VARDHAMAN COLLEGE OF ENGINEERING

(Autonomous)

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

Shamshabad-501218, Hyderabad

VCE-R19
DATA ANALYTICS USING R

LAB MANUAL
VII Semester
A5519
Prepared by
Mr C Satya Kumar
Mr A Ramesh
Mr GS Prasada Reddy
(Assistant Professor,CSE Dept)

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 Week-1: Introduction to R Lab, Basic Programming.

a).Write a R program to create a sequence of numbers from 20 to 50 and find the mean of
numbers from 20 to 60 and sum of numbers from 51 to 91

R Programming Code :
print("Sequence of numbers from 20 to 50:")
print(seq(20,50))
print("Mean of numbers from 20 to 60:")
print(mean(20:60))
print("Sum of numbers from 51 to 91:")
print(sum(51:91))

Sample Output:
[1] "Sequence of numbers from 20 to 50:"
[1] 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
[26] 45 46 47 48 49 50
[1] "Mean of numbers from 20 to 60:"
[1] 40
[1] "Sum of numbers from 51 to 91:"
[1] 2911

b). Write a R program to get the first 10 Fibonacci numbers.

R Programming Code :
Fibonacci <- numeric(10)
Fibonacci[1] <- Fibonacci[2] <- 1
for (i in 3:10) Fibonacci[i] <- Fibonacci[i - 2] + Fibonacci[i - 1]
print("First 10 Fibonacci numbers:")
print(Fibonacci)

Sample Output:
[1] "First 10 Fibonacci numbers:"
[1] 1 1 2 3 5 8 13 21 34 55

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 Week-1: Introduction to Loops

a). Write a R program to get all prime numbers up to a given number.

R Programming Code :

prime_numbers <- function(n) {

if (n >= 2) {
x = seq(2, n)
prime_nums = c()
for (i in seq(2, n)) {
if (any(x == i)) {
prime_nums = c(prime_nums, i)
x = c(x[(x %% i) != 0], i)
}
}
return(prime_nums)
}
else
{
stop("Input number should be at least 2.")
}
}
prime_numbers(12)

Sample Output:
[1] 2 3 5 7 11

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 Week-2: Programs using Vectors.

a)Write a R program to create a vector of a specified type and length. Create vector of
numeric, complex, logical and character types of length 6.

R Programming Code :

x = vector("numeric", 5)
print("Numeric Type:")
print(x)
c = vector("complex", 5)
print("Complex Type:")
print(c)
l = vector("logical", 5)
print("Logical Type:")
print(l)
chr = vector("character", 5)
print("Character Type:")
print(chr)

Sample Output:
[1] "Numeric Type:"
[1] 0 0 0 0 0
[1] "Complex Type:"
[1] 0+0i 0+0i 0+0i 0+0i 0+0i
[1] "Logical Type:"
[1] FALSE FALSE FALSE FALSE FALSE
[1] "Character Type:"
[1] "" "" "" "" ""

Week-2: Programs using Matrices.

a)Write a R program to create a matrix taking a given vector of numbers as input and
define the column and row names. Display the matrix.
R Programming Code:
row_names = c("row1", "row2", "row3", "row4")
col_names = c("col1", "col2", "col3", "col4")
M = matrix(c(1:16), nrow = 4, byrow = TRUE, dimnames = list(row_names, col_names))
print("Original Matrix:")
print(M)

Sample Output:
[1] "Original Matrix:"
col1 col2 col3 col4
row1 1 2 3 4
row2 5 6 7 8
row3 9 10 11 12
row4 13 14 15 16

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 Week-2: Programs using Factors.

a)Write a R program to find the levels of factor of a given vector

R Programming Code :

v = c(1, 2, 3, 3, 4, NA, 3, 2, 4, 5, NA, 5)

print("Original vector:")
print(v)
print("Levels of factor of the said vector:")
print(levels(factor(v)))

Sample Output:

[1] "Original vector:"

[1] 1 2 3 3 4 NA 3 2 4 5 NA 5
[1] "Levels of factor of the said vector:"
[1] "1" "2" "3" "4" "5"

Week-2: Programs using List

c).Write a R program to create a list containing strings, numbers, vectors and a logical values.

R Programming Code :

list_data = list("Python", "PHP", c(5, 7, 9, 11), TRUE, 125.17, 75.83)

print("Data of the list:")
print(list_data)

Sample Output:
[1] "Data of the list:"
[[1]]
[1] "Python"

[[2]]
[1] "PHP"

[[3]]
[1] 5 7 9 11

[[4]]
[1] TRUE

[[5]]
[1] 125.17

[[6]]
[1] 75.83

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 Week-3: Programs using Statics.

a) Apply all statistical concepts using R.

