R Projects and R Scripts

EE BIOL C177/C234

Chuliang Song

Today’s Menu 🎯

1. R Project: one home folder per analysis
2. R script: write, save, and rerun your code
3. Working directory & paths: how R finds your files, with here
4. Start fresh: restart R, rerun from the top

Setup 📦

Packages for this chapter

We’ll be relying on tidyverse, palmerpenguins, and here. If you haven’t installed them yet, run this in your R Console (not in your script):

pak::pak(c("tidyverse", "palmerpenguins", "here"))

Your Workspace

Three Things, Easy to Mix Up

	What it is	What you see	What you do with it
R Project	The “home” folder of one analysis	eeb_c234.Rproj	Double-click to open your work. No code in it!
R script	A text file of R code	07_workspace.R	Write code, save, run line by line
Console	Where R runs code right now	The > prompt	Quick tests. Nothing is saved.

🧪 Project = your lab bench  ·  Script = your written protocol  ·  Console = scratch paper

Most beginner confusion comes from mixing these three up: writing code into the .Rproj file, or doing everything in the Console and losing it.

Console or Script?

📝 Script: anything needed to reproduce a result

• library(tidyverse)
• reading data
• every transformation
• every plot

🗒️ Console: one-time or throwaway

• pak::pak("palmerpenguins") (install once per computer)
• ?filter (help pages)
• glimpse(penguins) (a quick peek)

If you closed RStudio right now, could you redo your analysis? Only if it’s in the script.

Create Your Course Project (once)

1. File > New Project… > New Directory > New Project
2. Directory name: eeb_c234 (no spaces), inside e.g. Documents
   • Not in Downloads, not inside another project
3. Click Create Project: RStudio restarts
4. ✅ Check: top-right corner says eeb_c234, not Project: (None)
5. Files pane → New Folder: data, then figures

Using Positron?

No .Rproj needed: File > Open Folder… and pick the project folder.

Your Project Folder

eeb_c234/                 <- the project folder
├── eeb_c234.Rproj        <- double-click this to open the project
├── 07_workspace.R        <- your script for this chapter
├── data/                 <- raw data files go here
└── figures/              <- saved plots go here

One project for the whole course. For research: one project per paper or analysis.

⚠️ Always Open the .Rproj File

Double-click eeb_c234.Rproj every time

(or File > Open Project…, or the project menu in the top-right corner)

• ❌ Double-clicking a .R file opens RStudio without the project → R looks for files in the wrong folder
• 👀 Top-right says Project: (None)? You’re not in your project
• 🪟 Windows hides file extensions: look for type R Project (blue cube icon)

Create & Save a Script

1. File > New File > R Script (Ctrl/Cmd + Shift + N)
2. Save right away (Ctrl/Cmd + S) as 07_workspace.R in the project folder
3. Red tab title with * = unsaved changes. Save often!

File names: no spaces, lowercase, numbered so they sort in order

✅ 07_workspace.R    ❌ My Script FINAL (2).R

Anatomy of a Script

# 07_workspace.R
# Setting up my course project
# Your Name, date

# Packages ----
library(tidyverse)
library(palmerpenguins)

# A first plot ----
ggplot(penguins, aes(x = bill_length_mm, y = bill_depth_mm)) +
    geom_point()

• # = comment: R ignores it; it’s a note to future you
• # Name ---- = section: jump around with the outline (Ctrl/Cmd + Shift + O)
• Read top to bottom: packages first, then data, then analysis

Running Code

Action	Windows / Linux	Mac
Run current line / selection	Ctrl + Enter	Cmd + Return
Run the whole script	Ctrl + Shift + Enter	Cmd + Shift + Return
Save	Ctrl + S	Cmd + S
Restart R	Ctrl + Shift + F10	Cmd + Shift + 0

• 💾 Saving ≠ running. Edited code does nothing until you run it
• 🔗 Cursor anywhere in a pipe → runs the whole pipe
• 📺 Output appears in the Console; plots in the Plots pane, never in the script
• ➕ A + in the Console = R is waiting for you to finish (missing ), ", or a trailing |>). Press Esc

Working Directory & Paths

Working directory = where R looks for files. With the project open, it’s the project folder.

getwd()   # should end in .../eeb_c234

read_csv("data/penguins_raw.csv")                                # ✅ relative: works on any computer
read_csv("C:/Users/ana/Desktop/eeb_c234/data/penguins_raw.csv")  # ❌ absolute: only on Ana's laptop

• 🚫 Never setwd() in a script: open the project instead
• ↗️ Use forward slashes /, even on Windows ("data\x.csv" is an error)
• 🔤 Spelling and capitalization must match: Data/ ≠ data/
• 🔍 Lost? list.files("data") shows what R can see

The here Package

By Jenny Bryan

here::here(): Paths from the Project Root

here::here()                             # .../eeb_c234
here::here("data", "penguins_raw.csv")   # .../eeb_c234/data/penguins_raw.csv
read_csv(here::here("data", "penguins_raw.csv"))

• 🏠 Always starts at the folder with the .Rproj file
• ✂️ One argument per folder: no slashes to get wrong
• 📄 Works the same in an .R script and in a .qmd in a subfolder

Start Fresh Every Time

Once: Tools > Global Options… > General

• Uncheck Restore .RData into workspace at startup
• Set Save workspace to .RData on exit → Never

Every time before you share or submit:

1. Restart R (Ctrl + Shift + F10 / Cmd + Shift + 0)
2. Run the whole script (Ctrl/Cmd + Shift + Enter)

No errors? Then anyone with your project folder can reproduce your results.

Your script, not your R session, is the record of your work.

Otherwise a script can “work” only because of an object made by hand in the Console last week.

When Things Go Wrong

What you see	Likely cause	Fix
'data/x.csv' does not exist in current working directory	Project not open, file not in data/, or a typo	Check the top-right corner; getwd(); list.files("data")
could not find function "ggplot"	Package not loaded (restarting R unloads everything)	Run the library() lines at the top
object 'my_data' not found	That line wasn’t run this session, or was only typed in the Console	Run the script from the top
Console shows + and nothing happens	Missing ) or ", or a trailing |>	Esc, fix, run again
Edited the script, output didn’t change	Saving is not running	Run the line again
Your files aren’t in the Files pane	RStudio opened from its icon or a .R file	Open eeb_c234.Rproj

Your Turn! 🏋️ Set Up Your Project

1. Create the R Project eeb_c234
2. Create folders data and figures
3. Turn off .RData saving/restoring
4. New script → save as 07_workspace.R → add a header, the library() lines, and a first plot
5. Run getwd() in the Console
6. Restart R, then run the whole script
7. Close RStudio; reopen by double-clicking eeb_c234.Rproj

✅ Top-right shows eeb_c234 · getwd() ends in eeb_c234 · packages load without errors (“Attaching packages” / “Conflicts” messages are normal)

From now on: every chapter gets its own script in this project (08_dplyr.R next).