Master in Data Science at Utica College

https://programs.online.utica.edu/programs/masters-data-science

Specific requirements

In this programming project, complete the following steps:

Data frame information

Description

Dataset of Social media ads describing users, whether users have purchased a product by clicking on the advertisements shown to them.

Content

Social media ads of 400 rows and 5 columns.

Headers

User ID

Character field which catpures the user account number.

Gender

Character field which indicates whether the user is female or male.

Age

The age of the user.

Estimated Salary

The estimated salary of the user.

Purchased

A binary field which indicates whether the user made the purchase.

Clearing R Studio Memory Usage

gc()
##           used (Mb) gc trigger (Mb) max used (Mb)
## Ncells  543103 29.1    1241057 66.3   621331 33.2
## Vcells 1025152  7.9    8388608 64.0  1600889 12.3
rm(list = ls())

Time Counter Start

start_time <- Sys.time()

Include the knitr package for integration of R code into Markdown

knitr::opts_chunk$set(echo = TRUE)

All the libraries used in this code

library(easypackages)
libraries("caret","caretEnsemble","caTools","class","cluster","data.tree","devtools","doSNOW","dplyr","e1071","factoextra","gbm","FNN","FSelector","ggalt","ggforce","ggfortify","ggplot2","gmodels","klaR","lattice","mlbench","modeest","nnet","neuralnet","outliers","parallel","psych","purrr","readr","rpart","rpart.plot","spatialEco","stats","tidyr","randomForest","ROSE","rsample","ROCR","pROC","glmnet","gridExtra","R6")

Import data

oldw <- getOption("warn")
options(warn = -1)
library(readr)
input_data <- read_csv("Social_Network_Ads.csv", 
    col_types = cols(
                      Age = col_number(), 
                      EstimatedSalary = col_number(), 
                      Gender = col_character(), 
                      Purchased = col_character(), 
                      `User ID` = col_character()
                    )
)
options(warn = -1) 

Numeric/character field separator

num.names <- input_data %>% select_if(is.numeric) %>% colnames()
ch.names <- input_data %>% select_if(is.character) %>% colnames()

Descriptive statistics before data processing

Dimension of data frame

dim(input_data)
## [1] 400   5

Structure of data frame

str(input_data)
## tibble [400 x 5] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
##  $ User ID        : chr [1:400] "15624510" "15810944" "15668575" "15603246" ...
##  $ Gender         : chr [1:400] "Male" "Male" "Female" "Female" ...
##  $ Age            : num [1:400] 19 35 26 27 19 27 27 32 25 35 ...
##  $ EstimatedSalary: num [1:400] 19000 20000 43000 57000 76000 58000 84000 150000 33000 65000 ...
##  $ Purchased      : chr [1:400] "0" "0" "0" "0" ...
##  - attr(*, "spec")=
##   .. cols(
##   ..   `User ID` = col_character(),
##   ..   Gender = col_character(),
##   ..   Age = col_number(),
##   ..   EstimatedSalary = col_number(),
##   ..   Purchased = col_character()
##   .. )

Summary statistics of data frame

summary(input_data)
##    User ID             Gender               Age        EstimatedSalary 
##  Length:400         Length:400         Min.   :18.00   Min.   : 15000  
##  Class :character   Class :character   1st Qu.:29.75   1st Qu.: 43000  
##  Mode  :character   Mode  :character   Median :37.00   Median : 70000  
##                                        Mean   :37.66   Mean   : 69743  
##                                        3rd Qu.:46.00   3rd Qu.: 88000  
##                                        Max.   :60.00   Max.   :150000  
##   Purchased        
##  Length:400        
##  Class :character  
##  Mode  :character  
##                    
##                    
## 

Glimpse of data frame

glimpse(input_data)
## Rows: 400
## Columns: 5
## $ `User ID`       <chr> "15624510", "15810944", "15668575", "15603246", "15...
## $ Gender          <chr> "Male", "Male", "Female", "Female", "Male", "Male",...
## $ Age             <dbl> 19, 35, 26, 27, 19, 27, 27, 32, 25, 35, 26, 26, 20,...
## $ EstimatedSalary <dbl> 19000, 20000, 43000, 57000, 76000, 58000, 84000, 15...
## $ Purchased       <chr> "0", "0", "0", "0", "0", "0", "0", "1", "0", "0", "...

Head of data frame

head(input_data)
## # A tibble: 6 x 5
##   `User ID` Gender   Age EstimatedSalary Purchased
##   <chr>     <chr>  <dbl>           <dbl> <chr>    
## 1 15624510  Male      19           19000 0        
## 2 15810944  Male      35           20000 0        
## 3 15668575  Female    26           43000 0        
## 4 15603246  Female    27           57000 0        
## 5 15804002  Male      19           76000 0        
## 6 15728773  Male      27           58000 0

Tail of data frame

tail(input_data)
## # A tibble: 6 x 5
##   `User ID` Gender   Age EstimatedSalary Purchased
##   <chr>     <chr>  <dbl>           <dbl> <chr>    
## 1 15757632  Female    39           59000 0        
## 2 15691863  Female    46           41000 1        
## 3 15706071  Male      51           23000 1        
## 4 15654296  Female    50           20000 1        
## 5 15755018  Male      36           33000 0        
## 6 15594041  Female    49           36000 1