R is known to be one of the most popular statistical programming languages. It is vital to

understand the in-built statistical functions in R. This section will outline the most common
statistical calculations that are performed by data scientists.

a.1 Filling Missing Values:

One of the most common tasks in a data science project is to fill the missing values. We can use
the is.na() to find the elements that are empty (NA or NAN):

vec <- c("test", NA, "another test")

is.na(vec)
This will print FALSE TRUE FALSE, indicating that the second element in NA.
To understand them better, is.na() will return all of those elements/objects that are NA. is.nan()
will return all of the NaN objects. It’s important to note that the NaN is an NA but an NA is not a
NaN.
Note: Many statistical functions such as mean, median, etc, take in an argument: na.rm which
indicates whether we want to remove the na (missing values).

The next few calculations will be based on the following two vectors:

A <- c(1,2,5,6.4,6.7,7,7,7,8,9,3,4,1.5,0,10,5.1,2.4,3.4, 4.5, 6.7)

B <- c(4,4.1,0,1.4,2,1,6.7,7,5,5,8,9,3,2,2.5,0,10,5.1,4.3,5.7)print(length(A)) #20
print(length(B)) #20
Both of the vectors, A and B, contain numerical values of 20 elements.

a.2 Mean

Mean is computed by summing the values in a collection and then dividing by the total number
of values:
my_mean <- mean(A)
print(my_mean)

a.3 Median

Median is the middle value in a sorted collection. If there are an even number of values then it’s
the average of the two middle values:

my_median <- median(A)

print(my_median)

a.4 Mode
A mode is the most frequent value. R is missing a standard built-in function to calculate the
mode. However, we can create a function to calculate it as shown below.

distinct_A <- unique(A)

matches <- match(A, distinct_A)
table_A <- tabulate(matches)
max_A <- which.max(table_A)

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mode<-distinct_A[max_A]
print(mode)

The function performs the following steps:

1. Computes the distinct values of the collection
2. Then it finds the frequency of each of the item and creates a table out of it
3. Lastly, it finds the index of the term that has the highest occurrence and returns it as the
mode.

a.5 Standard deviation

Standard deviation is the deviation of the values from the mean.

sd <- sd(A)
print(sd)

a.6 Variance
Variance is the square of the standard deviation:

var <- var(A)

print(var)

a.7 Correlation
Correlation helps us understand whether the collections have a relationship with each other
and whether they co-move with each other along with the strength of the relationship:

cor <- cor(A, B)

print(cor)
We can pass in a specific correlation method such as Kendall or Spearman. Pearson is the
default correlation method. Pass in the correlation method in the method argument.

a.8 Covariance
Covariance is created to inform us about the relationship between variables.

covariance <- cov(A, B)

print(covariance)

a.9 Standardise and normalise the data set

We are often required to normalise data such as by using min-max normalisation or calculate
the z-score using the standardisation mechanism. Standardising data means having a data set
with mean = 0 and standard deviation = 1. It requires subtracting the mean from each of the
observation and then dividing it by the standard deviation. We can use the scale function. If we
want to subtract the mean from each of the observation then set its center parameter to True. If
we want to standardise data then we need to set its scale parameter to True.
normal_A <- scale(A, center=TRUE, scale = FALSE)
print(normal_A)standard_A <- scale(A, center=TRUE, scale = TRUE)
print(standard_A)

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 Week-4: Programs using Linear Regression

Analysis: Dataset cars includes 50 observations with 2 variables - dist containing stoppping
distance in feet and speed containing speed of a car before applying the brakes in miles per
hour. Data were recorded in the 1920s.
summary(cars)
## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00
plot(cars$speed, cars$dist, xlab='Speed (mph)', ylab='Stopping Distance (ft)',
main='Stopping Distance vs. Speed')
Let us build a linear model and find the best fitting line.
cars_lm <- lm(cars$dist ~ cars$speed)
cars_lm
## Call:
## lm(formula = cars$dist ~ cars$speed)
## Coefficients:
## (Intercept) cars$speed
## -17.579 3.932
plot(cars$speed, cars$dist, xlab='Speed (mph)', ylab='Stopping Distance (ft)',
main='Stopping Distance vs. Speed')
abline(cars_lm)
summary(cars_lm)
## Call:
## lm(formula = cars$dist ~ cars$speed)
## Residuals:
## Min 1Q Median 3Q Max
## -29.069 -9.525 -2.272 9.215 43.201
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -17.5791 6.7584 -2.601 0.0123 *
## cars$speed 3.9324 0.4155 9.464 1.49e-12 ***
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Residual standard error: 15.38 on 48 degrees of freedom
## Multiple R-squared: 0.6511, Adjusted R-squared: 0.6438
## F-statistic: 89.57 on 1 and 48 DF, p-value: 1.49e-12
plot(cars_lm$fitted.values, cars_lm$residuals, xlab='Fitted Values', ylab='Residuals')
abline(0,0)
qqnorm(cars_lm$residuals)
qqline(cars_lm$residuals)
speed <- cars$speed
speed2 <- speed^2
dist <- cars$dist
cars_qm <- lm(dist ~ speed + speed2)
summary(cars_qm)
## Call:
## lm(formula = dist ~ speed + speed2)
## Residuals:

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## Min 1Q Median 3Q Max
## -28.720 -9.184 -3.188 4.628 45.152
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.47014 14.81716 0.167 0.868
## speed 0.91329 2.03422 0.449 0.656
## speed2 0.09996 0.06597 1.515 0.136
## Residual standard error: 15.18 on 47 degrees of freedom
## Multiple R-squared: 0.6673, Adjusted R-squared: 0.6532
## F-statistic: 47.14 on 2 and 47 DF, p-value: 5.852e-12
speedvalues <- seq(0, 25, 0.1)
predictedcounts <- predict(cars_qm,list(speed=speedvalues, speed2=speedvalues^2))
plot(speed, dist, pch=16, xlab='Speed (mph)', ylab='Stopping Distance (ft)')
lines(speedvalues, predictedcounts)
plot(cars_qm$fitted.values, cars_qm$residuals, xlab='Fitted Values', ylab='Residuals')
abline(0,0)
qqnorm(cars_qm$residuals)
qqline(cars_qm$residuals)

Week-5: Programs using Logistic Regression

The Dataset: mtcars(motor trend car road test) comprises fuel consumption, performance and 10
aspects of automobile design for 32 automobiles. It comes pre installed with dplyr package in R.

# Installing the package

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 install.packages("dplyr")

# Loading package
library(dplyr)

# Summary of dataset in package

summary(mtcars)

Performing Logistic regression on dataset

Logistic regression is implemented in R using glm() by training the model using features or
variables in the dataset.

# Installing the package

install.packages("caTools") # For Logistic regression
install.packages("ROCR") # For ROC curve to evaluate model

# Loading package
library(caTools)
library(ROCR)

# Splitting dataset
split <- sample.split(mtcars, SplitRatio = 0.8)
split

train_reg <- subset(mtcars, split == "TRUE")

test_reg <- subset(mtcars, split == "FALSE")

# Training model
logistic_model <- glm(vs ~ wt + disp,
data = train_reg,
family = "binomial")
logistic_model

# Summary
summary(logistic_model)

# Predict test data based on model

predict_reg <- predict(logistic_model,
test_reg, type = "response")
predict_reg

# Changing probabilities
predict_reg <- ifelse(predict_reg >0.5, 1, 0)

# Evaluating model accuracy

# using confusion matrix
table(test_reg$vs, predict_reg)

missing_classerr <- mean(predict_reg != test_reg$vs)

print(paste('Accuracy =', 1 - missing_classerr))

# ROC-AUC Curve
ROCPred <- prediction(predict_reg, test_reg$vs)

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 ROCPer <- performance(ROCPred, measure = "tpr",
x.measure = "fpr")

auc <- performance(ROCPred, measure = "auc")

auc <- [email protected][[1]]
auc

# Plotting curve
plot(ROCPer)
plot(ROCPer, colorize = TRUE,
print.cutoffs.at = seq(0.1, by = 0.1),
main = "ROC CURVE")
abline(a = 0, b = 1)

auc <- round(auc, 4)

legend(.6, .4, auc, title = "AUC", cex = 1)

wt influences dependent variables positively and one unit increase in wt increases the log of
odds for vs =1 by 1.44. disp influences dependent variables negatively and one unit increase in
disp decreases the log of odds for vs =1 by 0.0344. Null deviance is 31.755(fit dependent
variable with intercept) and Residual deviance is 14.457(fit dependent variable with all
independent variable). AIC(Alkaline Information criteria) value is 20.457 i.e the lesser the
better for the model. Accuracy comes out to be 0.75 i.e 75%.

