GitHub PullRequestReviewCommentEvent at 2014-08-21 18:17:49
Repository: bc
Actor: jdblischak
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/swcarpentry/bc/pulls/comments/16556795","id":16556795,"diff_hunk":"@@ -8,109 +8,91 @@ source(\"chunk_options.R\")\n opts_chunk$set(fig.path = \"figure/01-starting-with-data-\")\n ```\n \n-# Analyzing Patient Data\n+## Analyzing Patient Data\n \n We are studying inflammation in patients who have been given a new treatment for arthritis,\n and need to analyze the first dozen data sets. \n-The data sets are stored in `.csv` each row holds information for a single patient, and the columns represent successive days. \n+The data sets are stored in [comma-separated values](../../gloss.html#comma-separeted-values) (CSV) format: each row holds information for a single patient, and the columns represent successive days. \n The first few rows of our first file look like this:\n \n \t0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0\n \t0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1\n \t0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1\n \t0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1\n-\t0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1`\n+\t0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1\n \n-### We want to:\n+We want to:\n \n * load that data into memory,\n * calculate the average inflammation per day across all patients, and\n * plot the result.\n+\n To do all that, we'll have to learn a little bit about programming.\n \n-### Objectives\n-* Explain what a library is, and what libraries are used for.\n-* Load an R library and use the things it contains.\n+#### Objectives\n+\n * Read tabular data from a file into a program.\n * Assign values to variables.\n-* Learn about data types\n * Select individual values and subsections from data.\n-* Perform operations on arrays of data.\n+* Perform operations on a matrix of data.\n * Display simple graphs.\n \n-## Loading Data\n+### Loading Data\n \n-Words are useful, but what's more useful are the sentences and stories we use them to build. \n-Similarly, while a lot of powerful tools are built into languages like R, even more lives in the libraries they are used to build.\n-Importing a library is like getting a piece of lab equipment out of a storage locker and setting it up on the bench. \n-Once it's done, we can ask the library to do things for us.\n+To load our inflammation data, first we need to locate our data.\n+We can change the current working directory to the location of the CSV files using the function `setwd`.","path":"novice/r/01-starting-with-data.Rmd","position":50,"original_position":50,"commit_id":"a129eb213f17845517518107a3078a1f556b04ee","original_commit_id":"a129eb213f17845517518107a3078a1f556b04ee","user":{"login":"jdblischak","id":1608317,"avatar_url":"https://avatars.githubusercontent.com/u/1608317?v=2","gravatar_id":"9952931e69c37307ab4e1eb41dd14360","url":"https://api.github.com/users/jdblischak","html_url":"https://github.com/jdblischak","followers_url":"https://api.github.com/users/jdblischak/followers","following_url":"https://api.github.com/users/jdblischak/following{/other_user}","gists_url":"https://api.github.com/users/jdblischak/gists{/gist_id}","starred_url":"https://api.github.com/users/jdblischak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdblischak/subscriptions","organizations_url":"https://api.github.com/users/jdblischak/orgs","repos_url":"https://api.github.com/users/jdblischak/repos","events_url":"https://api.github.com/users/jdblischak/events{/privacy}","received_events_url":"https://api.github.com/users/jdblischak/received_events","type":"User","site_admin":false},"body":"> doesn't seem to work for me in rstudio.\r\n> have to do the Session > set working directory > choose source file location\r\n\r\n@chendaniely, what exactly did not work for you? Please elaborate.","created_at":"2014-08-21T18:17:49Z","updated_at":"2014-08-21T18:17:49Z","html_url":"https://github.com/swcarpentry/bc/pull/639#discussion_r16556795","pull_request_url":"https://api.github.com/repos/swcarpentry/bc/pulls/639","_links":{"self":{"href":"https://api.github.com/repos/swcarpentry/bc/pulls/comments/16556795"},"html":{"href":"https://github.com/swcarpentry/bc/pull/639#discussion_r16556795"},"pull_request":{"href":"https://api.github.com/repos/swcarpentry/bc/pulls/639"}}},"pull_request":{"url":"https://api.github.com/repos/swcarpentry/bc/pulls/639","id":19227034,"html_url":"https://github.com/swcarpentry/bc/pull/639","diff_url":"https://github.com/swcarpentry/bc/pull/639.diff","patch_url":"https://github.com/swcarpentry/bc/pull/639.patch","issue_url":"https://api.github.com/repos/swcarpentry/bc/issues/639","number":639,"state":"open","locked":false,"title":"Edits