krabberod / raukr

Jenny Bryan's instruction at RaukR: Advanced R for Bioinformatics Summer School

raukr

Agenda for Jenny Bryan's instruction at:

• RaukR: Advanced R for Bioinformatics Summer School
• 2019 June 10 - 20, Visby, Sweden

Pre-work

Please do the requested Git/GitHub prep in advance, as per email! Go here:

https://happygitwithr.com/workshops.html#pre-workshop-set-up

Git 1 of 2 (Tuesday June 11)

• Intro to GitHub and Git, with RStudio
• Using R Markdown and R with Git, GitHub, and RStudio (if time permits)

Slides

• git-and-github-early-usage.pdf

Activity prompts

• mostly instructor-led activities we'll do together
• Work on adding more exploration or a figure to your packages-report project
  • Keep working in the project we initiated on GitHub, then cloned, and practiced in.
  • Go through several cycles of: change R code, commit & push
  • Render to .md if you like.
  • We'll try to work up to finishing it with a README.Rmd and turning on GitHub Pages.
• A possible finished product, given more time: https://github.com/jennybc/wtf-packages-report-EXAMPLE
• Another version from Jim Hester that includes a proper Makefile https://github.com/jimhester/my-packages/tree/jims

Resources

• Git/GitHub motivator and explainer: "Excuse me, do you have a moment to talk about version control?"
  • PeerJ preprint: https://dx.doi.org/10.7287%2Fpeerj.preprints.3159v2
  • In The American Statistician: https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1399928
• New project, GitHub first
• Test drive R Markdown
• Render an R script

Iterating well with purrr (Wednesday June 12)

Slides on SpeakerDeck:

• https://speakerdeck.com/jennybc/purrr-workshop
• I'll be speaking from a lightly modified version of those slides, but it's close enough!

Jenny live code:

• rstd.io/jenny-live-code
• note: I've switched to an rstd.io shortlink, not bit.ly!

More of my purrr content:

• purrr tutorial
• Row-oriented workflows in R with the tidyverse

Git 2 of 2 (Thursday June 13)

• Introduce remotes and branches
• Useful Git workflows, esp. time travel

Slides

• git-and-github-daily-workflows.pdf version from rstudio::conf 2019, but close to what I will use

Resources

All link to Happy Git

• Branches
• Remotes
• Fork and clone
• Get upstream changes for a fork
• The Daily Workflows part
• Existing project, GitHub last

Where to find me online

• Jenny Bryan jennybryan.org | Github jennybc | Twitter jennybryan

Resources

Written versions of content are under open development here:

• Happy Git and GitHub for the useR (bookdown site)
• purrr tutorial
• What They Forgot to Teach You About R (bookdown site)

Links that are handy to us

• GitHub repo: https://github.com/jennybc/raukr
• GitHub Pages site, served from that repo: https://jennybc.github.io/raukr/
• Easy-to-type rstd.io short link to that GitHub Pages site: rstd.io/raukr

Exciting announcement about food!