richfitz's post http://nicercode.github.io/blog/2013-04-05-projects/), in a similar way that Docker containers are encouraged to be considered disposable.  The most appropriate management of this might end up varying considerably across different research communities, for my work the most sensible approach (to me at the moment) seems to be a sub-directory in `analysis` called `figures` or `output`, as @cboettig described above. I suppose a more generic version of that might be\r\n```\r\nanalysis/\r\n  ├─ input/\r\n  |   └─ my_rmd.Rmd\r\n  └─ output/\r\n    ├─ data-generated/\r\n    └─ figures/\r\n```\r\n\r\nBut I'm keen to see more real-world examples of what emerges from 'mangle of practice' when others organise their research to accompany publication.  I think that's where we'll get a lot of useful insight into some of these questions. I've been bothered by knitr's caching recently, so I'm giving `remake` a try on a current project as an alternative to that, though I'm wary of adding yet another dependency to my workflow..."}}