Variable data types

sapply(input_data,mode)
##         User ID          Gender             Age EstimatedSalary       Purchased 
##     "character"     "character"       "numeric"       "numeric"     "character"

Mean of each variable

lapply(input_data[,num.names],mean)
## $Age
## [1] 37.655
## 
## $EstimatedSalary
## [1] 69742.5

Median of each variable

lapply(input_data[,num.names],median)
## $Age
## [1] 37
## 
## $EstimatedSalary
## [1] 70000

Mode of each variable

lapply(input_data[,num.names],mfv)
## $Age
## [1] 35
## 
## $EstimatedSalary
## [1] 72000

Minimum value of each variable

lapply(input_data[,num.names],min)
## $Age
## [1] 18
## 
## $EstimatedSalary
## [1] 15000

Maximum value of each variable

lapply(input_data[,num.names],max)
## $Age
## [1] 60
## 
## $EstimatedSalary
## [1] 150000

Range of each variable

lapply(input_data[,num.names],range)
## $Age
## [1] 18 60
## 
## $EstimatedSalary
## [1]  15000 150000

Variance of each variable

lapply(input_data[,num.names],var)
## $Age
## [1] 109.8907
## 
## $EstimatedSalary
## [1] 1162602701

Standard deviation of each variable

lapply(input_data[,num.names],sd)
## $Age
## [1] 10.48288
## 
## $EstimatedSalary
## [1] 34096.96

Median absolute deviation of each variable

lapply(input_data[,num.names],mad)
## $Age
## [1] 11.8608
## 
## $EstimatedSalary
## [1] 31134.6

Data Processing

Converting character variables into factors

Explanation

To ensure that R’s data science models work correctly, all categorical dependent variables must be explicitly converted into factors. As for the independent variables, if the variable is both categorical and has more than two levels, then it should be converted into a factor.

input_data <- as.data.frame(lapply(input_data, function(x) if(is.character(x)){
  x=as.factor(x)
} else x))

Sorting data set

Explanation

Useful for examinating the data values. By sorting the data, one can tell if there are missing or corrupted data values.

input_data <- input_data[order(input_data[,1]),]
glimpse(input_data)
## Rows: 400
## Columns: 5
## $ User.ID         <fct> 15566689, 15569641, 15570769, 15570932, 15571059, 1...
## $ Gender          <fct> Female, Female, Female, Male, Female, Female, Male,...
## $ Age             <dbl> 35, 58, 26, 34, 33, 21, 40, 35, 58, 35, 48, 35, 41,...
## $ EstimatedSalary <dbl> 57000, 95000, 80000, 115000, 41000, 16000, 71000, 5...
## $ Purchased       <fct> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, ...
input_data <- input_data[order(-input_data[,1]),]
glimpse(input_data)
## Rows: 400
## Columns: 5
## $ User.ID         <fct> 15566689, 15569641, 15570769, 15570932, 15571059, 1...
## $ Gender          <fct> Female, Female, Female, Male, Female, Female, Male,...
## $ Age             <dbl> 35, 58, 26, 34, 33, 21, 40, 35, 58, 35, 48, 35, 41,...
## $ EstimatedSalary <dbl> 57000, 95000, 80000, 115000, 41000, 16000, 71000, 5...
## $ Purchased       <fct> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, ...

Replacing missing values with mean or NA

Explanation

These missing values could cause inaccuracies or errors when calculating data limits, central tendency, dispersion tendency, correlation, multicollinearity, p-values, z-scores, variance inflation factors, etc.

input_data <- as.data.frame(lapply(input_data, function(x) if(is.numeric(x) && is.na(x)){
  mean(x, na.rm = TRUE)
} else { if(is.character(x) && is.na(x)){x = "NA"} else x }
))
glimpse(input_data)
## Rows: 400
## Columns: 5
## $ User.ID         <fct> 15566689, 15569641, 15570769, 15570932, 15571059, 1...
## $ Gender          <fct> Female, Female, Female, Male, Female, Female, Male,...
## $ Age             <dbl> 35, 58, 26, 34, 33, 21, 40, 35, 58, 35, 48, 35, 41,...
## $ EstimatedSalary <dbl> 57000, 95000, 80000, 115000, 41000, 16000, 71000, 5...
## $ Purchased       <fct> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, ...

Scaling numeric variables

Explanation

These numeric variables are centered and standardized between -1 and 1. In order to correctly calculate the distances between data points, the values of each variable have to be on the same scale. Also, it is easier to fit smaller numbers onto the axes of a graph.

