Introduction to R

Topic 01 - Introduction to R DSA1101 Introduction to Data Science 1 / 58

 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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What is R?

It is an integrated suite of software facilitates for data manipulation, calculation

and graphical display.
Among other things it has

An eective data handling and storage facility.

A suite of operators for calculations on array, in particular, matrices.

A large, coherent, integrated collection of intermediate tools for data

analysis.

Graphical facilities for data analysis.

A well developed, simple and eective programming language.

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How To Start R?

Downloading R from https://www.r-project.org/

Double click the R's icon in the desktop to activate R (at least version 4.1.0
for our course).

After R is started, R console is open in the RGui window.

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RStudio

A free integrated development environment (IDE) for R

Have some features that makes it easier to work with

Note: R still needs to be installed before RStudio

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RStudio Suplements

DataCamp tutorial on Working with the Rstudio IDE

https:
//www.datacamp.com/courses/working-with-therstudio-ide-part-1

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Working Directory

The folder on your computer in which you are currently working.

R will read and write les from/to this folder.

In RStudio, use drop down menu to select working directory Session > Set
Working Directory > Choose Directory
Or
Files Pane > Navigating to a Directory > Clicking More > Set as
Working Directory

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How To Handle Data in R

Four most frequently used types of data objects:

Vector: set of elements of the same mode (logical; numeric; character).

Matrix: set of elements appearing in rows and columns, where the elements
are of the same mode.

Dataframe:
-Similar to the Matrix object but columns can have dierent modes.

-The rows contain dierent observations from your study or measurements

from your experiment;

-The columns contain the values of dierent variables which may be of

dierent modes.

List: generalization of a vector  represents a collection of data objects.

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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Creating a Vector in R: c function
To create a vector, the simplest way is using the concatenation c function.

> #creating a vector of numbers:

> number<-c(2,4,6,8,10); number
[1] 2 4 6 8 10
> # creating a vector of strings/characters:
> string<-c("weight", "height", "gender"); string
[1] "weight" "height" "gender"
> #creating a Boolean vector (T/F):
> logic<- c(T, T, F, F, T); logic
[1] TRUE TRUE FALSE FALSE TRUE
Appending item(s) to the existing vector:

What is c(number,12,14)? A vector of numbers.

What is c(string, 12,14)? A vector of strings where 12 and 14 are
treated as strings.

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Creating a Vector in R: numeric function

The numeric function creates a vector with all its elements being 0.

> number.2<-numeric(3)
> number.2
[1] 0 0 0
> c(number, number.2)
[1] 2 4 6 8 10 0 0 0

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Creating a Vector in R: rep function

The rep function replicates elements of vectors.

rep(a,b): replicate the item a by b times.

> #rep(a,b): replicate the item a by b times.

> number.3<-rep(2,3)
> number.3
[1] 2 2 2
> number.3<-rep(c(1,2),3)
> number.3
[1] 1 2 1 2 1 2
> rep(string,2)
[1] "weight" "height" "gender" "weight" "height" "gender"

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Creating a Vector in R: seq function
seq(from = a, to = b, by = c): from the number a to number b, create a
sequence of numbers evenly spread by a distance of c.
> seq(from=2, to=10, by=2)
[1] 2 4 6 8 10
> seq(from=2, to=10, length = 5)
[1] 2 4 6 8 10
> 1:5
[1] 1 2 3 4 5
> 1:5*2
[1] 2 4 6 8 10
> seq(2,10,2)
[1] 2 4 6 8 10
> seq(10)
[1] 1 2 3 4 5 6 7 8 9 10
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Suplements

DataCamp tutorial about variables in R:

https://campus.datacamp.com/courses/free-introduction-to-r/
chapter-1-intro-to-basics-1?ex=3

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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Creating a Matrix: matrix() function

Members in a matrix must be of the same mode (numeric or character).

matrix(v, nrow = r, ncol = c): take the values from vector v to create a
matrix with r rows and c columns.

By default, matrix is lled by column.

