Functions, packages, the tidyverse & objects

Day 3 - Wednesday, May 20, 2026

NoteToday: Wednesday May 20

Before class

• Perusall Assignment: Data Computing §3.1–3.5 (Click here).
• HW 0: Setup confirmation (Click here).

Plan for today

• Recap & reading R code
• Functions
• Packages and the tidyverse
• Histograms in ggplot2
• In-class activity

Helpful links

• Syllabus · AI policy · Schedule · Data Computing §3

Quick recap from yesterday

Yesterday we covered:

• The four panes of RStudio (Source, Console, Environment, Output)
• R as a calculator
• Data types (numeric, integer, character, logical)
• Data structures (vectors, lists, matrices, data frames, arrays)
• Creating objects with <-

Today we’ll build on that to start reading and writing real R code.

Reading R code

Yesterday’s textbook reading made one key point:

TipBefore you can write R code, you need to be able to read it.

Most people who write code start by copying and modifying existing code.

To do that well, you need to recognize a few key patterns and know what each piece of an expression is doing.

Five kinds of objects in R code

When you look at a line of R code, you’ll mostly see these five things:

1. Data tables - start with a capital letter (e.g., BabyNames)
2. Functions - always followed by an open parenthesis (e.g., filter(), mean())
3. Arguments - what’s inside the parentheses
4. Variables - the columns inside a data table (e.g., name, sex)
5. Constants - single values like "Arjun" or 1998

Note

The capital/lowercase convention is a style choice that is followed by the Data Computing textbook; but it is not strictly enforced by R.

Spot the parts

BabyNames %>%
  filter(name == "Arjun") %>%
  summarise(total = sum(count))

Try to identify:

• Data table?
• Functions?
• Variables?
• Constant?
• Named argument?

This single command counts the total number of babies named “Arjun” in the data: 5,578.

Spot the parts

BabyNames %>%
  filter(name == "Arjun") %>%
  summarise(total = sum(count))

Try to identify:

• Data table? BabyNames (starts with capital, no parentheses after it)
• Functions? filter, summarise, sum (each followed by an open parenthesis)
• Variables? name, count (lowercase, inside parentheses)
• Constant? "Arjun" (in quotes)
• Named argument? total = sum(count) (single = inside the function call)

This single command counts the total number of babies named “Arjun” in the data: 5,578.

Objects, revisited

An object is anything in R that has a name you can refer to later.

age_cutoff <- 21
my_numbers <- c(3, 7, 12, 4)
greeting   <- "hello, world"

Once an object exists, you can use its name anywhere you’d otherwise type the value:

age_cutoff + 5

[1] 26

mean(my_numbers)

[1] 6.5

Why bother naming things?

Compare:

# Hard to update, hard to read:
filter(students, age >= 21 & gpa >= 3.5 & credits >= 60)

vs.

# Easy to read and change:
age_min     <- 21
gpa_min     <- 3.5
credit_min  <- 60

filter(students,
       age     >= age_min,
       gpa     >= gpa_min,
       credits >= credit_min)

Good names make your code readable and easy to change later.

Example of naming conventions from Data Computing

Naming conventions from Data Computing.

Object type	Convention	Example
Data tables	Capitalized	BabyNames, Penguins
Variables / columns	lowercase	name, body_mass_g
Constants you create	lowercase, snake_case	age_cutoff, gpa_min

Warning

Object names must start with a letter and can only contain letters, numbers, _, and .. No spaces, no special characters, no starting with a number. This is a requirement, not a convention.

Functions

What is a function?

A function is a reusable chunk of code that takes some input, does something with it, and gives you back an output.

You’ve already used many functions:

sqrt(16)

[1] 4

mean(c(1, 2, 3, 4, 5))

[1] 3

c(1, 8, 4)

[1] 1 8 4

Every function call has the same three key elements: a name, followed by parentheses, with arguments inside.

Anatomy of a function call

function_name(argument1, argument2, name = value, ...)

• The name tells R which function to use.
• The arguments tell the function what to work on and how.
• Arguments are separated by commas.
• Some arguments are named (name = value); others are matched by position.

# Positional: round(x, digits)
round(3.14159, 2)

[1] 3.14

# Named: order doesn't matter
round(digits = 2, x = 3.14159)

[1] 3.14

Named vs. positional arguments

# Both of these work the same way:
seq(1, 10, 2)

[1] 1 3 5 7 9

seq(from = 1, to = 10, by = 2)

[1] 1 3 5 7 9

TipA good habit

• Use positional arguments for the obvious ones (the data, the first input).
• Use named arguments for everything else.

