Lecture 4

RStudio; R Basics

Byeong-Hak Choe

bchoe@geneseo.edu

SUNY Geneseo

September 5, 2024

Setting the DANL Tools

Setting the Tools

Posit Cloud

Posit Cloud (formerly RStudio Cloud) is a web service that delivers a browser-based experience similar to RStudio, the standard IDE for the R language.
For our course, we use Posit Cloud for the R programming component.
- If you want to install R and RStudio on your laptop, you use my office hours.

Setting the Tools

RStudio Environment

Script Pane is where you write R commands in a script file that you can save.
- An R script is simply a text file containing R commands.
- RStudio will color-code different elements of your code to make it easier to read.

Setting the Tools

RStudio Environment

Console Pane allows you to interact directly with the R interpreter and type commands where R will immediately execute them.

Setting the Tools

RStudio Environment

Environment Pane is where you can see the values of variables, data frames, and other objects that are currently stored in memory.
Type a <- 1 in Console, and then hit Enter.

Setting the Tools

RStudio Environment

Plots Pane contains any graphics that you generate from your R code.

Setting the Tools

R Packages and `tidyverse`

R packages are collections of R functions, compiled code, and data that are combined in a structured format.
Several R packages come with numerous pre-built functions that can perform a wide range of data analysis tasks.

Setting the Tools

`tidyverse`

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

tidyverse includes a lot of R packages, including ggplot2, dplyr, and tidyr.
The tidyverse packages work harmoniously together to make data manipulation, exploration, and visualization more.

Setting the Tools

Installing R packages with `install.packages("packageName")`

install.packages("tidyverse")

R packages can be easily installed from within R using a base-R function install.packages("packageName").
- To install the R package tidyverse, type and run the following command from R console:
While running the above codes, you may encounter the pop-up question, and you can answer “No”

Setting the Tools

Loading R packages with `library(packageName)`

library(tidyverse)
mpg

Once installed, a package is loaded into an R session using a base-R function library(packageName) so that R package’s functions and data can be used.
- To load the R package tidyverse, type and run the following commands from a R script:
mpg is the data.frame provided by the R package ggplot2, one of the R pakcages in tidyverse.
- Since tidyverse is installed, ggplot2 package is already installed.

Setting the Tools

RStudio Options Setting

This option menu is found by menus as follows:
- Tools \(>\) Global Options
Check the boxes as in the left.
Choose the option Never for Save workspace to .RData on exit:

Setting the Tools

Workflow: Naming and File Management

Save your class R script for each class.
I use the following style of file name for class R script:
- e.g., danl-101-lec-04-2024-0905.R
Do not have any space when you name a file.
- It is recommended to use all lower cases.

Setting the Tools

Workflow: Code and comment style

The two main principles for coding and managing data are:
- Make things easier for your future self.
- Don’t trust your future self.
The # mark is R’s comment character.
- In R scripts (*.R files), # indicates that the rest of the line is to be ignored.
- Write comments before the line that you want the comment to apply to.

Setting the DANL Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Windows
- Alt + - adds an assignment operator
- Ctrl + Enter runs a current line of code
- Ctrl + Shift + C makes a comment (#)
- Ctrl + Shift + R makes a section (# Section - - - -)

Mac
- option + - adds an assignment operator
- command + return runs a current line of code
- command + shift + C makes a comment (#)
- command + shift + R makes a section (# Section - - - -)

Setting the Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Ctrl (command for Mac Users) + Z undoes the previous action.
Ctrl (command for Mac Users) + Shift + Z redoes when undo is executed.

Setting the Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Ctrl (command for Mac Users) + F is useful when finding a phrase (and replace the phrase) in the RScript.

Setting the Tools

Workflow: Auto-completion

libr

Auto-completion of command is useful.
- Type libr in the RScript in RStudio and wait for a second.

Setting the Tools

Workflow: STOP icon

When the code is running, RStudio shows the STOP icon ( 🛑 ) at the top right corner in the Console Pane.
- Do not click it unless if you want to stop running the code.

R Basics

Values, Variables, and Types

A value is datum (literal) such as a number or text.
There are different types of values:
- 352.3 is known as a float or double;
- 22 is an integer;
- “Hello World!” is a string.