Function for standardizing data values

Standardization = (x - mean(x))/std(x)

input_data <- as.data.frame(lapply(input_data, function(x) if(is.numeric(x)){
  (x - mean(x)) / sd(x)
} else x))

str(input_data)
## 'data.frame':    400 obs. of  5 variables:
##  $ User.ID        : Factor w/ 400 levels "15566689","15569641",..: 1 2 3 4 5 6 7 8 9 10 ...
##  $ Gender         : Factor w/ 2 levels "Female","Male": 1 1 1 2 1 1 2 2 1 1 ...
##  $ Age            : num  -0.253 1.941 -1.112 -0.349 -0.444 ...
##  $ EstimatedSalary: num  -0.374 0.741 0.301 1.327 -0.843 ...
##  $ Purchased      : Factor w/ 2 levels "0","1": 1 2 1 1 1 1 2 1 2 1 ...
glimpse(input_data)
## Rows: 400
## Columns: 5
## $ User.ID         <fct> 15566689, 15569641, 15570769, 15570932, 15571059, 1...
## $ Gender          <fct> Female, Female, Female, Male, Female, Female, Male,...
## $ Age             <dbl> -0.25327018, 1.94078408, -1.11181315, -0.34866384, ...
## $ EstimatedSalary <dbl> -0.37371367, 0.74075518, 0.30083327, 1.32731773, -0...
## $ Purchased       <fct> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, ...

Descriptive statistics after data processing

Dimension of data frame

dim(input_data)
## [1] 400   5

Structure of data frame

str(input_data)
## 'data.frame':    400 obs. of  5 variables:
##  $ User.ID        : Factor w/ 400 levels "15566689","15569641",..: 1 2 3 4 5 6 7 8 9 10 ...
##  $ Gender         : Factor w/ 2 levels "Female","Male": 1 1 1 2 1 1 2 2 1 1 ...
##  $ Age            : num  -0.253 1.941 -1.112 -0.349 -0.444 ...
##  $ EstimatedSalary: num  -0.374 0.741 0.301 1.327 -0.843 ...
##  $ Purchased      : Factor w/ 2 levels "0","1": 1 2 1 1 1 1 2 1 2 1 ...

Summary statistics of data frame

summary(input_data)
##      User.ID       Gender         Age           EstimatedSalary     Purchased
##  15566689:  1   Female:204   Min.   :-1.87496   Min.   :-1.605495   0:257    
##  15569641:  1   Male  :196   1st Qu.:-0.75409   1st Qu.:-0.784308   1:143    
##  15570769:  1                Median :-0.06248   Median : 0.007552            
##  15570932:  1                Mean   : 0.00000   Mean   : 0.000000            
##  15571059:  1                3rd Qu.: 0.79606   3rd Qu.: 0.535458            
##  15573452:  1                Max.   : 2.13157   Max.   : 2.353802            
##  (Other) :394

Glimpse of data frame

glimpse(input_data)
## Rows: 400
## Columns: 5
## $ User.ID         <fct> 15566689, 15569641, 15570769, 15570932, 15571059, 1...
## $ Gender          <fct> Female, Female, Female, Male, Female, Female, Male,...
## $ Age             <dbl> -0.25327018, 1.94078408, -1.11181315, -0.34866384, ...
## $ EstimatedSalary <dbl> -0.37371367, 0.74075518, 0.30083327, 1.32731773, -0...
## $ Purchased       <fct> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, ...

Head of data frame

head(input_data)
##    User.ID Gender        Age EstimatedSalary Purchased
## 1 15566689 Female -0.2532702      -0.3737137         0
## 2 15569641 Female  1.9407841       0.7407552         1
## 3 15570769 Female -1.1118131       0.3008333         0
## 4 15570932   Male -0.3486638       1.3273177         0
## 5 15571059 Female -0.4440575      -0.8429637         0
## 6 15573452 Female -1.5887815      -1.5761669         0

Tail of data frame

tail(input_data)
##      User.ID Gender        Age EstimatedSalary Purchased
## 395 15811613 Female -0.1578765       0.1541926         0
## 396 15813113   Male  0.2236981       1.0926927         1
## 397 15814004   Male -1.0164195      -1.4588544         0
## 398 15814553   Male  1.8453904      -0.2857293         1
## 399 15814816   Male -0.6348448      -0.1097605         0
## 400 15815236 Female  0.7006665       1.7965678         1

Variable data types

sapply(input_data,mode)
##         User.ID          Gender             Age EstimatedSalary       Purchased 
##       "numeric"       "numeric"       "numeric"       "numeric"       "numeric"

Mean of each variable

lapply(input_data[,num.names],mean)
## $Age
## [1] -1.050681e-16
## 
## $EstimatedSalary
## [1] 6.539365e-18

Median of each variable

lapply(input_data[,num.names],median)
## $Age
## [1] -0.06248285
## 
## $EstimatedSalary
## [1] 0.007551993

Mode of each variable

lapply(input_data[,num.names],mfv)
## $Age
## [1] -0.2532702
## 
## $EstimatedSalary
## [1] 0.06620825

Minimum value of each variable

lapply(input_data[,num.names],min)
## $Age
## [1] -1.874962
## 
## $EstimatedSalary
## [1] -1.605495

Maximum value of each variable

lapply(input_data[,num.names],max)
## $Age
## [1] 2.131571
## 
## $EstimatedSalary
## [1] 2.353802

Range of each variable

lapply(input_data[,num.names],range)
## $Age
## [1] -1.874962  2.131571
## 
## $EstimatedSalary
## [1] -1.605495  2.353802

Variance of each variable

lapply(input_data[,num.names],var)
## $Age
## [1] 1
## 
## $EstimatedSalary
## [1] 1

Standard deviation of each variable

lapply(input_data[,num.names],sd)
## $Age
## [1] 1
## 
## $EstimatedSalary
## [1] 1

Median absolute deviation of each variable

lapply(input_data[,num.names],mad)
## $Age
## [1] 1.131445
## 
## $EstimatedSalary
## [1] 0.9131195

Plots and Graphs

Box plots

Explanation

This box plot reveals the mean value, minimum value, and maximum value of each variable.