Your future self will thank you when reading the code six weeks from now.

Getting help with a function

If you don’t remember what arguments a function takes:

?mean       # opens the help page
help(mean)  # same thing
??mean      # broader search if you're unsure of the name

Every help page has the same sections: Description, Usage, Arguments, Value, Examples.

Functions return values

Every function gives you back a value. You can store that value with <-:

x <- sqrt(16)
x

[1] 4

m <- mean(c(2, 4, 6, 8))
m

[1] 5

If you don’t assign the result, R just prints it to the console and it’s gone. The result will not be stored anywhere for you to access in the future.

WarningExample

mean(c(2, 4, 6, 8))   # prints 5, but doesn't save it anywhere

If you want to use that 5 later, you need m <- mean(c(2, 4, 6, 8)).

Functions inside functions

The output of one function can become the input to another:

sqrt(mean(c(1, 4, 9, 16, 25)))

[1] 3.316625

R works inside-out:

1. First c(1, 4, 9, 16, 25) makes a vector.
2. Then mean(...) of that vector is 11.
3. Then sqrt(11) is ≈ 3.317.

This nesting can get unreadable fast. Later on, we’ll see a cleaner way (the pipe).

Packages

What is a package?

Base R has a lot of features, but many useful tools live in packages.

A package is a bundle of:

• functions
• data sets
• documentation

Packages are written by someone in the R community and made available for everyone to use.

There are over 23,000 packages on CRAN (the main R package repository).

Installing vs. loading

There are two steps to using a package.

ImportantInstall once, load every session

• Install with install.packages("packagename") - do this once per computer.
• Load with library(packagename) - do this every time you start a new R session.

# Run this once, in the Console (NOT in your script):
install.packages("tidyverse")

# Run this at the top of every script or .qmd that uses it:
library(tidyverse)

Quotation marks matter: install.packages("tidyverse") (string), but library(tidyverse) (object).

Where do I install packages?

TipRun install.packages() in the Console, not in your script.

You only need to install once, so it doesn’t belong in a script that runs every time.

If your script needs a package, just put library(packagename) at the top.

What happens when you load a package?

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   3.5.1     ✔ 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()

These messages are fine. They mean: “Here are the packages I just loaded, and here are the function names that now point to a new place.”

The tidyverse

What is the tidyverse?

The tidyverse is a collection of R packages that share a common philosophy and work well together.

When you run library(tidyverse), you load all of them at once:

• ggplot2 - making plots
• dplyr - manipulating data tables
• tidyr - reshaping data
• readr - reading data files
• tibble - a nicer kind of data frame
• stringr - working with text
• forcats - working with categorical data
• purrr - applying functions across collections

We will use almost all of them this semester.

The tidyverse hex stickers

Each tidyverse package has its own hex sticker - a fun tradition in the R community.

Why use the tidyverse?

Two reasons:

1. Consistency. Tidyverse functions are designed to work the same way:
   • First argument is always the data.
   • Output is always a data frame (a “tibble”).
   • You can chain them together cleanly (more on that later).
2. Readability. Tidyverse code reads almost like English.

We’ll spend most of the semester learning to think in this style.

A taste of what’s coming

Don’t worry about understanding every line - just notice how readable this is:

library(palmerpenguins)

penguins |>
  filter(!is.na(body_mass_g)) |>
  group_by(species) |>
  summarize(
    n           = n(),
    avg_mass_g  = mean(body_mass_g)
  )

# A tibble: 3 × 3
  species       n avg_mass_g
  <fct>     <int>      <dbl>
1 Adelie      151      3701.
2 Chinstrap    68      3733.
3 Gentoo      123      5076.

This is the dplyr package in action. We’ll cover it in detail later this week.

ggplot2: a grammar of graphics

ggplot2 (part of the tidyverse) is the most popular plotting package in R.

It’s built on the idea of a grammar: you build up a plot by adding layers.

Every ggplot2 plot has at least three pieces:

1. Data - a data frame.
2. Aesthetics (aes(...)) - which variables map to which parts of the plot (x, y, color, fill, etc.).
3. Geometry (geom_*()) - what kind of plot (points, bars, lines, histograms…).

Histograms

A histogram shows the distribution of a single numeric variable by bucketing values into bins and counting how many fall in each bin.

It’s the right tool when you want to ask:

• What values are typical?
• Are there outliers?
• Is the distribution symmetric? Skewed? Bimodal?

In ggplot2, you make a histogram with geom_histogram().

