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8.3 Lab: Decision Trees 325 We see that the training error rate is 9 %. For classification trees, the deviance reported in the output of summary() is given by −2 ∑ ∑ n mk log ˆp mk , m k where n mk is the number of observations in the mth terminal node that belong to the kth class. A small deviance indicates a tree that provides a good fit to the (training) data. The residual mean deviance reported is simply the deviance divided by n−|T 0 |, which in this case is 400−27 = 373. One of the most attractive properties of trees is that they can be graphically displayed. We use the plot() function to display the tree structure, and the text() function to display the node labels. The argument pretty=0 instructs R to include the category names for any qualitative predictors, rather than simply displaying a letter for each category. > plot(tree.carseats) > text(tree.carseats ,pretty=0) The most important indicator of Sales appears to be shelving location, since the first branch differentiates Good locations from Bad and Medium locations. If we just type the name of the tree object, R prints output corresponding to each branch of the tree. R displays the split criterion (e.g. Price tree.carseats node), split , n, deviance, yval, (yprob) * denotes terminal node 1) root 400 541.5 No ( 0.590 0.410 ) 2) ShelveLoc : Bad,Medium 315 390.6 No ( 0.689 0.311 ) 4) Price < 92.5 46 56.53 Yes ( 0.304 0.696 ) 8) Income < 57 10 12.22 No ( 0.700 0.300 ) In order to properly evaluate the performance of a classification tree on these data, we must estimate the test error rather than simply computing the training error. We split the observations into a training set and a test set, build the tree using the training set, and evaluate its performance on the test data. The predict() function can be used for this purpose. In the case of a classification tree, the argument type="class" instructs R to return the actual class prediction. This approach leads to correct predictions for around 71.5 % of the locations in the test data set. > set.seed(2) > train=sample(1:nrow(Carseats), 200) > Carseats.test=Carseats[-train ,] > High.test=High[-train]
326 8. Tree-Based Methods > tree.carseats=tree(High∼.-Sales ,Carseats,subset=train) > tree.pred=predict(tree.carseats ,Carseats.test,type="class") > table(tree.pred ,High.test) High.test tree.pred No Yes No 86 27 Yes 30 57 > (86+57) /200 [1] 0.715 Next, we consider whether pruning the tree might lead to improved results. The function cv.tree() performs cross-validation in order to cv.tree() determine the optimal level of tree complexity; cost complexity pruning is used in order to select a sequence of trees for consideration. We use the argument FUN=prune.misclass in order to indicate that we want the classification error rate to guide the cross-validation and pruning process, rather than the default for the cv.tree() function, which is deviance. The cv.tree() function reports the number of terminal nodes of each tree considered (size) as well as the corresponding error rate and the value of the cost-complexity parameter used (k, which corresponds to α in (8.4)). > set.seed(3) > cv.carseats=cv.tree(tree.carseats ,FUN=prune.misclass) > names(cv.carseats) [1] "size" "dev" "k" "method" > cv.carseats $size [1] 19 17 14 13 9 7 3 2 1 $dev [1] 55 55 53 52 50 56 69 65 80 $k [1] -Inf 0.0000000 0.6666667 1.0000000 1.7500000 2.0000000 4.2500000 [8] 5.0000000 23.0000000 $method [1] "misclass" attr(,"class") [1] "prune" "tree.sequence" Note that, despite the name, dev corresponds to the cross-validation error rate in this instance. The tree with 9 terminal nodes results in the lowest cross-validation error rate, with 50 cross-validation errors. We plot the error rate as a function of both size and k. > par(mfrow=c(1,2)) > plot(cv.carseats$size ,cv.carseats$dev ,type="b") > plot(cv.carseats$k ,cv.carseats$dev ,type="b")
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Springer Texts in Statistics Gareth
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Gareth James • Daniela Witten •
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To our parents: Alison and Michael
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viii Preface disciplines who wish t
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x Contents 3 Linear Regression 59 3
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xii Contents 6.6 Lab 2: Ridge Regre
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xiv Contents 10.5 Lab 2: Clustering
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2 1. Introduction Wage 50 100 200 3
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4 1. Introduction Predicted Probabi
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6 1. Introduction of least squares,
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8 1. Introduction in order to contr
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10 1. Introduction In general, we w
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12 1. Introduction of A and B is de
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14 1. Introduction Name Auto Boston
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16 2. Statistical Learning Sales 5
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18 2. Statistical Learning Income Y
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20 2. Statistical Learning In this
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26 2. Statistical Learning additive
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28 2. Statistical Learning tistical
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30 2. Statistical Learning where ˆ
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32 2. Statistical Learning We now m
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34 2. Statistical Learning Y −10
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36 2. Statistical Learning 0.0 0.5
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38 2. Statistical Learning o o o o
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40 2. Statistical Learning o o o o
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42 2. Statistical Learning Error Ra
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44 2. Statistical Learning The matr
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46 2. Statistical Learning We will
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48 2. Statistical Learning [3,] 3 7
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50 2. Statistical Learning > plot(c
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52 2. Statistical Learning 2.4 Exer
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54 2. Statistical Learning (b) What
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56 2. Statistical Learning 9. This
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3 Linear Regression This chapter is
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3.1 Simple Linear Regression 3.1 Si
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3.1 Simple Linear Regression 63 3 2
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3.1 Simple Linear Regression 65 con
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3.1 Simple Linear Regression 67 In
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Quantity Value Residual standard er
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3.2 Multiple Linear Regression 71 a
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3.2 Multiple Linear Regression 73 Y
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3.2 Multiple Linear Regression 75 T
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3.2 Multiple Linear Regression 77 w
