Talk at R Summit and Workshop about using R Markdown and GitHub in your workflow

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How R Markdown + Git + GitHub changed my (teaching?) life R Summit & Workshop 2015 Dr. Jennifer (Jenny) Bryan Dept. of Statistics & Michael Smith Laboratories, UBC jenny@stat.ubc.ca @JennyBryan http://stat545-ubc.github.io @STAT545 http://www.stat.ubc.ca/~jenny/ @jennybc

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https://github.com/jennybc/2015-06-28_r-summit-talk GitHub repo for this talk gives a bunch of links + PDF of slides

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http://stat545-ubc.github.io https://github.com/STAT545-UBC/STAT545-UBC.github.io

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Most years of R use before developing and distributing a package

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What’s so great about (R) Markdown + Git(Hub)?

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weak links in the chain: process, packaging and presentation

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Do your work Get a presentable, web-friendly version for free Present-ability is BAKED IN … not a separate process you never get around to R + markdown

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stuff you need to write stuff people like to read

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stuff you need to write stuff people like to read

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stuff you need to write stuff people like to read foo.R foo.Rmd foo.md foo.html

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library(rmarkdown) render("foo.Rmd")

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library(rmarkdown) render("foo.R")

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foo.Rmd foo.html --- title: "Untitled" output: html_document --- foo.Rmd foo.md foo.html --- title: "Untitled" output: html_document: keep_md: yes --- foo.Rmd foo.md --- output: md_document: variant: markdown_github ---

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foo.R foo.html #’ — #’ title: "Untitled" #’ output: html_document #’ --- foo.R foo.md foo.html #’ --- #’ title: "Untitled" #’ output: #’ html_document: #’ keep_md: yes #’ --- foo.R foo.md #’ --- #’ output: #’ md_document: #’ variant: markdown_github #’ ---

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Markdown, and even Rmarkdown, are very privileged on GitHub Essentially rendered as HTML + =

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When I mark homework ... this is what I see.

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When I mark homework ... this is what I see.

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When I mark homework ... this is what I see.

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What’s so great about (R) Markdown + Git(Hub)?

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search linky-ness meta-stuff (comments, issues, …) What’s so great about Git(Hub)?

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Problem: NOTE from R CMD check when testing a package on Travis … but I am specifying my CRAN repo? * checking package dependencies ... NOTE No repository set, so cyclic dependency check skipped Hmm … maybe the CRAN environment variable isn’t consulted, maybe I need to set the CRAN repo set in .Rprofile … how do I that on Travis?

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Solution: Find a ton of other .travis.yml ﬁles that mention .Rprofile!

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Replies included discussion of why we have isTRUE() and the existence + history of various “truthy” things Included links to where all this occurs in the R source and when it was added

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https://github.com/wch/r-source/blob/trunk/src/main/util.c#L445-L452 https://github.com/wch/r-source/blob/trunk/src/main/util.c#L123-L129

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https://github.com/wch/r-source/commit/ 8fee9de69de30815457992145657797bf793b74f#diff- b98c76a66da58d25f4436ff77e8a2ac2R64 Github’s ease of search, navigation, & linking enriched this conversation

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Are the ofﬁcial examples for a function kind of thin? Search Github to see the function “in the wild”.

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Are the ofﬁcial examples for a function kind of thin? Search Github to see the function “in the wild”.

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Github Organization Content, website Shh… secret Discussion forum 1 repo per student

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Issues as discussion forum

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Issues to submit, peer review, and mark homework

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sorry about all those issues!

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The unreasonable effective of GitHub browsability Commit .md files and figures! They are not like .o files or executables. Get over it.

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When (intermediate) Markdown is no longer enough … .github.io

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+ = search linky-ness meta-stuff, e.g. issues reproducible presentable collaboration: “link, don’t attach” machine- and human-readable meta self-documentation