Intro to Data Science

Lab 1 – RStudio & Base R

A Guide to Your Process

Scheduling

Learning Objectives

Practice

Supporting Information

Class Discussion

Today’s Plan

• Installation Check (R + RStudio)
• Navigating RStudio
• RStudio Projects
• R Scripts
• “Base” R

Today’s Learning Objectives

After today’s session you will be able to:

• Set up RStudio on your computer
• Create an RStudio Project
• Use R Scripts
• Define fundamental base R terms
  • E.g., object, assign, function, arguments, etc.
• Solve simple arithmetic operations using R

Installation Check: R & RStudio

• Did anyone not get R installed?

• Did anyone not get RStudio installed?

• Once you have both installed, please open RStudio

R versus RStudio

R versus RStudio

• Access to fundamental R operations
• Not aesthetically pleasing
  • In my opinion
• Faster for very complex operations
  • Unlikely to matter for this course!

R versus RStudio

• Access to fundamental R operations
• Not aesthetically pleasing
  • In my opinion
• Faster for very complex operations
  • Unlikely to matter for this course!

• Access to fundamental R operations
• Allows custom aesthetics
• Has quality-of-life improvements
• Technically an “IDE”
  • Integrated Developer Environment

RStudio Layout

• Layout consisting of four panes
  • Each pane has tabs that do different things
  • You can customize which tabs are in each pane!
• To customize options:
  • In top menu, click “Tools”
  • Select “Global Options”
  • Select “Pane Layout”
• I recommend the following layout:

Practice: Choose Your Colors

• Tools Global Options Appearance

• Look through some of the available color schemes
  • Feel free to share the name of your favorites!

• Once you’ve picked one that you’re happy with:
  • Click “OK” (in bottom left)

RStudio Projects

• Projects are a special way of marking a folder on your computer for R

• You can still use the folder for other stuff though!

• RStudio will give you benefits if you use Projects

Why Use Projects?

• Sets default location for reading in / saving files
  • A.k.a. “importing” and “exporting” files

• Convenient separation among tasks you’re working on!
  • RStudio ‘remembers’ which files are a part of each Project
  • Even re-opens whatever files you had opened last time you used the Project!

• Lowers risk of mixing up data / script files

Practice: Create a Project

1. Make an empty folder on your computer to make the Project in

2. In RStudio, click “Project: (None)” in the top right corner
   • “New Project…” “Existing Directory” “Browse…” find the folder you made in step 1

3. If the name of the folder you made in step 1 shows up in the top right corner of RStudio, it worked!

Temperature Check

How are you Feeling?

R Scripts

• A code file is called a “script”
  • Microsoft Word : document – R : script

• Lines of code written in scripts can be re-used
  • I.e., “re-run”

• Scripts can be run line-by-line manually or run all at once
  • Running all at once = “sourcing” a script

Practice: Create an R Script

• Create an R script
  • “File” “New File” “R Script”

• Once created, save it as “316_week1.R”
  • “File” “Save”

• Note that the save location defaults to inside of your RStudio Project
  • Another reason to use Projects!

Base R Fundamentals

• “Base R” includes a set of core functions that are broadly useful
  • Reading in a CSV, taking an average, etc.

• R’s real power comes from “packages” with more advanced functions
  • These packages are not in base R
  • We’ll begin to cover these next week

• Base R is really useful in its own right!

Objects and Assignment

• You can do math in R directly

• More useful to use “objects” instead of direct values
  • object = alias for a value / set of values

• When we create an object we assign some value(s) to the object
  • Uses the assignment operator (<-)
  • Keyboard shortcut: Alt + hyphen

• After you create an object, you can use it in place of its value!

Object Example

We can make an object like so:

my_obj <- 52

Then when we use the name of the object later…

my_obj

[1] 52

… we get the value we assigned to it!

Objects Continued

• Useful because it lets you flexibly code

• If you know that an object only contains numbers, you can do general operations that work for any number

• If you had to use the actual value every time, complex operations would be brutal to code

Running Code

• How do you ‘actually’ run code?

