Chapter 4 Exercise 13

(a). Produce some numerical and graphical summaries of the Weekly data. Do there appear to be any patterns?

library(ISLR)
summary(Weekly)
##       Year           Lag1               Lag2               Lag3         
##  Min.   :1990   Min.   :-18.1950   Min.   :-18.1950   Min.   :-18.1950  
##  1st Qu.:1995   1st Qu.: -1.1540   1st Qu.: -1.1540   1st Qu.: -1.1580  
##  Median :2000   Median :  0.2410   Median :  0.2410   Median :  0.2410  
##  Mean   :2000   Mean   :  0.1506   Mean   :  0.1511   Mean   :  0.1472  
##  3rd Qu.:2005   3rd Qu.:  1.4050   3rd Qu.:  1.4090   3rd Qu.:  1.4090  
##  Max.   :2010   Max.   : 12.0260   Max.   : 12.0260   Max.   : 12.0260  
##       Lag4               Lag5              Volume            Today         
##  Min.   :-18.1950   Min.   :-18.1950   Min.   :0.08747   Min.   :-18.1950  
##  1st Qu.: -1.1580   1st Qu.: -1.1660   1st Qu.:0.33202   1st Qu.: -1.1540  
##  Median :  0.2380   Median :  0.2340   Median :1.00268   Median :  0.2410  
##  Mean   :  0.1458   Mean   :  0.1399   Mean   :1.57462   Mean   :  0.1499  
##  3rd Qu.:  1.4090   3rd Qu.:  1.4050   3rd Qu.:2.05373   3rd Qu.:  1.4050  
##  Max.   : 12.0260   Max.   : 12.0260   Max.   :9.32821   Max.   : 12.0260  
##  Direction 
##  Down:484  
##  Up  :605  
##            
##            
##            
## 
library(corrplot)
## corrplot 0.92 loaded
corrplot(cor(Weekly[,-9]), method="square")

(b). Use the full data set to perform a logistic regression with Direction as the response and the five lag variables plus Volume as predictors. Use the summary function to print the results. Do any of the predictors appear to be statistically significant? If so, which ones?

Weekly.fit<-glm(Direction~Lag1+Lag2+Lag3+Lag4+Lag5+Volume, data=Weekly,family='binomial')
summary(Weekly.fit)
## 
## Call:
## glm(formula = Direction ~ Lag1 + Lag2 + Lag3 + Lag4 + Lag5 + 
##     Volume, family = "binomial", data = Weekly)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.6949  -1.2565   0.9913   1.0849   1.4579  
## 
## Coefficients:
##             Estimate Std. Error z value Pr(>|z|)   
## (Intercept)  0.26686    0.08593   3.106   0.0019 **
## Lag1        -0.04127    0.02641  -1.563   0.1181   
## Lag2         0.05844    0.02686   2.175   0.0296 * 
## Lag3        -0.01606    0.02666  -0.602   0.5469   
## Lag4        -0.02779    0.02646  -1.050   0.2937   
## Lag5        -0.01447    0.02638  -0.549   0.5833   
## Volume      -0.02274    0.03690  -0.616   0.5377   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1496.2  on 1088  degrees of freedom
## Residual deviance: 1486.4  on 1082  degrees of freedom
## AIC: 1500.4
## 
## Number of Fisher Scoring iterations: 4

(c). Compute the confusion matrix and overall fraction of correct predictions. Explain what the confusion matrix is telling you about the types of mistakes made by logistic regression.

glm_probs_wk = predict(Weekly.fit, type = "response")
glm_pred_wk = rep("Down", length(glm_probs_wk)) 
glm_pred_wk[glm_probs_wk > 0.5] <- "Up"

table(glm_pred_wk, Weekly$Direction)
##            
## glm_pred_wk Down  Up
##        Down   54  48
##        Up    430 557
mean(glm_pred_wk == Weekly$Direction)
## [1] 0.5610652

(d). Now fit the logistic regression model using a training data period from 1990 to 2008, with Lag2 as the only predictor. Compute the confusion matrix and the overall fraction of correct predictions for the held out data (that is, the data from 2009 and 2010).