> v <- c(1:6) # a vector with 6 elements

> m <- matrix(v, nrow=2, ncol=3)
> m
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6

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Creating a Matrix: matrix() function

To ll the matrix by row instead of column, we need to specify byrow = TRUE.

> # to fill the matrix by rows:

> m <- matrix(v, nrow=2, ncol=3, byrow=T)
> m
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 4 5 6

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Creating a Matrix: rbind() functions

To bind a row (or many rows) onto a matrix, the command rbind() can be
used.

> a <- c(1,2,3,4)

> b <- c(5,6,7,8)
> # a and b are two vectors of the same length
> ab_row <- rbind(a,b)
> ab_row # each vector is one row of the matrix
[,1] [,2] [,3] [,4]
a 1 2 3 4
b 5 6 7 8

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Creating a Matrix: cbind() functions

> a <- c(1,2,3,4)

> b <- c(5,6,7,8)
To bind a column (or many columns) onto a matrix, the command cbind()
can be used.

> ab_col <- cbind(a,b)

> ab_col # each vector is one column of the matrix
a b
[1,] 1 5
[2,] 2 6
[3,] 3 7
[4,] 4 8

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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List in R

Lists are the objects which contain elements of dierent modes like
numbers, strings, vectors and another list inside it.

> list.1 <- list(10.5, TRUE, "Daisy")

> list.1
[[1]]
[1] 10.5

[[2]]
[1] TRUE

[[3]]
[1] "Daisy"

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List in R

> x = c(2,4,6,8) # vector length 4, numeric

> y = c(T, F, T) # vector length 3, logical
> list.2 = list(A = x, B = y)
> # Create a list using two vectors, x and y.
> # and assign names A, B to the members of the list
> list.2
$A
[1] 2 4 6 8

$B
[1] TRUE FALSE TRUE

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List in R

Refer to item in a list by index:

> list.2[1] # get the first item in the list

$A
[1] 2 4 6 8

Refer to an item by the name of the item:

> list.2$A # get item A (a vector) in the list

[1] 2 4 6 8

Refer to a member in an item of the list:

> list.2$A[1]
[1] 2

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List in R

> list.1[1] # this is an item of list, NOT numeric

[[1]]
[1] 10.5

> list.1[[1]] # this is numeric

[1] 10.5

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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A Dataframe in R

Dataframe is a list of vectors of equal length.

A dataframe has rows and columns:

▶ The rows contain dierent observations or measurements;
▶ The columns contain the values of dierent variables.

All the values of the same variable must go in the same column.

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Notes

Example: an experiment with three treatments (control, pre-heated and

pre-chilled), and four measurements per treatment. A table as below is
created based on the given measurements.

Is it a correct dataframe in R?

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A Dataframe in R

The correct dataframe for the example in the previous slide should be

This has 2 variables: measurements as the response variable and another

variable (called treatment) for three levels of experimental factor.

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Reading Data Files into R

The very rst step is to make sure that the le is under the working directory
that R is accessible to.

There are several ways of reading/importing data les into R:

read.table(le, header = FALSE, sep = "")

read.csv(le, header = TRUE, sep = ",")

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Open the le in Notepad

When you have a le, it's good to open that le in Notepad before
importing to R to know if the le has header; if the values are separated by
comma or by space, or by tab, etc.

Open the le crab.txt, we can observe that it has header, and the values
are separated by space.

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Import a File into R

Since the le has header, then we use: header = TRUE ; The values are
separated by space, hence we use sep = "".

> data1<-read.csv("~/Documents/Data/crab.txt", sep = "", header = TRUE

> # If you have set the working directory
> # setwd(C:/Data)
> # then you just need to have the code as
> # data1<-read.csv("crab.txt", sep = "", header = TRUE)

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Import a File into R

How the dataframe looks like:

> data1[1:4,] #first 4 rows

color spine width satell weight
1 3 3 28.3 8 3.05
2 4 3 22.5 0 1.55
3 2 1 26.0 9 2.30
4 4 3 24.8 0 2.10
> names(data1) # names of the columns
[1] "color" "spine" "width" "satell" "weight"

names(data1) returns a vector with 5 elements that are the names of 5

columns.