• You have two options!
  1. Click the “Run” button in the top right of the “Source” pane of RStudio
  2. Use the keyboard shortcut Command + Return (or for Windows users, Control + Return)

• Note that either option requires that you clicked somewhere in the line you want to run
  • Lines are numbered on the left of the “Source” pane

Practice: Object Assignment

Arithmetic

Object Practice

Practice: Object Assignment

Arithmetic

• Calculate 576 / 3

• Calculate (258 * 4) / 13

• Calculate 2 + 2 - 4

Object Practice

Practice: Object Assignment

Arithmetic

• Calculate 576 / 3

• Calculate (258 * 4) / 13

• Calculate 2 + 2 - 4

Object Practice

• Create an object called yy with a value of 55
  • Hint: remember to use the assignment operator (<-)

• Create an object called my_char with a value of “text”
  • What happens when you don’t include quotation marks around “text”?

Temperature Check

How are you Feeling?

Code Comments

• Coding languages all allow comments

• Comments are non-coding lines that explain what the code is doing in a human-readable way

• In R, comment lines start with a hashtag (#)

• Comments allow others to read your code and understand what is happening
  • Great for future you!!!

Code Comments

Code Example

Here are some example comments:

# Make an object with a value of 77
q <- 77

# Divide it by 7 and assign to a new object
p <- q / 7

• Any questions about comments before we continue?

Practice: Comments

• Add a comment at the top of your script with the course number and your name

• For each line of code you wrote earlier:
  • Add a comment line above it explaining what that line does
  • Use wording that makes sense to you!

• This lets your class notes be included directly with your code!
  • Though you’re of course welcome to take notes (or not) using whatever medium you prefer

Functions

• Programming wouldn’t be useful if you needed to do everything by hand

• Programming languages include functions to avoid arithmetic
  • Someone else has done the manual labor and made an object of that process!

• You can then use the function instead of doing the math yourself

• Functions use arguments to let users specify what they can modify

Function Example

• There is a function called round that rounds decimals either up or down

• round has two arguments:
  • x = the number(s) to round
  • digits = the number of digits to which to round x

• Let’s look at an example

# Round a decimal to 2 digits
round(x = 62.82379110, digits = 2)

[1] 62.82

Function Help

• Functions include help files built into R to help you use them!

• Can be accessed by typing a ? and then the function name
  • E.g., ?mean

• Type (and run) ?round and see what happens

Practice: Functions

• Base R includes an object called pi that includes the first 6 digits of π

• Using the round function, round pi to 3 digits

• Consult the help file for the square root function (sqrt)
  • What argument(s) does sqrt expect?

• What is the square root of pi?

• Don’t forget to add comments to each line in your script!

Vectors and Concatenation

• You can also make objects that contain several values
  • This type of object is called a vector

• You can make vectors using “concatenation”
  • [con-CAT-eh-nation]

• R does this with the c function
  • You need commas between each element of a vector
  • E.g., my_vector <- c(1, 2, 3, 4)

Object Classes

• Objects have a class that dictates what operations they support

• Math can only be done on “numeric” objects

• Text can be stored in “character” objects
  • But math can’t be done on characters!

• You can check an object’s current class with the class function
  • E.g., class(my_object)

Object Classes Cont.

• There are many classes
  • Most of which are beyond the scope of this class

• Let’s focus on 3 fundamental classes
  1. Numeric = numbers
  2. Character = text
  3. Factor = text but defines categorical groups

Class Coercion

• You can force (a.k.a. coerce) an object from one class to another

• The simplest functions to do this are all as.<desired class>()
  • E.g., as.numeric()

• Want to have your code treat a number like text?
  • my_text <- as.character(111)

• What happens when you try to force text into a number?
  • my_num <- as.numeric("hello")

Practice: Concatenation & Classes

• Concatenate the numbers 1, 4, 9, and 6 into a vector
  • Hint: remember the c function!

• What is the class of that vector?

• Concatenate “hello”, “world”, and the first vector into a new vector
  • What is the class of the new vector?

• Multiply the second vector by 16; what does this return?

Temperature Check

How are you Feeling?

Upcoming Due Dates

Due before lecture

(By midnight)

• Homework #1
• Read the British Ecological Society’s Reproducible Code Guide (p.1-12)

Due before lab

(By midnight)

• Muddiest Point #2
• Read the British Ecological Society’s Reproducible Code Guide (p.20-25)