{"action":"created","comment":{"url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/comments/71815615","id":71815615,"diff_hunk":"@@ -176,102 +172,55 @@ \\section{Data Management}\\label{sec:data}\n   treatment variable from \\texttt{1} vs.  \\texttt{2} to\n   \\texttt{untreated} vs. \\texttt{treated}, and replace artificial\n   codes for missing data, such as ``-99'', with \\texttt{NA}s,\n-  a shorthand code for ``Not Available'' that is used as a special variable\n-  in many programming languages \\cite{white2013}.\n+  a code used in most programming languages to indicate that data is ``Not Available''\n+  \\cite{white2013}.\n \n-  \\emph{Filenames}: Store\n-  especially useful metadata as part of the filename itself, while\n-  keeping the filename regular enough for easy pattern matching. For\n-  example, a filename like \\texttt{2016-05-alaska-b.csv} makes it easy\n-  for both people and programs to select by year or by location.\n+  \\emph{Filenames}: Store especially useful metadata as part of the filename itself, while\n+  keeping the filename regular enough for easy pattern matching. For example, a filename\n+  like \\texttt{2016-05-alaska-b.csv} makes it easy for both people and programs to select\n+  by year or by location.\n \n \\item\n-  \\recommend{Create analysis-friendly data}. Re-formatting data will\n-  eliminate processing steps between loading the\n-  data set and doing analyses.\n-\n-  \\emph{Split columns} that contain more\n-  than one variable's worth of information. For example, most analytical environments will read the value ``3.4 kg''\n-  as character data, rather than numeric. It should be split into two columns (the mass ``3.4'' and\n-  the units ``kg''), or record the units in the variable\n-  name and/or metadata.\n-\n-  \\emph{Combine columns} that only contain one variable's worth of\n-  information when taken together. This is\n-  characteristic of data that has been laid out for human eyeballs or\n-  for manual data entry.  For example, there might be one row per\n-  field site and then columns for measurements made at each of several\n-  time points. It is convenient to store this in a ``short and wide''\n-  form for data entry and inspection, but for most analyses it will be\n-  advantageous to gather these columns into a variable of\n-  measurements, plus an additional column that indicates the\n-  time point.\n-\n-  \\emph{Reformat values} to match your environment's built-in\n-  parsing rules. For example, use a date-time format that will be\n-  recognized automatically, or better yet, split dates into three\n-  columns (year, month, and day) for easier sorting and filtering.\n+  \\recommend{Create analysis-friendly data}: Analysis can be much easier if you are\n+  working with so-called ``tidy'' data \\cite{wickham2014}. Two key principles:\n \n-  \\begin{quote}\n-    \\noindent \\textbf{OpenRefine}\n-\n-    \\withurl{OpenRefine}{http://openrefine.org/}","path":"good-enough-practices-for-scientific-computing.tex","position":124,"original_position":124,"commit_id":"ac331a18a43782d7fe5e8c24b566b55f3831dd76","original_commit_id":"ac331a18a43782d7fe5e8c24b566b55f3831dd76","user":{"login":"jennybc","id":599454,"avatar_url":"https://avatars.githubusercontent.com/u/599454?v=3","gravatar_id":"","url":"https://api.github.com/users/jennybc","html_url":"https://github.com/jennybc","followers_url":"https://api.github.com/users/jennybc/followers","following_url":"https://api.github.com/users/jennybc/following{/other_user}","gists_url":"https://api.github.com/users/jennybc/gists{/gist_id}","starred_url":"https://api.github.com/users/jennybc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennybc/subscriptions","organizations_url":"https://api.github.com/users/jennybc/orgs","repos_url":"https://api.github.com/users/jennybc/repos","events_url":"https://api.github.com/users/jennybc/events{/privacy}","received_events_url":"https://api.github.com/users/jennybc/received_events","type":"User","site_admin":false},"body":"I removed this for two reasons. One, I'm not completely sold on OpenRefine. I appreciate that it writes a log file but I'm not completely convinced it's dramatically better than someone working in a spreadsheet. It seems to really shine at character/regex work, which we have not gotten into here at all. Two, we aren't mentioning other specific tools that I think are way more important, like R and Python. So this specific shout out just seemed odd to