A basic histogram

ggplot(penguins, aes(x = body_mass_g)) +
  geom_histogram()

Reading that code

ggplot(penguins, aes(x = body_mass_g)) +
  geom_histogram()

Breaking it down:

• ggplot(penguins, ...): start a plot using the penguins data.
• aes(x = body_mass_g): map the variable body_mass_g to the x-axis.
• + geom_histogram(): add a histogram layer.

Note

In ggplot2, you add layers with +, not with %>% or |>.

Controlling the bins

R will warn you: “stat_bin() using bins = 30. Pick better value with binwidth.”

You can control the number of bins two ways:

ggplot(penguins, aes(x = body_mass_g)) +
  geom_histogram(bins = 15)

# Or specify the width of each bin:
ggplot(penguins, aes(x = body_mass_g)) +
  geom_histogram(binwidth = 250)

Why the bin choice matters

WarningToo few bins

You lose detail and the shape gets oversmoothed.

Too many bins

You see noise and the shape gets jagged and hard to read.

There’s no single “right” answer. Try a few, and pick what tells the clearest story about your data.

Making it nicer

Add fill, color, and labels:

ggplot(penguins, aes(x = body_mass_g)) +
  geom_histogram(binwidth = 250, fill = "steelblue", color = "white") +
  labs(
    title = "Distribution of penguin body mass",
    x = "Body mass (g)",
    y = "Number of penguins"
  )

Anatomy of that command

Anatomy of a basic histogram in ggplot2.

Piece	What it does
ggplot(penguins, aes(x = body_mass_g))	Use the penguins data; put body_mass_g on x
geom_histogram(...)	Add the histogram layer
binwidth = 250	Each bar is 250 g wide
fill = "steelblue"	Bar color
color = "white"	Outline color
labs(...)	Title and axis labels

Tip

You can run ?geom_histogram in the Console to see every option.

Activity

Activity: your first histogram

You’ll work on this individually or with a neighbor for 20 minutes. We’ll regroup at the end.

Goal: Make a histogram of a real dataset and tweak it.

Setup:

1. Download the day3-activity.R starter file from Canvas.
2. Open RStudio.
3. Go to File > Open File... and open the script you downloaded.

Step 1 - Load packages

At the top of your script, type and run:

library(tidyverse)
library(palmerpenguins)

If palmerpenguins isn’t installed, run install.packages("palmerpenguins") in the Console first.

Step 2 - Look at the data

# Pick ONE of these to peek at the data:
glimpse(penguins)
View(penguins)
?penguins

What variables are in this data set? What does each row represent?

Step 3 - Make a default histogram

Pick a numeric variable from penguins (e.g., flipper_length_mm, bill_length_mm, bill_depth_mm).

ggplot(penguins, aes(x = flipper_length_mm)) +
  geom_histogram()

Step 4 - Tweak your histogram

Make at least three changes to your histogram:

• Try a different binwidth or bins value.
• Change the fill and color of the bars.
• Add a title and axis labels with labs(...).

Step 5 - Comment

Open a comment block in your script and write 2–3 sentences answering:

# What does the shape of your histogram tell you about the variable?
# Did changing the binwidth change the story?

To turn in:

Save your script (Cmd/Ctrl + S). Upload the .R file to the Canvas assignment page.

TipStuck?

• Read the error message - it’s usually a typo, missing +, or unmatched (.
• Ask a neighbor.
• Wave me down.

Activity debrief

Some things to look out for:

• Forgot + between layers: R thinks the line is finished.
• Used = instead of <-: works in some places, but breaks elsewhere.
• Typo in a variable name: R doesn’t guess. The spelling and capitalization must match exactly.
• Package not loaded: Error: could not find function "ggplot": run library(tidyverse).

Wrap-up: what we covered today

• Recognize the five kinds of objects in R code.
• Read and call functions, including named and positional arguments.
• Install and load packages.
• Recognize the tidyverse as a coherent collection of packages.
• Build a histogram in ggplot2 from scratch.

Wrap-up & looking ahead

Tomorrow: Quarto basics, writing reproducible documents.

Upcoming Deadlines

• Wed 5/20, 11:59 p.m. - HW 0: Setup
• Thurs 5/21, before class - DC §4.1–4.7
• Fri 5/22, in class - Quiz 1
  • Quiz 1 Practice
• Fri 5/22, 11:59 p.m. - HW 1: Basic R & Plots

Reach out

Stuck? Office hours, or email me (cgc5478@psu.edu) or Xinyue (xpw5228@psu.edu).

Reference

Syllabus · AI policy · Schedule · Data Computing