R Basics

Values, Variables, and Types

a <- 10    # The most popular assignment operator in R is `<-`.
a

A variable is a name that refers to a value.
- We can think of a variable as a box that has a value, or multiple values, packed inside it.
A variable is just a name!

R Basics

Objects

Sometimes you will hear variables referred to as objects.
Everything that is not a literal value, such as 10, is an object.

R Basics

Assignment

x <- 2
x < - 3

What is going on here?
The shortcut for the assignment <- is:
- Windows: Alt + -
- Mac: option + -

R Basics

Assignment

x <- 2
y <- x + 12

In programming code, everything on the right side needs to have a value.
- The right side can be a literal value, or a variable that has already been assigned a value, or a combination.
When R reads y <- x + 12, it does the following:
1. Sees the <- in the middle.
2. Knows that this is an assignment.
3. Calculates the right side (gets the value of the object referred to by x and adds it to 12).
4. Assigns the result to the left-side variable, y.

R Basics

Data Types

Logical: TRUE or FALSE.
Numeric: Numbers with decimals
Integer: Integers
Character: Text strings
Factor: Categorical values.
- Each possible value of a factor is known as a level.

R Basics

Data Containers

vector: 1D collection of variables of the same type
data.frame: 2D collection of variables of multiple types
- A data.frame is a collection of vectors.

R Basics

Data Types

orig_number <- 4.39898498
class(orig_number)
mod_number <- as.integer(orig_number)
class(mod_number)

# TRUE converts to 1; FALSE does to 0.
as.numeric(TRUE)
as.numeric(FALSE)

Sometimes we need to explicitly cast a value from one type to another.
- We can do this using built-in functions like as.character(), as.integer(), as.numeric(), and as.factor().

R Basics

myname <- "my_name"
class(myname) # returns the data **type** of an object.

Strings are known as character in R.
Use the double quotes (") or single quotes (') to wrap around the string
- Most IDE, including RStudio, automatically provides a pair of quotes when typing just one quote.

favorite.integer <- as.integer(2)
class(favorite.integer)

favorite.numeric <- as.numeric(8.8)
class(favorite.numeric)

Numbers have different classes.
- The most common two are integer and numeric. Integers are whole numbers.

class(TRUE)
class(FALSE)
favorite.numeric == 8.8
favorite.numeric == 9.9
class(favorite.numeric == 8.8)

We use the == to test for equality in R

a <- 1:10  # colon operator
b <- c("3", 4, 5)
beers <- c("BUD LIGHT", "BUSCH LIGHT", "COORS LIGHT", 
           "MILLER LITE", "NATURAL LIGHT")
class(a)
class(b)
class(beers)

We can create one-dimensional data structures called “vectors”.
c(...): Returns a vector that is constructed from one or more arguments, with the order of the vector elements corresponding to the order of the arguments.

beers <- as.factor(beers)
class(beers)

levels(beers)
nlevels(beers)

Factors store categorical data.
Under the hood, factors are actually integers that have a string label attached to each unique integer.
- For example, if we have a long list of Male/Female labels for each of our patients, this will be stored a “column” of zeros and ones by R.

Lecture 4

Setting the DANL Tools

Setting the Tools

Posit Cloud

Setting the Tools

RStudio Environment

Setting the Tools

RStudio Environment

Setting the Tools

RStudio Environment

Setting the Tools

RStudio Environment

Setting the Tools

R Packages and tidyverse

Setting the Tools

tidyverse

Setting the Tools

Installing R packages with install.packages("packageName")

Setting the Tools

Loading R packages with library(packageName)

Setting the Tools

RStudio Options Setting

Setting the Tools

Workflow: Naming and File Management

Setting the Tools

Workflow: Code and comment style

Setting the DANL Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Setting the Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Setting the Tools

Workflow: Shortcuts in Posit Cloud (RStudio)

Setting the Tools

Workflow: Auto-completion

Setting the Tools

Workflow: STOP icon

R Basics

R Basics

Values, Variables, and Types

R Basics

Values, Variables, and Types

R Basics

Objects

R Basics

Assignment

R Basics

Assignment

R Basics

Data Types

R Basics

Data Containers

R Basics

Data Types

R Basics

Data Types

R Packages and `tidyverse`

`tidyverse`

Installing R packages with `install.packages("packageName")`

Loading R packages with `library(packageName)`