Question 13:

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

library(ISLR2)
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  
##            
##            
##            
## 
cor(Weekly[,-9])
##               Year         Lag1        Lag2        Lag3         Lag4
## Year    1.00000000 -0.032289274 -0.03339001 -0.03000649 -0.031127923
## Lag1   -0.03228927  1.000000000 -0.07485305  0.05863568 -0.071273876
## Lag2   -0.03339001 -0.074853051  1.00000000 -0.07572091  0.058381535
## Lag3   -0.03000649  0.058635682 -0.07572091  1.00000000 -0.075395865
## Lag4   -0.03112792 -0.071273876  0.05838153 -0.07539587  1.000000000
## Lag5   -0.03051910 -0.008183096 -0.07249948  0.06065717 -0.075675027
## Volume  0.84194162 -0.064951313 -0.08551314 -0.06928771 -0.061074617
## Today  -0.03245989 -0.075031842  0.05916672 -0.07124364 -0.007825873
##                Lag5      Volume        Today
## Year   -0.030519101  0.84194162 -0.032459894
## Lag1   -0.008183096 -0.06495131 -0.075031842
## Lag2   -0.072499482 -0.08551314  0.059166717
## Lag3    0.060657175 -0.06928771 -0.071243639
## Lag4   -0.075675027 -0.06107462 -0.007825873
## Lag5    1.000000000 -0.05851741  0.011012698
## Volume -0.058517414  1.00000000 -0.033077783
## Today   0.011012698 -0.03307778  1.000000000
pairs(Weekly[,-9])

plot(Weekly$Year, Weekly$Volume)

It seems the only significant correlation would be between Year and Volume. When observed graphically, volume increases substantially over time. Meanwhile no visible relationship can be noted between Year and Lag variables, therefore there is no noticeably strong evidence that past returns are used to predict future returns.

b. Use the full data set to perform a logistic Regression. Summary function. Do any of the predictors appear to be statistically significant? If so, which ones?

glm.fit <- glm(Direction ~ . -Today, data = Weekly, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = Direction ~ . - Today, family = binomial, data = Weekly)
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)  
## (Intercept) 17.225822  37.890522   0.455   0.6494  
## Year        -0.008500   0.018991  -0.448   0.6545  
## Lag1        -0.040688   0.026447  -1.538   0.1239  
## Lag2         0.059449   0.026970   2.204   0.0275 *
## Lag3        -0.015478   0.026703  -0.580   0.5622  
## Lag4        -0.027316   0.026485  -1.031   0.3024  
## Lag5        -0.014022   0.026409  -0.531   0.5955  
## Volume       0.003256   0.068836   0.047   0.9623  
## ---
## 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: 1486.2  on 1081  degrees of freedom
## AIC: 1502.2
## 
## Number of Fisher Scoring iterations: 4

Based on the results, Lag2 appears to be statistically significant. Therefore if there was a positive return within the past 2 weeks, there is a higher likelihood that the market could go up today.

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.prob <- predict(glm.fit, type = "response")
glm.prob[1:10]
##         1         2         3         4         5         6         7         8 
## 0.6195813 0.6123878 0.5986601 0.4938106 0.6288351 0.5807001 0.5905994 0.5274874 
##         9        10 
## 0.5834212 0.5674230
contrasts(Weekly$Direction)
##      Up
## Down  0
## Up    1
glm.pred <- rep("Down", length(glm.prob))
glm.pred[glm.prob > 0.5] = "Up"

table(glm.pred, Weekly$Direction)
##         
## glm.pred Down  Up
##     Down   56  47
##     Up    428 558
mean(glm.pred == Weekly$Direction)
## [1] 0.56382

The confusion matrix tells us 2 things, the first that the market is predicted to go up in about 558 days, and that the logistic regression model will predict market direction about 56.4% of the time. Here the confusion matrix shows that the linear regression model was more likely to mistake down predictions, showing a total of 428 down days that were missclassified.