training.data = Weekly[Weekly$Year<2009,]
test.data = Weekly[Weekly$Year>2008,]
simpglm = glm(Direction~Lag2, data= training.data, family = "binomial")
summary(simpglm)
## 
## Call:
## glm(formula = Direction ~ Lag2, family = "binomial", data = training.data)
## 
## Deviance Residuals: 
##    Min      1Q  Median      3Q     Max  
## -1.536  -1.264   1.021   1.091   1.368  
## 
## Coefficients:
##             Estimate Std. Error z value Pr(>|z|)   
## (Intercept)  0.20326    0.06428   3.162  0.00157 **
## Lag2         0.05810    0.02870   2.024  0.04298 * 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1354.7  on 984  degrees of freedom
## Residual deviance: 1350.5  on 983  degrees of freedom
## AIC: 1354.5
## 
## Number of Fisher Scoring iterations: 4
logistic_probs <- predict(simpglm, test.data)
logistic_pred = rep("Down", length(test.data$Direction))
logistic_pred[logistic_probs > 0.5] <- "Up"
table(logistic_pred, test.data$Direction)
##              
## logistic_pred Down Up
##          Down   41 56
##          Up      2  5
mean(logistic_pred == test.data$Direction)
## [1] 0.4423077

(e). Repeat (d) using LDA

library(MASS)
lda_wkly <- lda(Direction ~ Lag2, data = training.data)
lda_probs <- predict(lda_wkly, test.data)
table(lda_probs$class, test.data$Direction)
##       
##        Down Up
##   Down    9  5
##   Up     34 56
mean(lda_probs$class == test.data$Direction)
## [1] 0.625

(f). Repeat (d) using QDA.

qda_wkly <- qda(Direction ~ Lag2, data = training.data)
qda_pred <- predict(qda_wkly, test.data)
table(qda_pred$class, test.data$Direction)
##       
##        Down Up
##   Down    0  0
##   Up     43 61
mean(qda_pred$class == test.data$Direction)
## [1] 0.5865385

(g). Repeat (d) using KNN with K = 1.

library(class)

train_10 <- (Weekly$Year< 2008)
Weekly.train <- Weekly[train_10,]
Weekly.test <- Weekly[!train_10,]

train.x_10 <- matrix(Weekly$Lag2[train_10])
test.x_10 <- matrix(Weekly$Lag2[!train_10])
train.direction_10 <- Weekly$Direction[train_10]
set.seed(1)
knn_pred_10 <- knn(train.x_10, test.x_10, train.direction_10, k=1)
table(knn_pred_10, Weekly.test$Direction)
##            
## knn_pred_10 Down Up
##        Down   32 38
##        Up     40 46
mean(knn_pred_10== Weekly.test$Direction)
## [1] 0.5

(h). Repeat (d) using naive Bayes.

library(naivebayes)
## Warning: package 'naivebayes' was built under R version 4.2.1
## naivebayes 0.9.7 loaded
naive_wkly <- naive_bayes(Direction ~ Lag2, data = Weekly)
naive.pred2 = predict(naive_wkly, newdata=test.data)
## Warning: predict.naive_bayes(): more features in the newdata are provided as
## there are probability tables in the object. Calculation is performed based on
## features to be found in the tables.
mean(naive.pred2 == test.data$Direction)
## [1] 0.5865385

(i). Which of these methods appears to provide the best results on this data? * The methods that have the highest accuracy rates are the Logistic Regression and Linear Discriminant Analysis; both having rates of 62.5%.

(j). Experiment with different combinations of predictors, including possible transformations and interactions, for each of the methods. Report the variables, method, and associated confusion matrix that appears to provide the best results on the held out data. Note that you should also experiment with values for K in the KNN classifier.

qda.fit2 = qda(Direction~Lag1 + Lag2 + Lag4, data= training.data)
qda.pred2 = predict(qda.fit2, newdata=test.data, type="response")
qda.class2 = qda.pred2$class
table(qda.class2, test.data$Direction)
##           
## qda.class2 Down Up
##       Down    9 20
##       Up     34 41
mean(qda.class2 == test.data$Direction)
## [1] 0.4807692
lda.fit2 = lda(Direction~Lag1 + Lag2 + Lag4, data= training.data)
lda.pred2 = predict(lda.fit2, newdata=test.data, type="response")
lda.class2 = lda.pred2$class
table(lda.class2, test.data$Direction)
##           
## lda.class2 Down Up
##       Down    9  7
##       Up     34 54
mean(lda.class2 == test.data$Direction)
## [1] 0.6057692