me.","created_at":"2016-07-22T01:32:35Z","updated_at":"2016-07-22T01:32:35Z","html_url":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing/pull/132#discussion_r71815615","pull_request_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/132","_links":{"self":{"href":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/comments/71815615"},"html":{"href":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing/pull/132#discussion_r71815615"},"pull_request":{"href":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/132"}}},"pull_request":{"url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/132","id":78411116,"html_url":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing/pull/132","diff_url":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing/pull/132.diff","patch_url":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing/pull/132.patch","issue_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/issues/132","number":132,"state":"open","locked":false,"title":"Reorganize and shorten data management section","user":{"login":"jennybc","id":599454,"avatar_url":"https://avatars.githubusercontent.com/u/599454?v=3","gravatar_id":"","url":"https://api.github.com/users/jennybc","html_url":"https://github.com/jennybc","followers_url":"https://api.github.com/users/jennybc/followers","following_url":"https://api.github.com/users/jennybc/following{/other_user}","gists_url":"https://api.github.com/users/jennybc/gists{/gist_id}","starred_url":"https://api.github.com/users/jennybc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennybc/subscriptions","organizations_url":"https://api.github.com/users/jennybc/orgs","repos_url":"https://api.github.com/users/jennybc/repos","events_url":"https://api.github.com/users/jennybc/events{/privacy}","received_events_url":"https://api.github.com/users/jennybc/received_events","type":"User","site_admin":false},"body":"Down to 16 pages from 17! I made some pretty big cuts/changes, but this was a section I drafted initially, so seemed OK. I'll make comments to point out where others might want to look.","created_at":"2016-07-22T01:03:11Z","updated_at":"2016-07-22T01:32:35Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c16e3c10828eb0596abf0d5310d1288e117a86d9","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/132/commits","review_comments_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/132/comments","review_comment_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/pulls/comments{/number}","comments_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/issues/132/comments","statuses_url":"https://api.github.com/repos/swcarpentry/good-enough-practices-in-scientific-computing/statuses/ac331a18a43782d7fe5e8c24b566b55f3831dd76","head":{"label":"swcarpentry:2-data-mgmt","ref":"2-data-mgmt","sha":"ac331a18a43782d7fe5e8c24b566b55f3831dd76","user":{"login":"swcarpentry","id":2238358,"avatar_url":"https://avatars.githubusercontent.com/u/2238358?v=3","gravatar_id":"","url":"https://api.github.com/users/swcarpentry","html_url":"https://github.com/swcarpentry","followers_url":"https://api.github.com/users/swcarpentry/followers","following_url":"https://api.github.com/users/swcarpentry/following{/other_user}","gists_url":"https://api.github.com/users/swcarpentry/gists{/gist_id}","starred_url":"https://api.github.com/users/swcarpentry/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swcarpentry/subscriptions","organizations_url":"https://api.github.com/users/swcarpentry/orgs","repos_url":"https://api.github.com/users/swcarpentry/repos","events_url":"https://api.github.com/users/swcarpentry/events{/privacy}","received_events_url":"https://api.github.com/users/swcarpentry/received_events","type":"Organization","site_admin":false},"repo":{"id":44908667,"name":"good-enough-practices-in-scientific-computing","full_name":"swcarpentry/good-enough-practices-in-scientific-computing","owner":{"login":"swcarpentry","id":2238358,"avatar_url":"https://avatars.githubusercontent.com/u/2238358?v=3","gravatar_id":"","url":"https://api.github.com/users/swcarpentry","html_url":"https://github.com/swcarpentry","followers_url":"https://api.github.com/users/swcarpentry/followers","following_url":"https://api.github.com/users/swcarpentry/following{/other_user}","gists_url":"https://api.github.com/users/swcarpentry/gists{/gist_id}","starred_url":"https://api.github.com/users/swcarpentry/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swcarpentry/subscriptions","organizations_url":"https://api.github.com/users/swcarpentry/orgs","repos_url":"https://api.github.com/users/swcarpentry/repos","events_url":"https://api.github.com/users/swcarpentry/events{/privacy}","received_events_url":"https://api.github.com/users/swcarpentry/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/swcarpentry/good-enough-practices-in-scientific-computing","description":"Minimalist 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