Lecture #4

Programming with R

Dr. Debasis Samanta

Associate Professor
Department of Computer Science & Engineering
 Quote of the day..

 What we think, we become.

 GAUTAMA BUDDHA, Sege

CS 40003: Data Analytics 2

Today’s discussion…
 R is an open source programming language and
software environment for statistical computing and
graphics.

 The R language is widely used among statisticians

and data miners for developing statistical software
and data analytics tools

CS 40003: Data Analytics 3

History of R
 Modelled after S & S-plus, developed at AT&T labs in late
1980s.

 R project was started by Robert Gentleman and Ross Ihaka

Department of Statistics, University of Auckland (1995).

 Currently maintained by R core development team – an

international team of volunteer developers (since 1997).
R resources

 http://www.r-project.org/

 http://cran.r-project.org/doc/contrib/Verzani-SimpleR.pdf
Download R and RStudio

 Download R :
http://cran.r-project.org/bin/

 Download RStudio :
http://www.rstudio.com/ide/download/desktop
Installation
Installing R on windows PC :

 Use internet browser to point to : http://mirror.aarnet.edu.au/pub/CRAN

 Under the heading Precompiled Binary Distributions, choose the link Windows.
 Next heading is R for Windows; choose the link base.
 Click on download option(R 3.4.1 for windows).
 Save this to the folder C:\R on your PC.
 When downloading is complete, close or minimize the Internet browser.
 Double click on R 3.4.1-win32.exe in C:\R to install.

Installing R on Linux:
 sudo apt-get install r-base-core
Installation
Installing RStudio:

 Go to www.rstudio.com and click on the "Download RStudio" button.

 Click on "Download RStudio Desktop.“

 Click on the version recommended for your system, or the latest Windows
version, and save the executable file. Run the .exe file and follow the
installation instructions.
Version

 Get R version
R.Version()

 Get RStudio version

RStudio: Toolbar at top > Help > About RStudio
A test run with R in Windows
 Double click the R icon on the Desktop and the R Console will open.
 Wait while the program loads. You observe something like this.

• You can type your own program at the prompt line >.
Getting help from R console

 help.start()
 help(topic)
 ?topic
 ??topic
R command in integrated environment
How to use R for simple maths
 > 3+5
 > 12 + 3 / 4 – 5 + 3*8
 > (12 + 3 / 4 – 5) + 3*8
 > pi * 2^3 – sqrt(4)
Note
 >factorial(4)  R ignores spaces
 >log(2,10)
 >log(2, base=10)
 >log10(2)
 >log(2)
How to store results of calculations for
future use
 > x = 3+5
 >x
 > y = 12 + 3 / 4 – 5 + 3*8
 >y
 > z = (12 + 3 / 4 – 5) + 3*8
>z
 > A <- 6 + 8 ## no space should be between < & -
 >a ## Note: R is case sensitive
 >A
Identifiers naming
 Don't use underscores ( _ ) or hyphens ( - ) in identifiers.
 The preferred form for variable names is all lower case letters
and words separated with dots (variable.name) but
variableName is also accepted.

 Examples:
avg.clicks GOOD
avgClicks OK
avg_Clicks BAD

 Function names have initial capital letters and no dots (e.g.,

FunctionName).
Using C command

 > data1 = c(3, 6, 9, 12, 78, 34, 5, 7, 7) ## numerical data

 > data1.text = c(‘Mon’, ‘Tue’, “Wed”) ## Text data
 ## Single or double quote both ok
 ##copy/paste into R console may not work
 > data1.text = c(data1.text, ‘Thu’, ‘Fri’)
Scan command for making data
 > data3 = scan() ## data separated by Space / Press
## Press Enter key twice to exit
 1: 4 5 7 8
 5: 2 9 4
 8: 3
 9: ## Read 8 items

 > data3
 [1] 4 5 7 8 2 9 4 3
Scan command for making data
 > d3 = scan(what = ‘character’)  > d3[6]='sat'
 1: mon 
 2: tue
 3: wed thu
 > d3
 5:  [1] "mon" "mon" "wed" "thu" NA
"sat"
 > d3 
 [1] "mon" "tue" "wed" "thu"  > d3[2]='tue'
 > d3[2]

 [1] "tue"
  > d3[5] = 'fri'
 > d3[2]='mon' 
  > d3
 > d3  [1] "mon" "tue" "wed" "thu" "fri"
 [1] "mon" "mon" "wed" "thu" "sat"
Concept of working directory
 >getwd()
 [1] "C:\Users\DSamanta\R\Database"

 > setwd('D:\Data Analytics\Project\Database)

 > dir() ## working directory listing

 >ls() ## Workspace listing of objects

 >rm(‘object’) ## Remove an element “object”, if exist

 > rm(list = ls()) ## Cleaning
Reading data from a data file
 > setwd("D:/arpita/data analytics/my work") #Set the working directory to file location
 > getwd()
 [1] "D:/arpita/data analytics/my work“
 > dir()
 [1] "Arv.txt" "DiningAtSFO" "LatentView-DPL" "TC-10-Rec.csv" "TC.csv"
 rm(list=ls(all=TRUE)) # Refresh session
 > data=read.csv('iris.csv', header = T, sep=",")
 (data = read.table(‘iris.csv', header = T, sep = ','))
 > ls()
 [1] "data"
 > str(data)
 'data.frame': 149 obs. of 5 variables:
 $ X5.1 : num 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 5.4 ...
 $ X3.5 : num 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 3.7 ...
 $ X1.4 : num 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 1.5 ...
 $ X0.2 : num 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 0.2 ...
 $ Iris.setosa: Factor w/ 3 levels "Iris-setosa",..: 1 1 1 1 1 1 1 1 1 1 ...
Accessing elements from a file
 > data$X5.1
 [1] 4.9 4.7 4.6 5.0 5.4 4.6 5.0 4.4 4.9 5.4 4.8 4.8 4.3 5.8 5.7
 > data$X5.1[7]=5.2
 > data$X5.1
 [1] 4.9 4.7 4.6 5.0 5.4 4.6 5.2 4.4 4.9 5.4 4.8 4.8 4.3 5.8 5.7
#Note: This change has happened in workspace only not in the file.
 How to make it permanent?
 write.csv / write.table
 >write.table(data, file =‘iris_mod.csv', row.names = FALSE, sep = ',')
 If row.names is TRUE, R adds one ID column in the beginning of file.
 So its suggested to use row.names = FALSE option
 >write.csv(data, file ==‘iris_mod.csv', row.names = TRUE) ## to test
Different data items in R
 Vector