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Import a Data File

If the rst line of the data le does not contain the names of the variables
ex_1.txt.
like the le

> data2<-read.table("~/Documents/Data/ex_1.txt", header = FALSE)

This is how data2 looks like where the columns are named by R.

> data2
V1 V2 V3 V4 V5
1 10 M 80 84 A
2 7 M 85 89 A
3 4 F 90 86 B
4 20 M 82 85 B
5 25 F 94 94 A
6 14 F 88 84 C

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Changing Names of Columns

> names(data2)
[1] "V1" "V2" "V3" "V4" "V5"

We can change the names of the columns

> names(data2) = c("Subject", "Gender", "CA1", "CA2", "HW")

> data2
Subject Gender CA1 CA2 HW
1 10 M 80 84 A
2 7 M 85 89 A
3 4 F 90 86 B
4 20 M 82 85 B
5 25 F 94 94 A
6 14 F 88 84 C

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Assessing Parts of a Dataframe

NAME[x, y]

NAME is the name of the dataframe.

x is to indicate the rows that we want to select. If it's not specify, then all
rows are selected.

y is to indicate the columns that we want to select. If it's not specify, then
all columns are selected.

x could be a number; a vector of numbers; or a condition; Similar for y.

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Assessing Parts of a Dataframe

The 2nd rows of a dataframe and all columns are listed.

> data2[2,] # 2nd rows

Subject Gender CA1 CA2 HW
2 7 M 85 89 A

Third column

> data2[,3]
[1] 80 85 90 82 94 88

Get a specic variable/column by the column name

> data2$CA1 # assess a column by its name

[1] 80 85 90 82 94 88

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Command attach()

Command attach(data2) could help us to assess every column of data2

by the name of the column.

However, the properties of each column inside data2 will be kept as when it
was attached.

> attach(data2)
> CA1
[1] 80 85 90 82 94 88

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Assessing Parts of a Dataframe

Selecting a specied column:

> data2[,1] # select only the first column

[1] 10 7 4 20 25 14

Select a few columns:

> data2[,2:4] # select columns from 2 to 4

Gender CA1 CA2
1 M 80 84
2 M 85 89
3 F 90 86
4 M 82 85
5 F 94 94
6 F 88 84

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Assessing Parts of a Dataframe

Selecting some specied observations (rows):

> data2[1:2,] # select row 1 to row 2

Subject Gender CA1 CA2 HW
1 10 M 80 84 A
2 7 M 85 89 A

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Assessing Parts of a Dataframe

Selecting some specic values in the data

> data2[3,3] # value at 3rd row & 3rd column

[1] 90
> data2[3,4] # value at 3rd row & 4th column
[1] 86

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Assessing Parts of a Dataframe by Conditions

Select all observations that are males:

> data2[Gender == "M",]

Subject Gender CA1 CA2 HW
1 10 M 80 84 A
2 7 M 85 89 A
4 20 M 82 85 B

Select all observations that are males and their CA2 is more than 85:

> data2[Gender == "M" & CA2 > 85,]

Subject Gender CA1 CA2 HW
2 7 M 85 89 A

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 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

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Common Commands

x and y are vectors. Some functions on vectors in R:

max(x): maximum value of vector x

min(x): minimum value of x

sum(x): total of all the values in x

mean(x): arithmetic average values in x

range(x): min(x) and max(x)

cor(x,y): correlation value between vectors x and y

sort(x): a sorted version of x

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Common Commands Used for a Dataframe

Read/import a dataframe into R: data = read.csv(crab.txt...)

names(data): to get the names of columns in data

attach(data)

colMeans(data): get the mean of every column, if all columns are numeric

which(data$x1 == 3): get the index of all the rows of data that the
column x1 has value 3.