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3.2 Multiple Linear Regression 79 i
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3.2 Multiple Linear Regression 81 S
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3.3 Other Considerations in the Reg
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x i = 3.3 Other Considerations in t
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3.4 The Marketing Plan 103 units wh
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y x 2 y x 2 3.5 Comparison of Linea
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3.5 Comparison of Linear Regression
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3.6 Lab: Linear Regression 109 p=1
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3.6 Lab: Linear Regression 111 Coef
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3.6 Lab: Linear Regression 113 > pl
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3.6 Lab: Linear Regression 115 > lm
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3.6 Lab: Linear Regression 117 > lm
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3.6 Lab: Linear Regression 119 Shel
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3.7 Exercises 121 (b) Answer (a) us
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3.7 Exercises 123 10. This question
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3.7 Exercises 125 (d) Create a scat
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4 Classification The linear regress
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4.2 Why Not Linear Regression? 129
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4.3 Logistic Regression 131 0 500 1
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4.3 Logistic Regression 133 β 1 do
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4.3 Logistic Regression 135 Coeffic
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4.3 Logistic Regression 137 Default
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4.4 Linear Discriminant Analysis 13
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4.5 A Comparison of Classification
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4.5 A Comparison of Classification
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4.6 Lab: Logistic Regression, LDA,
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4.7 Exercises 169 we will use obser
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4.7 Exercises 173 return(result) Th
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176 5. Resampling Methods 5.1 Cross
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178 5. Resampling Methods Mean Squa
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180 5. Resampling Methods LOOCV 10
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182 5. Resampling Methods Mean Squa
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184 5. Resampling Methods has highe
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186 5. Resampling Methods Error Rat
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188 5. Resampling Methods Y −2
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190 5. Resampling Methods Obs X Y Z
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192 5. Resampling Methods > mean((m
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194 5. Resampling Methods first is
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196 5. Resampling Methods Next, we
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198 5. Resampling Methods (f) When
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200 5. Resampling Methods predict.g
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6 Linear Model Selection and Regula
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6.1 Subset Selection 205 6.1 Subset
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6.1 Subset Selection 207 p = 20, th
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6.1 Subset Selection 209 #Variables
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6.1 Subset Selection 211 C p 10000
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6.1 Subset Selection 213 will lead
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6.2 Shrinkage Methods 215 obvious w
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6.2 Shrinkage Methods 217 regressio
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6.2 Shrinkage Methods 219 discussed
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6.2 Shrinkage Methods 221 respectiv
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6.2 Shrinkage Methods 223 Mean Squa
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6.2 Shrinkage Methods 225 To simpli
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6.2 Shrinkage Methods 227 (β j ) 0
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6.3 Dimension Reduction Methods 229
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6.4 Considerations in High Dimensio
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6.5 Lab 1: Subset Selection Methods
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6.6 Lab 2: Ridge Regression and the
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6.7 Lab 3: PCR and PLS Regression 2
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6.8 Exercises 259 final seven-compo
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6.8 Exercises 261 (a) As we increas
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6.8 Exercises 263 (d) Repeat (c), u
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7 Moving Beyond Linearity So far in
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|| 7.1 Polynomial Regression 267 De
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|| 7.2 Step Functions 269 Piecewise
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7.4 Regression Splines 271 7.4 Regr
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7.4 Regression Splines 273 plot is
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10.2 Principal Components Analysis
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10.2.4 Other Uses for Principal Com
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10.3 Clustering Methods 387 K=2 K=3
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10.3 Clustering Methods 389 Data St
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10.3 Clustering Methods 391 X2 −2
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10.3 Clustering Methods 393 0.0 0.5
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Algorithm 10.2 Hierarchical Cluster
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10.3 Clustering Methods 397 Average
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10.3 Clustering Methods 399 0 2 4 6
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10.4 Lab 1: Principal Components An
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10.4 Lab 1: Principal Components An
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10.5 Lab 2: Clustering 405 Cluster
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10.6 Lab 3: NCI60 Data Example 407
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10.7 Exercises 413 differ: for inst
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10.7 Exercises 415 (b) At a certain
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10.7 Exercises 417 10. In this prob
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Index C p , 78, 205, 206, 210-213 R
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Index 421 Wage, 1, 2, 9, 10, 14, 26
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Index 423 noise, 22, 228 non-linear
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Index 425 read.table(), 48, 49 regs
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