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.

train <-  (Weekly$Year < 2009)
weekly08 <- Weekly[!train,]

dim(weekly08)
## [1] 104   9
direction08 <- Weekly$Direction[!train]

glm.fit <- glm(Direction ~ Lag2, data = Weekly, family = binomial, subset = train)

glm.prob <-  predict(glm.fit, weekly08, type = "response")

glm.pred <- rep("Down", 104)
glm.pred[glm.prob > 0.5] <- "Up"

table(glm.pred, direction08)
##         direction08
## glm.pred Down Up
##     Down    9  5
##     Up     34 56
mean(glm.pred == direction08)
## [1] 0.625

e. d repeated using LDA

library(MASS)

lda.fit <- lda(Direction ~ Lag2, data = Weekly, subset = train)

lda.pred <-  predict(lda.fit, weekly08)
names(lda.pred)
## [1] "class"     "posterior" "x"
lda.class <- lda.pred$class
table(lda.class, direction08)
##          direction08
## lda.class Down Up
##      Down    9  5
##      Up     34 56
mean(lda.class == direction08)
## [1] 0.625

f. d repeated using QDA

qda.fit <- qda(Direction ~ Lag1, data = weekly08, subset = train)

qda.class <- predict(qda.fit, weekly08)$class

table(qda.class, direction08)
##          direction08
## qda.class Down Up
##      Down    1  3
##      Up     42 58
mean(qda.class == direction08)
## [1] 0.5673077

g. d repeated using KNN with K = 1

library(class)
train.X <- as.matrix(Weekly$Lag2[train])
test.X <- as.matrix(Weekly$Lag2[!train])

train.direction <- Weekly$Direction[train]

knn.pred <- knn(train = train.X,
                test = test.X,
                cl = train.direction,
                k = 1)
table(knn.pred, direction08)
##         direction08
## knn.pred Down Up
##     Down   21 30
##     Up     22 31
mean(knn.pred == direction08)
## [1] 0.5

h. d repeated using naive Bayes

library(e1071)
nb.fit <- naiveBayes(Direction ~ Lag1, data = weekly08, subset = train)

nb.class <-  predict(nb.fit, weekly08)
table(nb.class, direction08)
##         direction08
## nb.class Down Up
##     Down    1  3
##     Up     42 58
mean(nb.class == direction08)
## [1] 0.5673077

i. Which of these methods appears to provide the best results on this data?

Both Logistic Regression and LDA seem to provide the best results for the data both showing the highest prediction rate at 62.5%.

j. Experiment with different combination 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 KNN classifier.

logistic regression

glm.fit <- glm(Direction ~ Lag2, data = Weekly, family = binomial, subset = train)

glm.fit2 <- glm(Direction ~ Lag2 + Lag1, data = Weekly, family = binomial, subset = train)

glm.fit3 <- glm(Direction ~ Lag2 + Lag1 + Lag3, data = Weekly, family = binomial, subset = train)

glm.fit4 <- glm(Direction ~ Lag2 + Lag1 + Lag2 + Lag4, data = Weekly, family = binomial, subset = train)

glm.fit5 <- glm(Direction ~ Lag2 + Lag1 + Lag3 + Volume, data = Weekly, family = binomial, subset = train)

glm.fit6 <- glm(Direction ~ Lag2 + Volume, data = Weekly, family = binomial, subset = train)

train <- (Weekly$Year < 2009)
weekly.test <- Weekly[!train,]

models <-  list(
  glm1 = glm.fit,
  glm2 = glm.fit2,
  glm3 = glm.fit3,
  glm4 = glm.fit4,
  glm5 = glm.fit5,
  glm6 = glm.fit6
)

summary_table <- data.frame(Model = character(), accuracy = numeric())

for(i in names(models)) {
  prob <- predict(models[[i]], weekly.test, type = "response")
  pred <- ifelse(prob > .5, "Up", "Down")
  acc <-  mean(pred == weekly.test$Direction)
  summary_table <- rbind(summary_table, data.frame(Model = i, Accuracy = acc))
}

summary_table
##   Model  Accuracy
## 1  glm1 0.6250000
## 2  glm2 0.5769231
## 3  glm3 0.5769231
## 4  glm4 0.6057692
## 5  glm5 0.5192308
## 6  glm6 0.5384615

The best results for using the logistic regression is using Lag2 as the only variable.