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Common Plots

Topic 01 - Introduction to R DSA1101 Introduction to Data Science 46 / 58

 1 Introduction

2 Vectors in R

3 Matrices in R

4 Lists in R

5 Dataframes in R

6 Commonly Used Commands

7 Loops, Conditions and Functions in R

Topic 01 - Introduction to R DSA1101 Introduction to Data Science 47 / 58

 while loop

for loop

Conditioning with if...else

Dene a function

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while Loop: Examples

A simple while loop

> x = 1
> while(x<=3) {print("x is less than 4")
+ x = x+1}
[1] "x is less than 4"
[1] "x is less than 4"
[1] "x is less than 4"

Find the sum of rst 10 integers:

> x<-0; S<-0

> while(x<=10) {S<- S+ x
+ x<-x+1}
> S
[1] 55

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while Loop

The while loop is in the form of

while (condition) {expression}

How this loop works:

1 (condition) must evaluate to a TRUE or a FALSE.

2 If (condition) is TRUE, do all the steps inside the code block of

{expression}.

3 Check (condition) again

4 Repeat [2] and [3] above until (condition) is a FALSE.

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for Loop

Example: nd the sum of rst 10 integers

> S<-0; for(i in 1:10){S <-S+i}

> S
[1] 55

Find the mean

> x = c(2, 4, 3, 8, 10)

> l = length(x)
> S = 0
> for (i in 1:l){S = S + x[i]}
> ave = S/l; ave
[1] 5.4

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for Loop

The for loop is in the form of:

for (<variable> in <range>) {expression}

How this loop works:

Each time through the loop, <variable> takes a value

1 First time, <variable> starts at the smallest value in the range and do all
the steps inside the {expression}.

2 Next time, <variable> gets the previous value + 1, and do all the steps
inside the {expression}, until <variable> reaches the last value in the
range.

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if...else

Find the sum of all even numbers from 1 up to 100.

> x = c(1:100); S = 0

We'll identify all the even numbers in vector x and sum them up. For each
element x[i] of x, we'll check the remainder when it divides by 2; if the
remainder is 0, then we add that element x[i] to the sum S; if the
remainder is not 0, we do nothing to the sum.

> for (i in 1:length(x)){

+ if(x[i]%%2 ==0){S = S + x[i]} else {S = S}
+ }; print(S)
[1] 2550

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if...else

> x = c(1:10);

Vector x has 10 numbers from 1 to 10. We now need to create 3 vectors, S, M,

L where S contains all the values in x that are at most 3; M contains all the values
in x that are less than 8 but more than 3; L contains all the rest.

> # STEP 1: create 3 vectors S, M, L which has nothing yet

> S = numeric(0)
> M = numeric(0)
> L = numeric(0)

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if...else

STEP 2: checking each member of x[i]; then to append it to S, or M or L:

> for (i in 1:length(x)){
+ if (x[i] <=3){S = append(S, x[i])} else if (x[i]< 8)
+ {M = append(M, x[i])} else {L = append(L, x[i])}
+ }
> print(S)
[1] 1 2 3
> print(M)
[1] 4 5 6 7
> print(L)
[1] 8 9 10

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ifelse

> x = c(1:8);x
[1] 1 2 3 4 5 6 7 8

We need to replace each number in x by a word such that: if the number is odd,
we replace that number by the word odd; if the number is even, we then replace
it by the word even.

It could be done by the command ifelse()

> x = ifelse(x%%2 == 0, "even", "odd")

> x
[1] "odd" "even" "odd" "even" "odd" "even" "odd" "even"

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User-Dened Functions in R

Characteristics of a function:
-has a name
-has parameters
-has a body
-returns something

How to write/dene:
name <- function(parameters) { function body }

At the end of the function body, some command to ask for evaluation and
return normally be included.

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Function to calculate OR

We would want to form a function that helps us to calculate OR for a 2 ×2

matrix or table.

> OR<-function(x){
+ if(any(x==0)) {x<-x+0.5}
+ odds.ratio<-x[1,1]*x[2,2]/(x[2,1]*x[1,2])
+
+ return(odds.ratio) }
> #OR(table)
>

Function is named as OR.

It has one argument/parameter, x, which is a 2 ×2 matrix/table.

Question: write a function to nd the median of a given vector.

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