Exercise 14

(a). Create a binary variable, mpg01, that contains a 1 if mpg contains a value above its median, and a 0 if mpg contains a value below its median. You can compute the median using the median() function. Note you may find it helpful to use the data.frame() function to create a single data set containing both mpg01 and the other Auto variables

library(dplyr)
## 
## Attaching package: 'dplyr'
## The following object is masked from 'package:MASS':
## 
##     select
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
Auto <- as_tibble(ISLR::Auto)
Auto_mpg01 <- Auto %>% 
  mutate(mpg01 = ifelse(mpg > median(mpg), 1, 0))

(b). Explore the data graphically in order to investigate the association between mpg01 and the other features. Which of the other features seem most likely to be useful in predicting mpg01? Scatterplots and boxplots may be useful tools to answer this question. Describe your findings.

library(tidyverse)
## Warning: package 'tidyverse' was built under R version 4.2.1
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6     ✔ purrr   0.3.4
## ✔ tibble  3.1.6     ✔ stringr 1.4.0
## ✔ tidyr   1.2.0     ✔ forcats 0.5.2
## ✔ readr   2.1.2
## Warning: package 'readr' was built under R version 4.2.1
## Warning: package 'forcats' was built under R version 4.2.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ✖ dplyr::select() masks MASS::select()
Auto_mpg01 %>% 
  ggplot(aes(cut_number(mpg01, 2), displacement)) + 
  geom_boxplot()

Auto_mpg01 %>% 
  ggplot(aes(cut_number(mpg01, 2), horsepower)) + 
  geom_boxplot()

Auto_mpg01 %>% 
  ggplot(aes(cut_number(mpg01, 2), weight)) + 
  geom_boxplot()

Auto_mpg01 %>% 
  ggplot(aes(cut_number(mpg01, 2), acceleration)) + 
  geom_boxplot()

ggplot(Auto_mpg01) +
  geom_count(aes(cut_number(mpg01, 2), cylinders))

ggplot(Auto_mpg01) +
  geom_boxplot(aes(cut_number(mpg01, 2), cylinders))

Auto_mpg01 %>% 
  ggplot(aes(cut_number(mpg01, 2), mpg)) + 
  geom_boxplot()

* To predict mpg01, can use mpg obviously. there seems to be neg corr with cylnders and displacement, horsepower, and weight but positive correlation with acceleration.

(c). Split the data into a training set and a test set.

train <- (Auto_mpg01$year %% 2 == 0)
train_auto <- Auto_mpg01[train,]
test_auto <- Auto_mpg01[!train,]

(d). Perform LDA on the training data in order to predict mpg01 using the variables that seemed most associated with mpg01 in (b). What is the test error of the model obtained?

# LDA Models
lda_auto <- lda(mpg01 ~ cylinders + displacement + horsepower + weight, 
                data = Auto_mpg01,
                subset = train)
lda_auto_pred <- predict(lda_auto, test_auto)
table(lda_auto_pred$class, test_auto$mpg01)
##    
##      0  1
##   0 86  9
##   1 14 73
# test error rate is 
1 - mean(lda_auto_pred$class == test_auto$mpg01)
## [1] 0.1263736

(e). Perform QDA on the training data in order to predict mpg01 using the variables that seemed most associated with mpg01 in (b). What is the test error of the model obtained?

qda_auto <- qda(mpg01 ~ cylinders + displacement + horsepower + weight, 
                data = Auto_mpg01,
                subset = train)
qda_auto_pred <- predict(qda_auto, test_auto)
table(qda_auto_pred$class, test_auto$mpg01)
##    
##      0  1
##   0 89 13
##   1 11 69
# test error rate is 
1 - mean(qda_auto_pred$class == test_auto$mpg01)
## [1] 0.1318681

(f). Perform logistic regression on the training data in order to predict mpg01 using the variables that seemed most associated with mpg01 in (b). What is the test error of the model obtained?