Week 6: Implement Decision trees

#read data file
mydata= read.csv("C:\\Users\\german_credit.csv")
# Check attributes of data
str(mydata)

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'data.frame': 1000 obs. of 21 variables:
$ Creditability : Factor w/ 2 levels "0","1": 2 2 2 2
$ Account.Balance : int 1 1 2 1 1 1 1 1 4 2 ...
$ Duration.of.Credit..month. : int 18 9 12 12 12 10 8 6 18 24 ...
$ Payment.Status.of.Previous.Credit: int 4 4 2 4 4 4 4 4 4 2 ...
$ Purpose : int 2 0 9 0 0 0 0 0 3 3 ...
$ Credit.Amount : int 1049 2799 841 2122 2171 2241
$ Value.Savings.Stocks : int 1 1 2 1 1 1 1 1 1 3 ...
$ Length.of.current.employment : int 2 3 4 3 3 2 4 2 1 1 ...
$ Instalment.per.cent : int 4 2 2 3 4 1 1 2 4 1 ...
$ Sex...Marital.Status : int 2 3 2 3 3 3 3 3 2 2 ...
$ Guarantors : int 1 1 1 1 1 1 1 1 1 1 ...
$ Duration.in.Current.address : int 4 2 4 2 4 3 4 4 4 4 ...
$ Most.valuable.available.asset : int 2 1 1 1 2 1 1 1 3 4 ...
$ Age..years. : int 21 36 23 39 38 48 39 40 65 23 ...
$ Concurrent.Credits : int 3 3 3 3 1 3 3 3 3 3 ...
$ Type.of.apartment : int 1 1 1 1 2 1 2 2 2 1 ...
$ No.of.Credits.at.this.Bank : int 1 2 1 2 2 2 2 1 2 1 ...
$ Occupation : int 3 3 2 2 2 2 2 2 1 1 ...
$ No.of.dependents : int 1 2 1 2 1 2 1 2 1 1 ...
$ Telephone : int 1 1 1 1 1 1 1 1 1 1 ...
$ Foreign.Worker : int 1 1 1 2 2 2 2 2 1 1 ...
# Check number of rows and columns
dim(mydata)
# Make dependent variable as a factor (categorical)
mydata$Creditability = as.factor(mydata$Creditability)
# Split data into training (70%) and validation (30%)
dt = sort(sample(nrow(mydata), nrow(mydata)*.7))
train<-mydata[dt,]
val<-mydata[-dt,] # Check number of rows in training data set
nrow(train)
# To view dataset
edit(train)
# Decision Tree Model
library(rpart)
mtree <- rpart(Creditability~., data = train, method="class", control = rpart.control(minsplit =
20, minbucket = 7, maxdepth = 10, usesurrogate = 2, xval =10 ))

mtree

#Plot tree
plot(mtree)
text(mtree)

#Beautify tree
library(rattle)
library(rpart.plot)
library(RColorBrewer)

#view1
prp(mtree, faclen = 0, cex = 0.8, extra = 1)

#view2 - total count at each node

tot_count <- function(x, labs, digits, varlen)

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{paste(labs, "\n\nn =", x$frame$n)}

prp(mtree, faclen = 0, cex = 0.8, node.fun=tot_count)

#view3- fancy Plot

rattle()
fancyRpartPlot(mtree)

############################
########Pruning#############
############################

printcp(mtree)
bestcp <- mtree$cptable[which.min(mtree$cptable[,"xerror"]),"CP"]

# Prune the tree using the best cp.

pruned <- prune(mtree, cp = bestcp)

# Plot pruned tree

prp(pruned, faclen = 0, cex = 0.8, extra = 1)

# confusion matrix (training data)

conf.matrix <- table(train$Creditability, predict(pruned,type="class"))
rownames(conf.matrix) <- paste("Actual", rownames(conf.matrix), sep = ":")
colnames(conf.matrix) <- paste("Pred", colnames(conf.matrix), sep = ":")
print(conf.matrix)

#Scoring
library(ROCR)
val1 = predict(pruned, val, type = "prob")
#Storing Model Performance Scores
pred_val <-prediction(val1[,2],val$Creditability)

# Calculating Area under Curve

perf_val <- performance(pred_val,"auc")
perf_val

# Plotting Lift curve

plot(performance(pred_val, measure="lift", x.measure="rpp"), colorize=TRUE)

# Calculating True Positive and False Positive Rate

perf_val <- performance(pred_val, "tpr", "fpr")

# Plot the ROC curve

plot(perf_val, col = "green", lwd = 1.5)

#Calculating KS statistics
ks1.tree <- max(attr(perf_val, "y.values")[[1]] - (attr(perf_val, "x.values")[[1]]))
ks1.tree
# Advanced Plot
prp(pruned, main="Decision Tree",
extra=106,
nn=TRUE,
fallen.leaves=TRUE,

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branch=.5,
faclen=0,
trace=1,
shadow.col="gray",
branch.lty=3,
split.cex=1.2,
split.prefix="is ",
split.suffix="?",
split.box.col="lightgray",
split.border.col="darkgray",
split.round=.5)

Decision Tree

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