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sr320: June 05, 2018 at 10:37AM


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5 June, 2018 17:35

Hackweek Day 2: R/R Markdown Notes

  • R Studio server exists on Emu and Roadrunner
  • Multiple people can log on at the same time
  • Commits associated with whatever user configured everything in the command line
  • Could potentially convert https repos to ssh to avoid having to long in all the time………this seems really confusing.

Special tab in R Studio server for Terminal! R Project –> Version Control –> Git –> Create Project based on previously existing repository

  • allows you to push from R Studio itself
  • Can also push from Github Desktop

R Markdown

  • Ctrl + alt + i –> create new {r} chunk
  • Can set other keyboard shortcuts for bash, etc.

Ctrl + shift + enter –> run chunk

  • Slightly different than ctrl + enter for normal R scripts

Preference for R vs. R Markdown: you can get in the habit of just running everything in R Markdown Easier to render HTML vs. pdf

  • pdf requires other packages to be installed beforehand
  • Packages exist on Linux machines!

Use Markdown to add plain text, photos, etc. Can also insert Bash and Python cells

  • Easier to do Bash in R Markdown instead of doing R in Jupyter

Knit: creates HTML/pdf and runs the code

  • Open in Browser –> view in Browser
  • Automatically puts HTML in same directory as Rmd file
  • htmlpreview.github.io/? –> prefix before any HTML file to view it –> can use that link in notebooks, etc.
  • Rmd automatically renders (because markdown), but you don’t get the output from the R chunks

Can also make the output as a slide instead of an HTML file –> Knit and create slides

  • knitter:kable() makes tables prettier
  • Keeps writing code so it goes off the slide
  • Options to put in to wrap or adjust width, but those options may or may not work…?

GOAL: USE R MARKDOWN FOR ALL PAPER SCRIPTS AND REPOSITORIES Add Terminal tab to R Studio

  • Tools –> Terminal –> Move focus to Terminal (shift + alt + t)
  • Need R Studio version 1.1 or higher

steven@roadrunner:~/SR-R/hackweek-p2$ git config –global credential.helper…

steven@roadrunner:~/SR-R/hackweek-p2$ git config –global credential.helper ‘cache –timeout=1000000000’

keeping stuff in Rstudio

`steven@roadrunner:~/SR-R/hackweek-p2$ git config –global credential.helper ‘cache –timeout=1000000000’`

More Panopto

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Testing Panopto

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