Observation

It appears that both Age and Estimated Salary are pretty much centered at 0. However, if it is broken down by the factor level of the target variable Purchased, each predictor variable appears to have a higher mean for transactions in which the customers did make a purchase.

oldw <- getOption("warn")
options(warn = -1)
boxplot(input_data[,num.names])

options(warn = oldw)
oldw <- getOption("warn")
options(warn = -1)
ggplot(data = input_data, aes(y=Age)) + geom_boxplot(aes(fill=Purchased))+ggtitle("Box Plot of Age")

ggplot(data = input_data, aes(y=EstimatedSalary)) + geom_boxplot(aes(fill=Purchased))+ggtitle("Box Plot of Estimated Salary")

options(warn = oldw)

Histograms

Explanation

The purpose of these histograms is to see the frequency of each predictor variable under each factor level of the target variable.

Observation

It appears that the majority of the purchases were made by customers who have low salaries.

oldw <- getOption("warn")
options(warn = -1)
hist(input_data$Age, main = "Histogram of Age", xlab="Age")

hist(input_data$EstimatedSalary, main = "Histogram of Estimated Salary", xlab="Estimated Salary")

options(warn = oldw)
oldw <- getOption("warn")
options(warn = -1)
ggplot(data = input_data, aes(x=Age, fill=Purchased, color=Purchased)) + geom_histogram(alpha=0.6)+ggtitle("Histogram of Age")

ggplot(data = input_data, aes(x=EstimatedSalary, fill=Purchased, color=Purchased)) + geom_histogram(alpha=0.6)+ggtitle("Histogram of Estimated Salary")

options(warn = oldw)

Grubbs’s Outlier Test

Explanation

This is a test to check for the existence of outliers associated with each independent variable in the data frame. This test is based on Z-Scores. The function’s null hypothesis is that there are no outliers. If the p-value is smaller than 0.05, then the null hypothesis could be rejected, and the alternative hypothesis that there is at least one outlier could be accepted. The two-tail test is carried out for this data frame.

Observation

All variables have p-values smaller than 0.05. Given a significant cut-off point of 0.05, all these variables have outliers.

# Detect outliers via z-score
grubbs.test(input_data$Age,two.sided=TRUE,type=11)
## 
##  Grubbs test for two opposite outliers
## 
## data:  input_data$Age
## G = 4.0065, U = 0.9798, p-value < 2.2e-16
## alternative hypothesis: -1.87496245115082 and 2.1315714052895 are outliers
grubbs.test(input_data$EstimatedSalary,two.sided=TRUE,type=11)
## 
##  Grubbs test for two opposite outliers
## 
## data:  input_data$EstimatedSalary
## G = 3.95930, U = 0.97965, p-value < 2.2e-16
## alternative hypothesis: -1.60549502203623 and 2.35380219630219 are outliers

Correlation Analysis

Explanation

The correlation statistics reveal the degree of associations between variables in the data set. Given a range between 0 and 1, a correlation value less than 0.5 in either direction indicates a weak correlation, and a value equal to or greater than 0.5 in either direction indicates a moderate to strong correlation.

Observation

It appears that none of the variables have correlation coefficient greater than 0.5.

Correlation Plot

oldw <- getOption("warn")
options(warn = -1)
pairs.panels(input_data[,num.names],gap=0,bg=c("green","red","yellow","blue","pink","purple"),pch= 21, cex=0.5)

options(warn = oldw)

Correlation Table

oldw <- getOption("warn")
options(warn = -1)
cor(input_data[,num.names])
##                      Age EstimatedSalary
## Age             1.000000        0.155238
## EstimatedSalary 0.155238        1.000000
options(warn = oldw)

Preparation of Training and Test Data Sets

Explanation

The purpose of creating separate data sets for training and testing the model is because we want to see how differently the model would perform with data that it has never seen before.

oldw <- getOption("warn")
options(warn = -1)

set.seed(123)
df <- input_data[,c(3,4,5)]
ind <- sample(2, nrow(input_data), replace=T, prob=c(0.6,0.4))
df_sample_train <- df[ind==1,]
df_sample_test <- df[ind==2,]
options(warn = oldw)

Single-Layer Perceptrons Neural Network

Using Neuralnet

Explanation

As the “neural” part of their name suggests, they are brain-inspired systems which are intended to replicate the way that we humans learn. Neural networks consist of input and output layers, as well as (in most cases) a hidden layer consisting of neurons that transform the input into something that the output layer can use. In case of a single-layer perceptrons, there is no hidden layer. They are excellent tools for finding patterns which are far too complex or numerous for a human programmer to extract and teach the machine to recognize.