LDA

lda.fit <- lda(Direction ~ Lag2, data = Weekly, family = binomial, subset = train)

lda.fit1 <- lda(Direction ~ Lag2 + Lag1, data = Weekly, family = binomial, subset = train)

lda.fit2 <- lda(Direction ~ Lag2 + Volume, data = Weekly, family = binomial, subset = train)

lda.fit3 <- lda(Direction ~ Lag2 + Lag1 +Lag3, data = Weekly, family = binomial, subset = train)

lda.fit4 <- lda(Direction ~ Lag2 + Lag1 + Lag3 + Lag4, data = Weekly, family = binomial, subset = train)

lda.fit5 <- lda(Direction ~ Lag2 + Lag1 + Lag3 + Lag4 + Lag5, data = Weekly, family = binomial, subset = train)


direction08 <- Weekly$Direction[!train]

models <- list (lda.fit, lda.fit1, lda.fit2, lda.fit3, lda.fit4, lda.fit5)

results <- data.frame()

for(i in seq_along(models)) {
lda.pred <-  predict(models[[i]], weekly08)
lda.class <- lda.pred$class
cm <- table(lda.class, direction08)
acc <- mean(lda.class == direction08)

results <- rbind(results, data.frame(model = paste0("LDA", i), accuracy = acc))
print(cm)
}
##          direction08
## lda.class Down Up
##      Down    9  5
##      Up     34 56
##          direction08
## lda.class Down Up
##      Down    7  8
##      Up     36 53
##          direction08
## lda.class Down Up
##      Down   20 25
##      Up     23 36
##          direction08
## lda.class Down Up
##      Down    8  9
##      Up     35 52
##          direction08
## lda.class Down Up
##      Down    7  8
##      Up     36 53
##          direction08
## lda.class Down Up
##      Down    9 13
##      Up     34 48
results
##   model  accuracy
## 1  LDA1 0.6250000
## 2  LDA2 0.5769231
## 3  LDA3 0.5384615
## 4  LDA4 0.5769231
## 5  LDA5 0.5769231
## 6  LDA6 0.5480769

The best results for using the LDA model is using Lag2 as the only variable.

QDA

qda.fit <- qda(Direction ~ Lag2, data = Weekly, family = binomial, subset = train)

qda.fit1 <- qda(Direction ~ Lag2 + Lag1, data = Weekly, family = binomial, subset = train)

qda.fit2 <- qda(Direction ~ Lag2 + Volume, data = Weekly, family = binomial, subset = train)

qda.fit3 <- qda(Direction ~ Lag2 + Lag1 +Lag3, data = Weekly, family = binomial, subset = train)

qda.fit4 <- qda(Direction ~ Lag2 + Lag1 + Lag3 + Lag4, data = Weekly, family = binomial, subset = train)

qda.fit5 <- qda(Direction ~ Lag2 + Lag1 + Lag3 + Lag4 + Lag5, data = Weekly, family = binomial, subset = train)

direction08 <- Weekly$Direction[!train]

models <- list (qda.fit, qda.fit1, qda.fit2, qda.fit3, qda.fit4, qda.fit5)

results <- data.frame()

for(i in seq_along(models)) {
qda.pred <-  predict(models[[i]], weekly08)
qda.class <- qda.pred$class
cm <- table(qda.class, direction08)
acc <- mean(qda.class == direction08)