to make novice R lesson 01 more similar to novice Python lesson 01.","user":{"login":"jdblischak","id":1608317,"avatar_url":"https://avatars.githubusercontent.com/u/1608317?v=2","gravatar_id":"9952931e69c37307ab4e1eb41dd14360","url":"https://api.github.com/users/jdblischak","html_url":"https://github.com/jdblischak","followers_url":"https://api.github.com/users/jdblischak/followers","following_url":"https://api.github.com/users/jdblischak/following{/other_user}","gists_url":"https://api.github.com/users/jdblischak/gists{/gist_id}","starred_url":"https://api.github.com/users/jdblischak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdblischak/subscriptions","organizations_url":"https://api.github.com/users/jdblischak/orgs","repos_url":"https://api.github.com/users/jdblischak/repos","events_url":"https://api.github.com/users/jdblischak/events{/privacy}","received_events_url":"https://api.github.com/users/jdblischak/received_events","type":"User","site_admin":false},"body":"I have made edits so that the first R lesson more closely follows the Python lesson. It covers all the same topics save two:\r\n\r\n  + Loading external packages - omitted because none of the operations in the lesson require loading an external package.\r\n  + How to display three plots side-by-side - omitted because this is more complicated in R. This would require discussing how to set and reset `par` options, which is not a beginner topic.\r\n\r\nHere's how you can quickly compare the two rendered files:\r\n\r\n```\r\n# clone bc repo\r\ngit clone git@github.com:swcarpentry/bc.git\r\n# create and switch to new branch\r\ngit checkout -b review-pr\r\n# add remote\r\ngit remote add jdb git@github.com:jdblischak/bc.git\r\n# pull changes from my branch\r\ngit pull jdb 01-starting-with-data\r\n# build site locally\r\nmake site\r\n```\r\nThen compare the rendered files  `_site/novice/r/01-starting-with-data.html` and `_site/novice/python/01-numpy.html`.","created_at":"2014-08-01T18:48:00Z","updated_at":"2014-08-21T18:17:49Z","closed_at":null,"merged_at":null,"merge_commit_sha":"5551743fde9466b6059081486bc6904d9efcb576","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/swcarpentry/bc/pulls/639/commits","review_comments_url":"https://api.github.com/repos/swcarpentry/bc/pulls/639/comments","review_comment_url":"https://api.github.com/repos/swcarpentry/bc/pulls/comments/{number}","comments_url":"https://api.github.com/repos/swcarpentry/bc/issues/639/comments","statuses_url":"https://api.github.com/repos/swcarpentry/bc/statuses/a129eb213f17845517518107a3078a1f556b04ee","head":{"label":"jdblischak:01-starting-with-data","ref":"01-starting-with-data","sha":"a129eb213f17845517518107a3078a1f556b04ee","user":{"login":"jdblischak","id":1608317,"avatar_url":"https://avatars.githubusercontent.com/u/1608317?v=2","gravatar_id":"9952931e69c37307ab4e1eb41dd14360","url":"https://api.github.com/users/jdblischak","html_url":"https://github.com/jdblischak","followers_url":"https://api.github.com/users/jdblischak/followers","following_url":"https://api.github.com/users/jdblischak/following{/other_user}","gists_url":"https://api.github.com/users/jdblischak/gists{/gist_id}","starred_url":"https://api.github.com/users/jdblischak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdblischak/subscriptions","organizations_url":"https://api.github.com/users/jdblischak/orgs","repos_url":"https://api.github.com/users/jdblischak/repos","events_url":"https://api.github.com/users/jdblischak/events{/privacy}","received_events_url":"https://api.github.com/users/jdblischak/received_events","type":"User","site_admin":false},"repo":{"id":19242938,"name":"bc","full_name":"jdblischak/bc","owner":{"login":"jdblischak","id":1608317,"avatar_url":"https://avatars.githubusercontent.com/u/1608317?v=2","gravatar_id":"9952931e69c37307ab4e1eb41dd14360","url":"https://api.github.com/users/jdblischak","html_url":"https://github.com/jdblischak","followers_url":"https://api.github.com/users/jdblischak/followers","following_url":"https://api.github.com/users/jdblischak/following{/other_user}","gists_url":"https://api.github.com/users/jdblischak/gists{/gist_id}","starred_url":"https://api.github.com/users/jdblischak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdblischak/subscriptions","organizations_url":"https://api.github.com/users/jdblischak/orgs","repos_url":"https://api.github.com/users/jdblischak/repos","events_url":"https://api.github.com/users/jdblischak/events{/privacy}","received_events_url":"https://api.github.com/users/jdblischak/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jdblischak/bc","description":"Template 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