Interpretation

After training the model with 100 repeats and layers of 5 neurons each, the model predictively ability reached 81.4% accuracy, 83.64% sensitivity, 80% specificity, and a Kappa statistic of 0.61. An accuracy percentage of 81.4% means that the model can predict 81.4% of both the true negatives and true positives. A sensitivity of 83.64% means that the model can predict 83.64% of the true positives. A specificity percentage of 80% means that the model can predict 80% of the true negatives. A Kappa statistic of 0.61 means that the instances classified by the model matched the output labels 61% of the time. If compared to the Raw Implementation, Neuralnet has a slightly lower accuracy percentage.

oldw <- getOption("warn")
options(warn = -1)

# Making sure the target variable is in numeric format
df_sample_train$Purchased = as.integer(as.character(df_sample_train$Purchased))
df_sample_test$Purchased = as.integer(as.character(df_sample_test$Purchased))

# neuralnet cannot accept y~. as formula
nn_train <- neuralnet(formula=Purchased~Age+EstimatedSalary, data=df_sample_train, hidden=0, act.fct = "logistic", linear.output=FALSE, rep=100) #linear.output=FALSE is neccessary for classifcation NN

# Neural Network Result
head(as.data.frame(nn_train$result.matrix), n=5)
##                                  V1            V2            V3           V4
## error                  11.059271306  11.059077415  11.059273842 11.059229745
## reached.threshold       0.009878695   0.009526415   0.008802204  0.007929586
## steps                  72.000000000 116.000000000 107.000000000 85.000000000
## Intercept.to.Purchased -1.006527757  -1.011272341  -1.007888882 -1.007248311
## Age.to.Purchased        4.006363167   4.028986345   4.007153594  4.010458597
##                                   V5            V6           V7          V8
## error                   11.059131503  11.059176898  11.05910045 11.05931784
## reached.threshold        0.007663115   0.008140279   0.00930926  0.00966322
## steps                  120.000000000 102.000000000 120.00000000 92.00000000
## Intercept.to.Purchased  -1.008061746  -1.008012441  -1.01078711 -1.00443101
## Age.to.Purchased         4.019883048   4.015286049   4.02410662  4.00366746
##                                  V9           V10           V11           V12
## error                  11.059179190  11.059050019  11.059081449  11.059059468
## reached.threshold       0.008646881   0.007810222   0.007006843   0.007861171
## steps                  96.000000000 111.000000000 108.000000000 107.000000000
## Intercept.to.Purchased -1.009798139  -1.011458163  -1.008765157  -1.011095941
## Age.to.Purchased        4.016044608   4.030347374   4.025778819   4.028973482
##                                  V13           V14           V15           V16
## error                   11.059127002  11.059290044  11.059255970  11.059084280
## reached.threshold        0.008629314   0.009958285   0.007425126   0.009433234
## steps                  112.000000000 107.000000000 102.000000000 113.000000000
## Intercept.to.Purchased  -1.008292553  -1.004707178  -1.005246477  -1.011846904
## Age.to.Purchased         4.020296384   4.006203957   4.008012917   4.026686478
##                                  V17           V18         V19          V20
## error                   11.059183685  11.059232360 11.05939523 11.059123561
## reached.threshold        0.008535515   0.009924924  0.00982961  0.008416146
## steps                  105.000000000 111.000000000 86.00000000 79.000000000
## Intercept.to.Purchased  -1.007249153  -1.006193608 -1.00354962 -1.007991301
## Age.to.Purchased         4.014390540   4.009608047  3.99641299  4.020698857
##                                  V21          V22           V23         V24
## error                   11.059107956 11.059250437  11.059127493 11.05926220
## reached.threshold        0.007885998  0.009286286   0.008915809  0.00893357
## steps                  121.000000000 72.000000000 128.000000000 84.00000000
## Intercept.to.Purchased  -1.008778114 -1.005559764  -1.009618147 -1.00496661
## Age.to.Purchased         4.022518545  4.008062405   4.020619209  4.00713336
##                                  V25           V26           V27           V28
## error                   11.059175740  11.059123856  11.059190724  11.059162277
## reached.threshold        0.008977766   0.009387454   0.007896632   0.009352247
## steps                  129.000000000 115.000000000 105.000000000 103.000000000
## Intercept.to.Purchased  -1.007423130  -1.008407412  -1.007448084  -1.007310327
## Age.to.Purchased         4.015124755   4.020663260   4.013901789   4.016473573
##                                 V29           V30           V31        V32
## error                  11.059140872  11.059235960  11.059133854 11.0591071
## reached.threshold       0.008489665   0.009809328   0.008095016  0.0077181
## steps                  95.000000000 107.000000000 102.000000000 92.0000000
## Intercept.to.Purchased -1.009790875  -1.005153554  -1.007789333 -1.0089469
## Age.to.Purchased        4.019473280   4.009439585   4.019574344  4.0226565
##                                  V33           V34           V35           V36
## error                   11.059073928  11.059066837  11.059111638  11.059089444
## reached.threshold        0.009518364   0.009080503   0.008105408   0.009073575
## steps                  120.000000000 113.000000000 116.000000000 124.000000000
## Intercept.to.Purchased  -1.010238614  -1.010669648  -1.009939504  -1.009851693
## Age.to.Purchased         4.026935181   4.027905744   4.022498859   4.026730873
##                                 V37           V38          V39         V40
## error                  11.059276054  11.059054313 11.059254331 11.05913086
## reached.threshold       0.008816792   0.008932634  0.009187266  0.00887198
## steps                  54.000000000 130.000000000 78.000000000 93.00000000
## Intercept.to.Purchased -1.006248820  -1.011345959 -1.007836465 -1.00765028
## Age.to.Purchased        4.006126549   4.031683647  4.008473298  4.01990797
##                                  V41           V42        V43          V44
## error                   11.059205989  11.059247338 11.0592275 11.059144909
## reached.threshold        0.009200441   0.009507909  0.0091811  0.008959096
## steps                  117.000000000 107.000000000 93.0000000 96.000000000
## Intercept.to.Purchased  -1.005700066  -1.006330977 -1.0076605 -1.008868768
## Age.to.Purchased         4.012272016   4.008352184  4.0105129  4.018531654
##                                V45           V46           V47          V48
## error                  11.05921139  