results <- rbind(results, data.frame(model = paste0("QDA", i), accuracy = acc))
print(cm)
}
##          direction08
## qda.class Down Up
##      Down    0  0
##      Up     43 61
##          direction08
## qda.class Down Up
##      Down    7 10
##      Up     36 51
##          direction08
## qda.class Down Up
##      Down   32 44
##      Up     11 17
##          direction08
## qda.class Down Up
##      Down    6 10
##      Up     37 51
##          direction08
## qda.class Down Up
##      Down    9 16
##      Up     34 45
##          direction08
## qda.class Down Up
##      Down   10 23
##      Up     33 38
results
##   model  accuracy
## 1  QDA1 0.5865385
## 2  QDA2 0.5576923
## 3  QDA3 0.4711538
## 4  QDA4 0.5480769
## 5  QDA5 0.5192308
## 6  QDA6 0.4615385

KNN with different K values

train.X <- as.matrix(Weekly$Lag2[train])
test.X <- as.matrix(Weekly$Lag2[!train])

train.direction <- Weekly$Direction[train]
test.direction <- Weekly$Direction[!train]

kval <-  c(1,3,5,7,9,11,13)

results <- data.frame()

for(k in kval){
  knn.pred <- knn(train = train.X,
                test = test.X,
                cl = train.direction,
                k = k)
  
  cm <- table(knn.pred, test.direction)
  acc <- mean(knn.pred == test.direction)
  
  results <- rbind(results, 
                   data.frame(
                     k=k,
                     accuracy = acc
                     ))
  print(cm)
}
##         test.direction
## knn.pred Down Up
##     Down   21 29
##     Up     22 32
##         test.direction
## knn.pred Down Up
##     Down   16 19
##     Up     27 42
##         test.direction
## knn.pred Down Up
##     Down   15 21
##     Up     28 40
##         test.direction
## knn.pred Down Up
##     Down   16 19
##     Up     27 42
##         test.direction
## knn.pred Down Up
##     Down   17 20
##     Up     26 41
##         test.direction
## knn.pred Down Up
##     Down   19 21
##     Up     24 40
##         test.direction
## knn.pred Down Up
##     Down   20 19
##     Up     23 42
results
##    k  accuracy
## 1  1 0.5096154
## 2  3 0.5576923
## 3  5 0.5288462
## 4  7 0.5576923
## 5  9 0.5576923
## 6 11 0.5673077
## 7 13 0.5961538

Question 14. In this problem, you will develop a model to predict whether a given car gets high or low gas mileage based on the Auto data set.

a. Create a binary variable, mpg1, that contains a 1 if mpg contains a value above its median, and a 0 if mpg contains a value below its median.

library(ISLR2)
Auto$mpg01 <-  ifelse(Auto$mpg > median(Auto$mpg), 1, 0)

Auto$horsepower[Auto$horsepower == "?"] <- NA
Auto$horsepower <- as.numeric(Auto$horsepower)
Auto <- na.omit(Auto)

head(Auto)
##   mpg cylinders displacement horsepower weight acceleration year origin
## 1  18         8          307        130   3504         12.0   70      1
## 2  15         8          350        165   3693         11.5   70      1
## 3  18         8          318        150   3436         11.0   70      1
## 4  16         8          304        150   3433         12.0   70      1
## 5  17         8          302        140   3449         10.5   70      1
## 6  15         8          429        198   4341         10.0   70      1
##                        name mpg01
## 1 chevrolet chevelle malibu     0
## 2         buick skylark 320     0
## 3        plymouth satellite     0
## 4             amc rebel sst     0
## 5               ford torino     0
## 6          ford galaxie 500     0
table(Auto$mpg01)
## 
##   0   1 
## 196 196

b. Explore the data graphically in order to investigate the association between mpg01 and the 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)

pairs(Auto[,c("mpg01", "cylinders", "displacement", "horsepower", "weight", "acceleration", "year")])

boxplot(cylinders ~ mpg01, data = Auto)

boxplot(displacement ~ mpg01, data = Auto)

boxplot(horsepower ~ mpg01, data = Auto)

boxplot(weight ~ mpg01, data = Auto)

boxplot(acceleration ~ mpg01, data = Auto)