logistic_auto <- glm(mpg01 ~ cylinders + displacement + horsepower + weight,
                     data = Auto_mpg01,
                     subset = train,
                     family = binomial)

logistic_probs_auto <- predict(logistic_auto, test_auto, type = "response")
logistic_pred_auto <- rep(0,length(test_auto$mpg01))
logistic_pred_auto[logistic_probs_auto > 0.5] <- 1

table(logistic_pred_auto, test_auto$mpg01)
##                   
## logistic_pred_auto  0  1
##                  0 89 11
##                  1 11 71
# test error rate is 
1 - mean(logistic_pred_auto == test_auto$mpg01)
## [1] 0.1208791

(g). Perform naive Bayes on the training data in order to predict mpg01 using the variables that seemed most associated with mpg01 in (b). What is the test error of the model obtained?

naive_auto <- naive_bayes(as.factor(mpg01) ~ cylinders + displacement + horsepower + weight, data = Auto_mpg01, subset = train)
naive_auto_pred <- predict(naive_auto, test_auto)
## Warning: predict.naive_bayes(): more features in the newdata are provided as
## there are probability tables in the object. Calculation is performed based on
## features to be found in the tables.
table(naive_auto_pred, test_auto$mpg01)
##                
## naive_auto_pred  0  1
##               0 88 11
##               1 12 71
# test error rate is 
1 - mean(naive_auto_pred == test_auto$mpg01)
## [1] 0.1263736

(h). Perform KNN on the training data, with several values of K, in order to predict mpg01. Use only the variables that seemed most associated with mpg01 in (b). What test errors do you obtain? Which value of K seems to perform the best on this data set?

train_auto_X <- cbind(
  Auto_mpg01$cylinders, 
  Auto_mpg01$displacement, 
  Auto_mpg01$horsepower,
  Auto_mpg01$weight
)[train,]

test_auto_X <- cbind(
  Auto_mpg01$cylinders, 
  Auto_mpg01$displacement, 
  Auto_mpg01$horsepower,
  Auto_mpg01$weight
)[!train,]

set.seed(1)
knn_auto1 <- knn(train_auto_X, test_auto_X, train_auto$mpg01, k = 1)
table(knn_auto1, test_auto$mpg01)
##          
## knn_auto1  0  1
##         0 83 11
##         1 17 71
#test error
1 - mean(knn_auto1 == test_auto$mpg01)
## [1] 0.1538462
knn_auto10 <- knn(train_auto_X, test_auto_X, train_auto$mpg01, k = 10)
table(knn_auto10, test_auto$mpg01)
##           
## knn_auto10  0  1
##          0 77  7
##          1 23 75
#test error
1 - mean(knn_auto10 == test_auto$mpg01)
## [1] 0.1648352
knn_auto100 <- knn(train_auto_X, test_auto_X, train_auto$mpg01, k = 100)
table(knn_auto100, test_auto$mpg01)
##            
## knn_auto100  0  1
##           0 81  7
##           1 19 75
#test error
1 - mean(knn_auto100 == test_auto$mpg01)
## [1] 0.1428571
knn_auto5 <- knn(train_auto_X, test_auto_X, train_auto$mpg01, k = 5)
table(knn_auto5, test_auto$mpg01)
##          
## knn_auto5  0  1
##         0 82  9
##         1 18 73
#test error
1 - mean(knn_auto5 == test_auto$mpg01)
## [1] 0.1483516

Exercise 16

predicting whether a given census tract has a crime rate above or below the median.

attach(Boston)
median_crime = median(crim)
#We will create crim_lvl variable that takes on two values: "0" or "1".
#"0" if crime rate below median and "1" if above median.
crim_lvl <- rep(0, 506)
crim_lvl[crim > median_crime] = 1
crim_lvl <- as.factor(crim_lvl)
Boston_2 <- data.frame(Boston, crim_lvl)

Set up Training and Test Sets

set.seed(1)
train_13 <- rbinom(506, 1, 0.7)
Boston_2 <- cbind(Boston_2, train_13)
Boston.train <- Boston_2[train_13 == 1,]
Boston.test <- Boston_2[train_13 == 0,]