11.059242766  11.059201632 11.059246191
## reached.threshold       0.00912173   0.009348176   0.009317124  0.009868915
## steps                  64.00000000 114.000000000 107.000000000 93.000000000
## Intercept.to.Purchased -1.00491760  -1.005797868  -1.007471503 -1.004757171
## Age.to.Purchased        4.01210141   4.008730425   4.012656237  4.008592087
##                                  V49           V50           V51           V52
## error                   11.059088590  11.059157952  11.059139168  11.059261879
## reached.threshold        0.008861396   0.009942644   0.008284701   0.009738609
## steps                  133.000000000 120.000000000 126.000000000 100.000000000
## Intercept.to.Purchased  -1.010047730  -1.008739082  -1.009395624  -1.005501414
## Age.to.Purchased         4.025021035   4.017138241   4.019430435   4.006995212
##                                V53          V54          V55           V56
## error                   11.0591753 11.059156254 11.059270126  11.059125669
## reached.threshold        0.0088874  0.007893245  0.007403058   0.008106747
## steps                  123.0000000 91.000000000 68.000000000 103.000000000
## Intercept.to.Purchased  -1.0070434 -1.007005796 -1.005872437  -1.008471847
## Age.to.Purchased         4.0151658  4.017252139  4.007083764   4.020497573
##                                 V57           V58          V59          V60
## error                  11.059164471  11.059130525 11.059124230 11.059499082
## reached.threshold       0.007942492   0.009869703  0.008022102  0.009552857
## steps                  87.000000000 108.000000000 92.000000000 78.000000000
## Intercept.to.Purchased -1.007035919  -1.008052746 -1.007053770 -1.002765724
## Age.to.Purchased        4.017583273   4.019958137  4.020922476  3.989445276
##                                  V61          V62           V63           V64
## error                   11.059150516 11.059353768  11.059162291  11.059092731
## reached.threshold        0.009785793  0.009855779   0.009974099   0.008524386
## steps                  114.000000000 71.000000000 115.000000000 122.000000000
## Intercept.to.Purchased  -1.008014812 -1.003634544  -1.009080940  -1.009754426
## Age.to.Purchased         4.017726739  3.999511593   4.018721663   4.024437987
##                                  V65           V66           V67          V68
## error                   11.059256877  11.059190496  11.059198918  11.05931855
## reached.threshold        0.009738715   0.008999318   0.008678656   0.00959872
## steps                  112.000000000 114.000000000 105.000000000 103.00000000
## Intercept.to.Purchased  -1.006005691  -1.008494164  -1.006820358  -1.00479096
## Age.to.Purchased         4.008971221   4.014114396   4.012879827   4.00231099
##                                  V69           V70          V71          V72
## error                   11.059100756  11.059214127 11.059258918 11.059078436
## reached.threshold        0.007339124   0.009071242  0.009827834  0.009287193
## steps                  135.000000000 116.000000000 83.000000000 96.000000000
## Intercept.to.Purchased  -1.008468014  -1.005710128 -1.005368740 -1.007704454
## Age.to.Purchased         4.023398911   4.011460883  4.007252144  4.028457519
##                                 V73         V74           V75          V76
## error                  11.059244271 11.05913767  11.059144002 11.059194838
## reached.threshold       0.009669865  0.00959015   0.009495725  0.009368973
## steps                  89.000000000 98.00000000 101.000000000 98.000000000
## Intercept.to.Purchased -1.006597594 -1.00893448  -1.008595483 -1.006273727
## Age.to.Purchased        4.008644078  4.01925848   4.018504538  4.013242732
##                                  V77           V78           V79          V80
## error                   11.059216156  11.059121216  11.059114383  11.05914935
## reached.threshold        0.009860672   0.007376398   0.009687434   0.00838519
## steps                  103.000000000 104.000000000 113.000000000 132.00000000
## Intercept.to.Purchased  -1.006790540  -1.007329814  -1.009378170  -1.00919436
## Age.to.Purchased         4.012875154   4.021193415   4.021900737   4.01833290
##                                  V81           V82           V83          V84
## error                   11.059100580  11.059112829  11.059172910 11.059241979
## reached.threshold        0.007774792   0.009745111   0.009008136  0.008861744
## steps                  110.000000000 113.000000000 114.000000000 87.000000000
## Intercept.to.Purchased  -1.009898955  -1.008686120  -1.007190100 -1.006500568
## Age.to.Purchased         4.023685515   4.024063864   4.015391776  4.008961686
##                                 V85           V86           V87           V88
## error                  11.059372397  11.059169628  11.059133490  11.059187086
## reached.threshold       0.009612282   0.009087914   0.008460542   0.009939838
## steps                  89.000000000 102.000000000 110.000000000 103.000000000
## Intercept.to.Purchased -1.005302285  -1.007468174  -1.008204051  -1.006872383
## Age.to.Purchased        3.998509222   4.015726700   4.019590761   4.015884598
##                                 V89          V90           V91           V92
## error                  11.059145678 11.059161225  11.059118063  11.059151681
## reached.threshold       0.009395439  0.009087876   0.009929384   0.009394086
## steps                  99.000000000 87.000000000 107.000000000 112.000000000
## Intercept.to.Purchased -1.007008656 -1.005994505  -1.009394197  -1.008183405
## Age.to.Purchased        4.020360277  4.017091738   4.021515176   4.017625178
##                                V93          V94           V95          V96
## error                  11.05917573 11.059337089  11.059067051 11.059221958
## reached.threshold       0.00761517  0.009872248   0.007027954  0.009484249
## steps                  99.00000000 92.000000000 100.000000000 69.000000000
## Intercept.to.Purchased -1.00578702 -1.002985662  -1.010854645 -1.006204334
## Age.to.Purchased        4.01558741  4.001046420   4.028027010  4.010605359
##                                V97           V98           V99         V100
## error                  11.05920347  11.059145541  11.059138904 11.059170688
## reached.threshold       0.00851572   0.008946364   0.007672549  0.009795812
## steps                  89.00000000 109.000000000 120.000000000 99.000000000
## Intercept.to.Purchased -1.00615017  -1.010049422  -1.007932043 -1.007962992
## Age.to.Purchased        4.01248547   4.019147446   4.019085605  4.015656871
# Neural Network Plot 
plot(nn_train, rep="best") #rep="best" must be included