 Matrix

 Data Frame

 List
Vectors in R
 >x=c(1,2,3,4,56)
 >x
 > x[2]
 > x = c(3, 4, NA, 5)
 >mean(x)
 [1] NA
 >mean(x, rm.NA=T)
 [1] 4
 > x = c(3, 4, NULL, 5)
 >mean(x)
 [1] 4
More on Vectors in R
 >y = c(x,c(-1,5),x)
 >length(x)
 >length(y)
 There are useful methods to create long vectors whose elements are in
arithmetic progression:
 > x=1:20
 >x

 If the common difference is not 1 or -1 then we can use the seq function
 > y=seq(2,5,0.3)
 >y
 [1] 2.0 2.3 2.6 2.9 3.2 3.5 3.8 4.1 4.4 4.7 5.0
 > length(y)
 [1] 11
More on Vectors in R
 > x=1:5
 It is very easy to
 > mean(x) add/subtract/multiply/divide two
 [1] 3 vectors entry by entry.
 >x  > y=c(0,3,4,0)
 [1] 1 2 3 4 5  > x+y
 > x^2  [1] 1 5 7 4 5
 [1] 1 4 9 16 25  > y=c(0,3,4,0,9)
 > x+y
 > x+1
 [1] 1 5 7 4 14
 [1] 2 3 4 5 6  Warning message:
 > 2*x  In x + y : longer object length is not a
 [1] 2 4 6 8 10 multiple of shorter object length
 > exp(sqrt(x))  > x=1:6
 [1] 2.718282 4.113250 5.652234  > y=c(9,8)
7.389056 9.356469  > x+y
 [1] 10 10 12 12 14 14
Matrices in R
 Same data type/mode – number , character, logical
 a.matrix <- matrix(vector, nrow = r, ncol = c, byrow = FALSE,
dimnames = list(char-vector-rownames, char-vector-col-names))
## dimnames is optional argument, provides labels for rows & columns.
 > y <- matrix(1:20, nrow = 4, ncol = 5)
 >A = matrix(c(1,2,3,4),nrow=2,byrow=T)
 >A
 >A = matrix(c(1,2,3,4),ncol=2)
 >B = matrix(2:7,nrow=2)
 >C = matrix(5:2,ncol=2)
 >mr <- matrix(1:20, nrow = 5, ncol = 4, byrow = T)
 >mc <- matrix(1:20, nrow = 5, ncol = 4)
 >mr
 >mc
More on matrices in R
 >dim(B) #Dimension
 >nrow(B)
 >ncol(B)
 >A+C
 >A-C
 >A%*%C #Matrix multiplication. Where will be the result?
 >A*C #Entry-wise multiplication
 >t(A) #Transpose
 >A[1,2]
 >A[1,]
 >B[1,c(2,3)]
 >B[,-1]
Lists in R
 Vectors and matrices in R are two ways to work with a
collection of objects.

 Lists provide a third method. Unlike a vector or a matrix a

list can hold different kinds of objects.

 One entry in a list may be a number, while the next is a

matrix, while a third is a character string (like "Hello R!").

 Statistical functions of R usually return the result in the

form of lists. So we must know how to unpack a list using
the $ symbol.
Examples of lists in R
 >x = list(name="Arun Patel", nationality="Indian",
height=5.5, marks=c(95,45,80))

 >names(x)
 >x$name

 >x$hei #abbreviations are OK

 >x$marks
 >x$m[2]
Data frame in R
 A data frame is more general than a matrix, in that different
columns can have different modes (numeric, character, factor,
etc.).
 >d <- c(1,2,3,4)
 >e <- c("red", "white", "red", NA)
 >f <- c(TRUE,TRUE,TRUE,FALSE)
 >myframe <- data.frame(d,e,f)
 >names(myframe) <- c("ID","Color","Passed") # Variable names
 >myframe
 >myframe[1:3,] # Rows 1 , 2, 3 of data frame
 >myframe[,1:2] # Col 1, 2 of data frame
 >myframe[c("ID","Color")] #Columns ID and color from data frame
 >myframe$ID # Variable ID in the data frame
Factors in R
 In R we can make a variable is nominal by making it a factor.

 The factor stores the nominal values as a vector of integers in the

range [ 1... k] (where k is the number of unique values in the nominal
variable).

 An internal vector of character strings (the original values) mapped to

these integers.

 # Example: variable gender with 20 "male" entries and

# 30 "female" entries
>gender <- c(rep("male",20), rep("female", 30))
>gender <- factor(gender)
# Stores gender as 20 1’s and 30 2’s
 # 1=male, 2=female internally (alphabetically)
# R now treats gender as a nominal variable
>summary(gender)
Functions in R

 >g = function(x,y) (x+2*y)/3

 >g(1,2)
 >g(2,1)
 Any question?

You may post your question(s) at the “Discussion Forum”

maintained in the course Web page!

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