Logistic Regression

log_13_fits <- glm(crim_lvl~nox + age + dis + medv, data = Boston.train, family = binomial)
summary(log_13_fits)
## 
## Call:
## glm(formula = crim_lvl ~ nox + age + dis + medv, family = binomial, 
##     data = Boston.train)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -2.17404  -0.35742   0.00278   0.26418   2.53635  
## 
## Coefficients:
##               Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -24.900404   4.019591  -6.195 5.84e-10 ***
## nox          38.426015   5.859800   6.558 5.47e-11 ***
## age           0.016253   0.009966   1.631   0.1029    
## dis           0.309361   0.164026   1.886   0.0593 .  
## medv          0.087237   0.028230   3.090   0.0020 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 499.02  on 359  degrees of freedom
## Residual deviance: 210.55  on 355  degrees of freedom
## AIC: 220.55
## 
## Number of Fisher Scoring iterations: 7
log_13_fits <- glm(crim_lvl~nox + dis + medv, data = Boston.train, family = binomial)
summary(log_13_fits)
## 
## Call:
## glm(formula = crim_lvl ~ nox + dis + medv, family = binomial, 
##     data = Boston.train)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -2.19958  -0.39388   0.00252   0.26563   2.48475  
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -23.94414    3.89175  -6.153 7.63e-10 ***
## nox          39.78032    5.77733   6.886 5.75e-12 ***
## dis           0.23393    0.15697   1.490  0.13615    
## medv          0.07713    0.02678   2.880  0.00398 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 499.02  on 359  degrees of freedom
## Residual deviance: 213.25  on 356  degrees of freedom
## AIC: 221.25
## 
## Number of Fisher Scoring iterations: 7
log_13_fits <- glm(crim_lvl~nox  + medv, data = Boston.train, family = binomial)
summary(log_13_fits)
## 
## Call:
## glm(formula = crim_lvl ~ nox + medv, family = binomial, data = Boston.train)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -2.17657  -0.38729   0.00523   0.30375   2.65695  
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -19.74864    2.42833  -8.133  4.2e-16 ***
## nox          33.97633    3.88025   8.756  < 2e-16 ***
## medv          0.06605    0.02524   2.617  0.00887 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 499.02  on 359  degrees of freedom
## Residual deviance: 215.41  on 357  degrees of freedom
## AIC: 221.41
## 
## Number of Fisher Scoring iterations: 6
log_13_prob <- predict(log_13_fits, Boston.test, type = 'response')
log_13_preds <- rep(0, 146)
log_13_preds[log_13_prob > 0.5] = 1

dat <- matrix(data=table(log_13_preds, Boston.test$crim_lvl), nrow=2, ncol=2, 
              dimnames=list(c("Below median", "Above median"), c("Below", "Above")))
names(dimnames(dat)) <- c("predicted", "observed")
print(dat)
##               observed
## predicted      Below Above
##   Below median    63    16
##   Above median    12    55
#Error rate:
(16+12)/146
## [1] 0.1917808

LDA

lda_13_fits <- lda(crim_lvl~nox + age+ dis+medv, data = Boston_2, subset= (train_13==1))
lda_13_preds <- predict(lda_13_fits, Boston.test)
lda_13_class <- lda_13_preds$class

dat <- matrix(data=table(lda_13_class, Boston.test$crim_lvl), nrow=2, ncol=2, 
              dimnames=list(c("Below median", "Above median"), c("Below", "Above")))
names(dimnames(dat)) <- c("predicted", "observed")
print(dat)
##               observed
## predicted      Below Above
##   Below median    62    14
##   Above median    13    57
#Error rate:
(14 + 13)/146
## [1] 0.1849315

KNN For k=3

train.x_13 <- cbind(Boston.train$nox, Boston.train$tax, Boston.train$pratio)
test.x_13 <- cbind(Boston.test$nox, Boston.test$tax, Boston.test$pratio)
set.seed(1)
knn_pred_13 <- knn(train.x_13, test.x_13, Boston.train$crim_lvl, k=3)
table(knn_pred_13, Boston.test$crim_lvl)
##            
## knn_pred_13  0  1
##           0 71  5
##           1  4 66
#Error rate:
(4 + 5)/146
## [1] 0.06164384

For k=5

knn_pred_13_2 <- knn(train.x_13, test.x_13, Boston.train$crim_lvl, k=5)
table(knn_pred_13_2, Boston.test$crim_lvl)
##              
## knn_pred_13_2  0  1
##             0 69  5
##             1  6 66
#Error rate:
(5 + 6)/146
## [1] 0.07534247