# Test the neural network on some test data
nn_pred <- compute(nn_train, df_sample_test)

options(warn = oldw)

Confusion Matrix

Explanation

Comparison between the predicted values and actual observed values. Calculate the average accuracy statistics.

oldw <- getOption("warn")
options(warn = -1)
# nn_pred$net.result
pred_simo <- ifelse(nn_pred$net.result>0.5, 1, 0)
# head(pred_simo, n=5)
table(pred_simo)
## pred_simo
##  0  1 
## 90 66
table(df_sample_test$Purchased)
## 
##   0   1 
## 101  55
# table(Predicted=pred_simo,Actual=df_sample_test$Purchased)
confusionMatrix( table(Predicted=pred_simo,Actual=df_sample_test$Purchased), positive='1' )
## Confusion Matrix and Statistics
## 
##          Actual
## Predicted  0  1
##         0 81  9
##         1 20 46
##                                           
##                Accuracy : 0.8141          
##                  95% CI : (0.7441, 0.8718)
##     No Information Rate : 0.6474          
##     P-Value [Acc > NIR] : 3.674e-06       
##                                           
##                   Kappa : 0.6105          
##                                           
##  Mcnemar's Test P-Value : 0.06332         
##                                           
##             Sensitivity : 0.8364          
##             Specificity : 0.8020          
##          Pos Pred Value : 0.6970          
##          Neg Pred Value : 0.9000          
##              Prevalence : 0.3526          
##          Detection Rate : 0.2949          
##    Detection Prevalence : 0.4231          
##       Balanced Accuracy : 0.8192          
##                                           
##        'Positive' Class : 1               
## 
options(warn = oldw)

Single-Layer Perceptrons Neural Network

Raw Implementation

Description

This is the raw implementation of a Single-Layer Perceptions Neural Network. This implementation is inspired by my own understanding of how a neural network works.

Interpretation

After training the model with 10 neurons, learning rate of 0.001, and 100,000 iterations, the model was able to achieve a 95% accuracy. Since there is only one layer of neurons, there might be a problem with overfitting. However, the testing result is surprisingly good. When running the model against the test data, it was able to achieve an 83% accuracy.

oldw <- getOption("warn")
options(warn = -1)

# Making sure the target variable is in the factor format
df_sample_train$Purchased = as.factor(as.character(df_sample_train$Purchased))
df_sample_test$Purchased = as.factor(as.character(df_sample_test$Purchased))

# This functin is to convert the matrix values to a scale between -1 and 1
standardFN <- function(x) 1 / (1 + exp(-x))

# X is a matrix of predictor variable values. wgt1 and wgt2 are matrices of the assigned weights.
feedforwardNN <- function(x, wgt1, wgt2) {
# This function does both a compound multiplication and a sum product of weights+bias (wgt1,wgt2) with the input data values. At the final stage, it sum up each resulting row of products into a single column. A a vector of random bias values between 0 and 1 is used. By default, runif generates random numbers between 0 and 1.
# The cbind function adds a bias vector of 1's to the matrix. R matrix multiplication of A %*% B requires that total column number of A must match total row number of B.
  
