CSE3506 Essentials of Data Analytics

Name : Shivam Batra

Reg. No. : 19BPS1131
Lab Exercise: 5

Objective: Applying logistic regression to predict red wine.

Methods -

1. Exploratory data analysis (EDA)

2. Data preparation

3. Modeling -> Logistic regression

4. ROC Curve

STEPS:

#Importing the dataset

data <- read.csv('winequality-red.csv', sep = ';')
str(data)

## 'data.frame': 1599 obs. of 12 variables:

## $ fixed.acidity : num 7.4 7.8 7.8 11.2 7.4 7.4 7.9 7.3 7.8 7.5 ...
## $ volatile.acidity : num 0.7 0.88 0.76 0.28 0.7 0.66 0.6 0.65 0.58 0.5 ...
## $ citric.acid : num 0 0 0.04 0.56 0 0 0.06 0 0.02 0.36 ...
## $ residual.sugar : num 1.9 2.6 2.3 1.9 1.9 1.8 1.6 1.2 2 6.1 ...
## $ chlorides : num 0.076 0.098 0.092 0.075 0.076 0.075 0.069 0.065 0.073 0.071 ...
## $ free.sulfur.dioxide : num 11 25 15 17 11 13 15 15 9 17 ...
## $ total.sulfur.dioxide: num 34 67 54 60 34 40 59 21 18 102 ...
## $ density : num 0.998 0.997 0.997 0.998 0.998 ...
## $ pH : num 3.51 3.2 3.26 3.16 3.51 3.51 3.3 3.39 3.36 3.35 ...
## $ sulphates : num 0.56 0.68 0.65 0.58 0.56 0.56 0.46 0.47 0.57 0.8 ...
## $ alcohol : num 9.4 9.8 9.8 9.8 9.4 9.4 9.4 10 9.5 10.5 ...
## $ quality : int 5 5 5 6 5 5 5 7 7 5 ...

#Format outcome variable

data$quality <- ifelse(data$quality >= 7, 1, 0)
data$quality <- factor(data$quality, levels = c(0, 1))

#Descriptive statistics
summary(data)
## fixed.acidity volatile.acidity citric.acid residual.sugar
## Min. : 4.60 Min. :0.1200 Min. :0.000 Min. : 0.900
## 1st Qu.: 7.10 1st Qu.:0.3900 1st Qu.:0.090 1st Qu.: 1.900
## Median : 7.90 Median :0.5200 Median :0.260 Median : 2.200
## Mean : 8.32 Mean :0.5278 Mean :0.271 Mean : 2.539
## 3rd Qu.: 9.20 3rd Qu.:0.6400 3rd Qu.:0.420 3rd Qu.: 2.600
## Max. :15.90 Max. :1.5800 Max. :1.000 Max. :15.500
## chlorides free.sulfur.dioxide total.sulfur.dioxide density
## Min. :0.01200 Min. : 1.00 Min. : 6.00 Min. :0.9901
## 1st Qu.:0.07000 1st Qu.: 7.00 1st Qu.: 22.00 1st Qu.:0.9956
## Median :0.07900 Median :14.00 Median : 38.00 Median :0.9968
## Mean :0.08747 Mean :15.87 Mean : 46.47 Mean :0.9967
## 3rd Qu.:0.09000 3rd Qu.:21.00 3rd Qu.: 62.00 3rd Qu.:0.9978
## Max. :0.61100 Max. :72.00 Max. :289.00 Max. :1.0037
## pH sulphates alcohol quality
## Min. :2.740 Min. :0.3300 Min. : 8.40 0:1382
## 1st Qu.:3.210 1st Qu.:0.5500 1st Qu.: 9.50 1: 217
## Median :3.310 Median :0.6200 Median :10.20
## Mean :3.311 Mean :0.6581 Mean :10.42
## 3rd Qu.:3.400 3rd Qu.:0.7300 3rd Qu.:11.10
## Max. :4.010 Max. :2.0000 Max. :14.90

Univariate analysis

#Dependent variable
#Frequency plot
par(mfrow=c(1,1))
barplot(table(data[[12]]),
main = sprintf('Frequency plot of the variable: %s',
colnames(data[12])),
xlab = colnames(data[12]),
ylab = 'Frequency')
#Check class BIAS
table(data$quality)

##
## 0 1
## 1382 217

round(prop.table((table(data$quality))),2)

