1.1 What is GitHub?

• Cloud-based version control system

• But what is version control?

    - Simple analogy: Google Drive for developers
  	  - Track and manage changes to your code
  	  - Version control lets developers safely work through branching and merging
  	  - Work with online Git repository
  	  - Make changes in your own branch
  	  - Merge with online cloud branch
  	  - Changes are tracked and can be reverted if needed

1.2 Why GitHub?

• Don't really have a choice—industry standard!
• Cloud backup
• Collaboration, version control
• Don't have to reinvent the wheel: use existing Git repos
• Community review of your code
• Other uses: GitHub forum, hosting websites, GitHub Classroom, etc.

1.3 Setup for RStudio

Make your account and install into RStudio

• Sign up at www.github.com
• In console: install.packages("devtools") - If this doesn't work, you might need to update your R - Update at https://www.r-project.org/

Start your first project

• Create a new GitHub Repository
• (If collaborative) Open options in your repo -> Share with collaborators
• In the GitHub repo: Clone or Download -> Copy the repo link
• In RStudio: File -> New Project -> Version Control -> Git -> Paste the link
• Check out Git tab in top right corner alongside Environment, History, and Connections

Quick note

• Gitignore: what local files or filetypes should Git ignore in prompting you to Commit in the Git tab? (e.g., *.Rproj in your .gitignore)
• Readme: let people know what cool thing you're building in your readme.md

More information: https://www.datacamp.com/community/tutorials/git-setup

1.4 Three Main Git Functions

1. Commit: create a new commit containing the current contents of the index and the given log message describing the changes (https://git-scm.com/docs/git-commit)
2. Push: push the local version of directory into your Git directory, i.e, your repo (https://git-scm.com/docs/git-push)
3. Pull: pull the current online version of the project into your local directory. Used when the online version has been edited since you last clones/pulled. Maintains both the changes in the online version and your local version

Very simple guide on the workflow: http://rogerdudler.github.io/git-guide/

A more detailed guide: https://happygitwithr.com/rstudio-git-github.html

1.5 Working with Git from the Shell

Use man git in Shell for help

• Commit: git commit -m "Commit message"
• Push: git push origin master
• Pull: git pull

1.6 More Resources

• GitHub Cheat Sheet: https://education.github.com/git-cheat-sheet-education.pdf
• A solid introduction: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668

2.1 What is Rmd?

“R Markdown is a file format for making dynamic documents with R. An R Markdown document is written in markdown (an easy-to-write plain text format) and contains chunks of embedded R code, like the document below.” - https://rmarkdown.rstudio.com/articles_intro.html

2.2 Why Rmd?

• This is written in Rmd! So cool!
• Using Rscripts is cumbersome: Rmd lets you analyze and present data in one go
• Can publish as html, pdf, and word doc
• Automatically LaTeXs if you publish to pdf
• Can handle complex scientific and mathematic notation

2.3 Setup

Very simple. Next time you make a new file, make it a R Markdown file instead of a R script and save it as x.Rmd

2.4 Chunks and Chunk Options

Chunks

A mini-R-script in the middle of your text, headings, etc. in Markdown

E.g.:

	library(tidyverse)
	# Making a random dummy dataframe
	x <- data.frame(replicate(5,sample(0:1,1000,rep=TRUE)))
	# Print three rows of our dummy df
	x[1:3,]
	

	##   X1 X2 X3 X4 X5
	## 1  1  0  0  0  0
	## 2  1  1  0  1  0
	## 3  0  1  1  1  0
	

Chunk Options

You might not want to show your code, the warnings, and messages but show the output—Rmd let's you control that.

E.g.: There's a hidden chunk below but you'll only see the table it outputs:

Global Options

You can also initialize a setup chunk with global chunk options like below.

knitr::opts_chunk$set(include = TRUE, warning = FALSE) # Random chunk options

Here's a cheat sheet!

2.5 Knitting to Different File Formats

• Cmd or Ctrl + Shift + K to knit to chosen format
• Use the Knit button in the RStudio toolbar to knit to some other format

• Alternately, edit the YAML header at the top of the file. Options include:

  output:

    pdf_document: default
  	
  	  word_document: default
  	
  	  html_document: default

2.6 More Resources

• Xie, Yihue. R Markdown: The Definite Guide (written in Bookdown!)
• R for Data Science (R4DS) Chapter on Rmds