  set.seed(123) # Set reproduciblity for runif.
  cal1 <- cbind(runif(nrow(x)), x) %*% wgt1 # Result in a matrix of n columns
  calSD <- standardFN(cal1) 
  cal2 <- cbind(runif(nrow(calSD)), calSD) %*% wgt2 # Result in a matrix of 1 column  
  list(output = standardFN(cal2), cal1=cal1, cal2=cal2, calSD=calSD)
}

backpropagateNN <- function(x, y, yHAT, wgt1, wgt2, m1, learnRate) {
# Using the the differences between predicted outputs and the actual outputs to re-calcuate the weights.
# Since R matrix mulitplication requires that matrix A's number of columns must match with matrix B's number of rows, matrix A in this case has to be tranpsosed.
# y is either a 0 or 1. yHAT is a numeric value between -1 and 1.

  set.seed(123) # Set reproduciblity for runif.
  nm1  <- (yHAT - y) %*% t(wgt2[-1, , drop = FALSE])
  nwgt1 <- t(cbind(runif(nrow(x)), x)) %*% (m1 * (1 - m1) * nm1)
  nwgt2 <- t(cbind(runif(nrow(x)), m1)) %*% (yHAT - y)
  wgt1 <- wgt1 - learnRate * nwgt1
  wgt2 <- wgt2 - learnRate * nwgt2
  list(wgt1 = wgt1, wgt2 = wgt2)
}

# Defaults of 1 neuron, learn rate of 0.01, and 10 iteration
trainNN <- function(x, y, neurons = 1, learnRate = 0.01, iterates = 10) {
  set.seed(123) # Set reproducibility for rnorm.
  inp <- ncol(x) + 1 # Number of inputs
  wgt1 <- matrix(0.1*rnorm(inp * neurons), inp, neurons) # First initial weight matrix of 'inp' rows and 'neurons' columns
  wgt2 <- as.matrix(0.1*rnorm(neurons + 1)) # Second initial weight matrix. A single-column matrix of (neurons + 1) rows.
  
  for (i in 1:iterates) {
    ff <- feedforwardNN(x, wgt1, wgt2)
    bp <- backpropagateNN(x, y,
                          yHAT = ff$output,
                          wgt1, wgt2,
                          m1 = ff$calSD,
                          learnRate = learnRate)
    wgt1 <- bp$wgt1; wgt2 <- bp$wgt2
  }
  list(output = ff$output, wgt1 = wgt1, wgt2 = wgt2)
}

x <-data.matrix(df_sample_train[,c(1, 2)]) # Matrix of inputs   
y <- df_sample_train$Purchased == '1' # Boolean of outputs

# Training the algorithm with 10 neurons, learn rate of 0.001, and 100,000 iterations
nnOBJ <- trainNN(x, y, neurons = 10, learnRate = 0.001, iterates = 1e5) 

# Model Accuracy Percentage
mean((nnOBJ$output > .5) == y)
## [1] 0.9467213
# Plotting the training result
gridTrainBG <- expand.grid(x1 = seq(min(df_sample_train$Age)-1,
                             max(df_sample_train$Age)+1,
                             by = .03),
                    x2 = seq(min(df_sample_train$EstimatedSalary)-1,
                             max(df_sample_train$EstimatedSalary)+1,
                             by = .03))

gridTrainOBJ <- feedforwardNN(x = data.matrix(gridTrainBG[, c('x1', 'x2')]), wgt1 = nnOBJ$wgt1, wgt2 = nnOBJ$wgt2)

gridTrainBG$class <- factor( (gridTrainOBJ$output > .5) * 1, labels = levels(df_sample_train$Purchased) )

ggplot() + 
geom_point(data = gridTrainBG, aes(x=x1, y=x2, colour = class), size = .25) + 
geom_point(data = df_sample_train, aes(x=Age, y=EstimatedSalary, colour = Purchased)) +
labs(x = 'Age', y = 'Estimated Salary') +
ggtitle("Single-Layer Neural Network Training Result") 

# Pediction Accuracy Percentage
y <- df_sample_test$Purchased == '1' # Boolean of outputs
testOBJ <- feedforwardNN(x = data.matrix(df_sample_test[,1:2]), wgt1 = nnOBJ$wgt1, wgt2 = nnOBJ$wgt2)
mean((testOBJ$output > .5) == y)
## [1] 0.8269231
# Plotting the testing result
gridTestBG <- expand.grid(x1 = seq(min(df_sample_test$Age)-1,
                             max(df_sample_test$Age)+1,
                             by = .03),
                    x2 = seq(min(df_sample_test$EstimatedSalary)-1,
                             max(df_sample_test$EstimatedSalary)+1,
                             by = .03))

gridTestOBJ <- feedforwardNN(x = data.matrix(gridTestBG[, c('x1', 'x2')]), wgt1 = nnOBJ$wgt1, wgt2 = nnOBJ$wgt2)
gridTestBG$class <- factor( (gridTestOBJ$output > .5) * 1, labels = levels(df_sample_test$Purchased) )

ggplot() + 
geom_point(data = gridTestBG, aes(x=x1, y=x2, colour = class), size = .25) + 
geom_point(data = df_sample_test, aes(x=Age, y=EstimatedSalary, colour = Purchased)) +
labs(x = 'Age', y = 'Estimated Salary') +
ggtitle("Single-Layer Neural Network Testing Result") 

options(warn = oldw)

Process Runtime

end_time <- Sys.time()
end_time - start_time
## Time difference of 57.20434 secs