Introduction to Toolkit

ISI-BUDS 2025

hello woRld

Object assignment operator

my_apples <- 4

	Windows	Mac
Shortcut	Alt + -	Option + -

R is case-sensitive

My_apples

Error: object 'My_apples' not found

If something comes in quotes, it is not defined in R.

n_apples <- c(7, my_apples, 3)

names <- c("Menglin", "Gloria", "Robert")

data.frame(person = names, apple_count = n_apples)

   person apple_count
1 Menglin           7
2  Gloria           4
3  Robert           3

Vocabulary

do(something)

do() is a function;
something is the argument of the function.

do(something, colorful)

do() is a function;
something is the first argument of the function;
colorful is the second argument of the function.

Getting Help

In order to get any help we can use ? followed by function (or object) name.

?c

Tip

You should not copy paste code from my slides or from the internet. Part of learning to code is building up your muscle memory.

tidyverse style guide

canyoureadthissentence?

tidyverse style guide

n_apples <- c(7, my_apples, 3)

names <- c("Menglin", "Gloria", "Robert")

data.frame(person = names, 
           apple_count = n_apples)

After function names do not leave any spaces.
Before and after operators (e.g. <-, =) leave spaces.
Put a space after a comma, not before.
Object names are all lower case, with words separated by an underscore.

Tip

You can let RStudio do the indentation for your code.

RStudio Setup

Literate Programming

Quarto

markdown


_Hello world_ 

__Hello world__

~~Hello world~~

Hello world

Hello world

~~Hello world~~

Quarto parts

Slides for this program

Slides that you are currently looking at are also written in Quarto. You can take a look at them on our GitHub organization in the program-2025 repo.

R packages

Phone apps vs. R packages

When you buy a new phone it comes with some apps pre-installed.

Calendar
Email
Messages

If you want to use a different app you can install it.

Instagram
GMail
BlueSky

When you download R for the first time to your computer. It comes with some packages already installed. You can also install many other R packages.

R packages

What do R packages have? All sorts of things but mainly

functions
datasets

R packages

Try running the following code:

beep()

Error in beep(): could not find function "beep"

Why are we seeing this error?

Installing packages

Using `install.packages()`

In your Console, install the beepr package

install.packages("beepr")

We do this in the Console because we only need to do it once.

Using Packages pane

Packages Pane > Install

Letting RStudio Install

If you save your file and using a package RStudio will tell you that you have not installed the package.

Using packages

Using beep() from beepr

Option 1

library(beepr)
beep()

More common usage.

Useful if you are going to use multiple functions from the same package. E.g. we have used many functions (ggplot, aes, geom_…) from the ggplot2 package. In such cases, usual practice is to put the library name in the first R chunk in the .Rmd file.

Using beep() from beepr

Option 2

beepr::beep()

Useful when you are going to use a function once or few times. Also useful if there are any conflicts. For instance if there is some other package in your environment that has a beep() function that prints the word beep, you would want to distinguish the beep function from the beepr package and the beep function from the other imaginary package.

Open Source

Any one around the world can create R packages.
Good part: We are able to do pretty much anything R because someone from around the world has developed the package and shared it.
Bad part: The language can be inconsistent.
Good news: We have tidyverse.

Tidyverse

The tidyverse is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar, and data structures. tidyverse.org

Tidyverse

In short, tidyverse is a family of packages. From practical stand point, you can install many tidyverse packages at once (and you did this).

We can also load multiple tidyverse packages all at the same time.

library(tidyverse)

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.2     ✔ tibble    3.2.1
✔ lubridate 1.9.4     ✔ tidyr     1.3.1
✔ purrr     1.0.4     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Version Control

Does this look familiar?

hw1
hw1_final
hw1_final2
hw1_final3
hw1_finalwithfinalimages
hw1_finalestfinal

What if we tracked our file with better names for each version and have only 1 file hw1?

hw1 added questions 1 through 5
hw1 changed question 1 image
hw1 fixed typos

We will call the descriptions in italic commit messages.

git vs. GitHub

git allows us to keep track of different versions of a file(s).
GitHub is a website where we can store (and share) different versions of the files.

Demo

Tip

Always use .Rproj file to open projects. Then open the appropriate .qmd / .R file from the Files pane. If you don’t open .Rproj file you will not be able to see the Git pane.

Cloning a repo

repo is a short form of repository. Repositories contain all of your project’s files as well as each file’s revision history.

For this course our weekly repos (lecture code, activity etc.) are hosted on Github.

To clone a GitHub repo to our computer, we first copy the cloning link as shown in screencast then start an RStudio project using that link.

Cloning a repo pulls (downloads) all the elements of a repo available at that specific time.

Commits

Once you make changes to your repo (e.g. take notes during lecture, answer an activity question) you can take a snapshot of your changes with a commit.

This way if you ever have to go back in version history you have your older commits to get back to.

This is especially useful, for instance, if you want to go back to an earlier solution you have committed.

Push

All the commits you make will initially be local (i.e. on your own computer).

In order for us to see your commits and your final submission on any file, you have to push your commits. In other words upload your files at the stage in that specific time.

(An incomplete) Git/GitHub glossary

Git: is software for tracking changes in any set of files

GitHub: is an internet host for Git projects.

repo: is a short form of repository. Repositories contain all of your project’s files as well as each file’s revision history.

clone: Cloning a repo pulls (downloads) all the elements of a repo available at that specific time.

commit: A snapshot of your repo at a specific point in time. We distinguish each commit with a commit message.

push: Uploads the latest “committed” state of your repo to GitHub.

Do you git it?

Introduction to Toolkit

hello woRld

Object assignment operator

R is case-sensitive

Vocabulary

Getting Help

tidyverse style guide

tidyverse style guide

RStudio Setup

Literate Programming

Quarto

markdown

Quarto parts

Quarto parts

Quarto parts

Quarto parts

Quarto parts

Quarto parts

Quarto parts

Slides for this program

R packages

Phone apps vs. R packages

R packages

R packages

Using install.packages()

Using Packages pane

Letting RStudio Install

Using beep() from beepr

Using beep() from beepr

Open Source

Tidyverse

Tidyverse

Version Control

git vs. GitHub

Demo

Cloning a repo

Commits

Push

(An incomplete) Git/GitHub glossary

Using `install.packages()`