boxplot(year ~ mpg01, data = Auto)

cor(Auto[,c("mpg01", "cylinders", "displacement", "horsepower", "weight", "acceleration", "year")])
##                   mpg01  cylinders displacement horsepower     weight
## mpg01         1.0000000 -0.7591939   -0.7534766 -0.6670526 -0.7577566
## cylinders    -0.7591939  1.0000000    0.9508233  0.8429834  0.8975273
## displacement -0.7534766  0.9508233    1.0000000  0.8972570  0.9329944
## horsepower   -0.6670526  0.8429834    0.8972570  1.0000000  0.8645377
## weight       -0.7577566  0.8975273    0.9329944  0.8645377  1.0000000
## acceleration  0.3468215 -0.5046834   -0.5438005 -0.6891955 -0.4168392
## year          0.4299042 -0.3456474   -0.3698552 -0.4163615 -0.3091199
##              acceleration       year
## mpg01           0.3468215  0.4299042
## cylinders      -0.5046834 -0.3456474
## displacement   -0.5438005 -0.3698552
## horsepower     -0.6891955 -0.4163615
## weight         -0.4168392 -0.3091199
## acceleration    1.0000000  0.2903161
## year            0.2903161  1.0000000

Autos with higher mpg, more fuel efficient, would be those with fewer cylinders, lower engine displacement, lower horsepower, lighter in weight, and newer models. While there doesn’t seem to be too much of an impact on mpg from acceleration.

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

set.seed(1)
train <- sample(1:nrow(Auto),nrow(Auto)/2)

auto.train <- Auto[train,]
auto.test <- Auto[-train,]

mpg01.test <- 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.fit <- lda(mpg01 ~ cylinders + displacement + horsepower + weight + year, data = auto.train)

lda.pred <- predict(lda.fit, auto.test)
table(lda.pred$class, mpg01.test)
##    mpg01.test
##      0  1
##   0 81  4
##   1 21 90
mean(lda.pred$class != mpg01.test)
## [1] 0.127551

test error: 12.8%

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.fit <- qda(mpg01 ~ cylinders + displacement + horsepower + weight + year, data = auto.train)

qda.pred <-  predict(qda.fit, auto.test)
table(qda.pred$class, mpg01.test)
##    mpg01.test
##      0  1
##   0 89  8
##   1 13 86
mean(qda.pred$class != mpg01.test)
## [1] 0.1071429

test error: 10.7

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?

glm.fit <- glm(mpg01 ~ cylinders + displacement + horsepower + weight + year, data = auto.train, family = binomial)

glm.prob <- predict(glm.fit, auto.test, type = "response")
glm.pred <- ifelse(glm.prob > .5, 1, 0)

table(glm.pred, mpg01.test)
##         mpg01.test
## glm.pred  0  1
##        0 91  7
##        1 11 87
mean(glm.pred != mpg01.test)
## [1] 0.09183673

test error: 9.2%

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?

nb.fit <- naiveBayes(as.factor(mpg01) ~ cylinders + displacement + horsepower + weight + year, data = auto.train)

nb.pred <-  predict(nb.fit, auto.test)
table(nb.pred, mpg01.test)
##        mpg01.test
## nb.pred  0  1
##       0 88  9
##       1 14 85
mean(nb.pred != mpg01.test)
## [1] 0.1173469

test error: 11.7%

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.X <- scale(auto.train[,c("cylinders", "displacement", "horsepower", "weight", "year")])
test.X <- scale(auto.test[,c("cylinders", "displacement", "horsepower", "weight", "year")])
train.Y <- auto.train$mpg01

kval <-  c(1,3,5,7,9,11,13)

err <-  numeric(length(kval))

for(i in seq_along(kval)){
  pred <- knn(train.X, test.X, train.Y, k = kval[i])
  err[i] <-  mean(pred != mpg01.test)
}

data.frame(K = kval, test_error = err)
##    K test_error
## 1  1 0.10714286
## 2  3 0.10204082
## 3  5 0.09693878
## 4  7 0.10204082
## 5  9 0.10204082
## 6 11 0.10204082
## 7 13 0.10204082

From the test errors obtained, K = 5 would be the k value chosen to run the model since it gives the lowest test error with minimum smoothing.

