What is R?

• A programming language for statistical computing and graphics
• Free, open source
• Base installation + thousands of user-created add-on packages for specialized tasks

What is an IDE?

One application window that manages a whole bunch of things you use while writing code.

• text editor for your scripts, often with with syntax highlighting that makes it easier to read and spot errors.

• console where the code runs

• view of the environment: objects, files, plots, help pages

• many other features

RStudio

• Purpose-built IDE for R — probably the friendliest place to start
• Runs R code, manages your files, and helps you write documents in R Markdown or LaTeX

VS Code

• A more general-purpose IDE that works with essentially any language
• R, Python, Julia, Stata, LaTeX, shell scripts
• Connects to a remote machine and edits files there as if they were local.
• Agentic AI tools can run inside VS Code, which is pretty helpful sometimes.

The Problem with Microsoft Word and Google Docs

• Equations are painful, and they break when you move the file
• Citations and cross-references drift out of sync as the paper changes
• You spend a lot of time fussing with formatting and it often looks bad anyway
• AI tools and git based version control work best with plain text files

LaTeX

• A janky programming language for writing and typesetting documents.

• You write plain text and a compiler produces a PDF.

• Totally absurd and rickety.

• And yet…many advantages and you grow to like it a bit.

• Makes math writing easy:$\hat{\beta} = (X'X)^{-1}X'y$

• Bibliographies and citations are super easy to manage.

\begin{equation}
  \hat{\beta} = (X'X)^{-1} X'y
\end{equation}

Markdown

• A much lighter markup language: **bold**, # Heading, - bullet
• Readable as plain text before it is rendered into anything
• Could be the wave of the future for academic writing because its so simple. But…LaTeX is pretty grizzled and tenecious.

Overleaf

• A gift that made LaTeX more accessible and friendly.
• LaTeX in a browser: nothing to install, and it compiles for you
• Google-Docs-style collaboration

File naming in the state of nature

analysis.R
analysis_final.R
analysis_final_kosali.R
analysis_final_kosali_cw.R
analysis_final_kosali_cw_ks_final.R
analysis_submission_kosali_cw_ks_final_cw.R
analysis_please_god_let_this_be_the_one.R

What is Git? What is GitHub?

A formal version control system developed by Linus Torvalds – the same guy who created Linux. (So…it’s good, right?)

• Repository — a folder that contains your project, including all the files and a hidden folder that tracks changes
• Remote repository — a copy of your repository on a server somewhere, usually GitHub
• History — every saved version, with a note on what changed and why
• Pull — get the latest version from a remote repository
• Commit — save a version of your project, with a note on what changed
• Push — send your saved version to a remote repository
• Diff — compare changes between two versions

GitHub is a website that hosts git repositories.

This is how software developers manage their code.

And now us too.

What “Agentic” Means

• A chatbot answers a question and hands you text to paste somewhere

• An agentic tool has access to your project: it reads your files, edits them, runs code, and reads the errors

• Claude Code and Codex run in a terminal or inside your IDE

What the Shell Is

• A text interface to your computer: you type a command, it does the thing
• Same machine, same files, no icons in the way
• macOS has Terminal, Windows has PowerShell
• Linux has Terminal as well

Enough Commands to Survive

pwd                  # where am I?
ls                   # what's here?
cd code              # go into the code folder
cd ..                # go back up one
mkdir raw_data       # make a folder
cp a.csv b.csv       # copy
mv old.R new.R       # move or rename
rm junk.csv          # delete, with no undo

rm does not use a trash can. Look twice before you press return.

Running R from the Shell

Rscript code/main.r

• Runs the script start to finish in a fresh session, with no RStudio involved

When Your Laptop Is Not Enough

• Restricted use data that cannot leave a secure server
• Huge data set that will not fit in RAM
• A job that would run for three days, during which you would like to use your laptop

What is a super computer?

• Many machines, sitting in a room, sharing storage.
• Lots of capacity and strange terminology.
• Weird and old school but easier than it sounds.

Recap

• R is a statistical programming environment.
• RStudio or VS Code are IDE that make it easier to write code and documents.
• LaTeX and Markdown are tools for technical writing. Overleaf is Google Docs for LaTeX.
• Git and GitHub is a version control system.