##
## 0 1
## 0.86 0.14

#Independent variable
#Boxplots
par(mfrow=c(3,4))
for (i in 1:(length(data)-1)){
boxplot(x = data[i],
horizontal = TRUE,
main = sprintf('Boxplot of the variable: %s',
colnames(data[i])),
xlab = colnames(data[i]))
}
#Histograms
par(mfrow=c(3,4))
for (i in 1:(length(data)-1)){
hist(x = data[[i]],
main = sprintf('Histogram of the variable: %s',
colnames(data[i])),
xlab = colnames(data[i]))
}
 Bivariate analysis

#Correlation matrix
library(ggcorrplot)

## Loading required package: ggplot2

ggcorrplot(round(cor(data[-12]), 2),
type = "lower",
lab = TRUE,
title =
'Correlation matrix of the red wine quality dataset')
Data preparation

#Missing values
sum(is.na(data))

## [1] 0

#Outliers
#Identifing outliers
is_outlier <- function(x) {
return(x < quantile(x, 0.25) - 1.5 * IQR(x) |
x > quantile(x, 0.75) + 1.5 * IQR(x))
}
outlier <- data.frame(variable = character(),
sum_outliers = integer(),
stringsAsFactors=FALSE)
for (j in 1:(length(data)-1)){
variable <- colnames(data[j])
for (i in data[j]){
sum_outliers <- sum(is_outlier(i))
}
row <- data.frame(variable,sum_outliers)
outlier <- rbind(outlier, row)
}
outlier

## variable sum_outliers
## 1 fixed.acidity 49
## 2 volatile.acidity 19
## 3 citric.acid 1
## 4 residual.sugar 155
## 5 chlorides 112
## 6 free.sulfur.dioxide 30
## 7 total.sulfur.dioxide 55
## 8 density 45
## 9 pH 35
## 10 sulphates 59
## 11 alcohol 13

#Identifying the percentage of outliers

for (i in 1:nrow(outlier)){
if (outlier[i,2]/nrow(data) * 100 >= 5){
print(paste(outlier[i,1],
'=',
round(outlier[i,2]/nrow(data) * 100, digits = 2),
'%'))
}
}

## [1] "residual.sugar = 9.69 %"

## [1] "chlorides = 7 %"

#Inputting outlier values

for (i in 4:5){
for (j in 1:nrow(data)){
if (data[[j, i]] > as.numeric(quantile(data[[i]], 0.75) +
1.5 * IQR(data[[i]]))){
if (i == 4){
data[[j, i]] <- round(mean(data[[i]]), digits = 2)
} else{
data[[j, i]] <- round(mean(data[[i]]), digits = 3)
}
}
}
}

Modeling
#Splitting the dataset into the Training set and Test set
#Stratified sample
data_ones <- data[which(data$quality == 1), ]
data_zeros <- data[which(data$quality == 0), ]
#Train data
set.seed(123)
train_ones_rows <- sample(1:nrow(data_ones), 0.8*nrow(data_ones))
train_zeros_rows <- sample(1:nrow(data_zeros), 0.8*nrow(data_ones))
train_ones <- data_ones[train_ones_rows, ]
train_zeros <- data_zeros[train_zeros_rows, ]
train_set <- rbind(train_ones, train_zeros)
table(train_set$quality)

##
## 0 1
## 173 173

#Test Data
test_ones <- data_ones[-train_ones_rows, ]
test_zeros <- data_zeros[-train_zeros_rows, ]
test_set <- rbind(test_ones, test_zeros)
table(test_set$quality)

##
## 0 1
## 1209 44

Logistic regression

#Logistic Regression
lr = glm(formula = quality ~.,
data = train_set,
family = binomial)
#Predictions
prob_pred = predict(lr,
type = 'response',
newdata = test_set[-12])
library(InformationValue)
optCutOff <- optimalCutoff(test_set$quality, prob_pred)[1]
y_pred = ifelse(prob_pred > optCutOff, 1, 0)

#Making the confusion matrix

cm_lr = table(test_set[, 12], y_pred)
cm_lr

## y_pred
## 0 1
## 0 1207 2
## 1 43 1

#Accuracy
accuracy_lr = (cm_lr[1,1] + cm_lr[1,1])/
(cm_lr[1,1] + cm_lr[1,1] + cm_lr[2,1] + cm_lr[1,2])
accuracy_lr

## [1] 0.9816999

#ROC curve
library(ROSE)

## Loaded ROSE 0.0-4

par(mfrow = c(1, 1))

roc.curve(test_set$quality, y_pred)

## Area under the curve (AUC): 0.511