Question 16.

Using the Boston data set, fit classification models in order to predict whether a given census tract has a crime rate above or below the median. Explore logistic regression, LDA, naive Bayes, and KNN models using various subsets of the predictors. Describe your findings.

Boston$crim01 <-  ifelse(Boston$crim > median(Boston$crim), 1,0) 
table(Boston$crim01)
## 
##   0   1 
## 253 253
pairs(Boston,)

boxplot(zn ~ crim01, data = Boston)

boxplot(indus ~ crim01, data = Boston)

boxplot(nox ~ crim01, data = Boston)

boxplot(rm ~ crim01, data = Boston)

boxplot(dis ~ crim01, data = Boston)

boxplot(rad ~ crim01, data = Boston)

boxplot(tax ~ crim01, data = Boston)

boxplot(ptratio ~ crim01, data = Boston)

boxplot(lstat ~ crim01, data = Boston)

boxplot(medv ~ crim01, data = Boston)

Based on the plots, the variables that are significant in relation to crime rates are the following: index of accessibility to radial highways (rad), property tax, proportion of non-retail business acres (indus), nitrogen oxides concentration (nox), distances to employment centers (dis), and lower population status (lstat).

set.seed(1)

train <- sample(1:nrow(Boston), nrow(Boston)/2)
boston.train <- Boston[train,]
boston.test <- Boston[-train,]

crim01.test <- Boston$crim01[-train]

fitting logistic regression

glm.fit <- glm(crim01 ~ rad + tax + indus + nox + dis + lstat, data = boston.train, family = binomial)

glm.prob <- predict(glm.fit, newdata = boston.test, type = "response")

glm.pred <- ifelse(glm.prob > .5, 1, 0)

table(glm.pred, crim01.test)
##         crim01.test
## glm.pred   0   1
##        0 109  17
##        1  17 110
mean(glm.pred != crim01.test)
## [1] 0.1343874

fitting LDA

lda.fit <- lda(crim01 ~ rad + tax + indus + nox + dis + lstat, data = boston.train)

lda.pred <- predict(lda.fit, boston.test)$class

table(lda.pred, crim01.test)
##         crim01.test
## lda.pred   0   1
##        0 120  33
##        1   6  94
mean(lda.pred != crim01.test)
## [1] 0.1541502

fitting Naive Bayes

library(e1071)

nb.fit <- naiveBayes(as.factor(crim01) ~ rad + tax + indus + nox + dis + lstat, data = boston.train)

nb.pred <- predict(nb.fit, boston.test)

table(nb.pred, crim01.test)
##        crim01.test
## nb.pred   0   1
##       0 119  39
##       1   7  88
mean(nb.pred != crim01.test)
## [1] 0.1818182

fitting KNN

train.X <- scale(boston.train[, c("rad", "tax", "indus",  "nox", "dis", "lstat")])

test.X <- scale(boston.test[, c("rad", "tax", "indus", "nox", "dis", "lstat")], center = attr(train.X, "scaled:center"), scale  = attr(train.X, "scaled:scale"))

train.Y <- boston.train$crim01

kval <- c(1,3,5,7,9,11,13,15)

err <- numeric(length(kval))

for(i in seq_along(kval)){
  pred <- knn(train.X,
              test.X,
              train.Y,
              k = kval[i])

  err[i] <- mean(pred != crim01.test)
}

data.frame(K = kval, Test_Error = err)
##    K Test_Error
## 1  1 0.07114625
## 2  3 0.05138340
## 3  5 0.07905138
## 4  7 0.09090909
## 5  9 0.09881423
## 6 11 0.07509881
## 7 13 0.09486166
## 8 15 0.11462451