# Fitting Classification Trees
library(tree)
library(ISLR)
attach(Carseats)
High=ifelse(Sales<=8,"No","Yes")
Carseats=data.frame(Carseats,High)
tree.carseats=tree(High~.-Sales,Carseats)
summary(tree.carseats)
##
## Classification tree:
## tree(formula = High ~ . - Sales, data = Carseats)
## Variables actually used in tree construction:
## [1] "ShelveLoc" "Price" "Income" "CompPrice" "Population"
## [6] "Advertising" "Age" "US"
## Number of terminal nodes: 27
## Residual mean deviance: 0.4575 = 170.7 / 373
## Misclassification error rate: 0.09 = 36 / 400
plot(tree.carseats)
text(tree.carseats,pretty=0,cex=0.8)#pretty=0表示输出定性预测变量的类别名而不是首字母
tree.carseats
## node), split, n, deviance, yval, (yprob)
## * denotes terminal node
##
## 1) root 400 541.500 No ( 0.59000 0.41000 )
## 2) ShelveLoc: Bad,Medium 315 390.600 No ( 0.68889 0.31111 )
## 4) Price < 92.5 46 56.530 Yes ( 0.30435 0.69565 )
## 8) Income < 57 10 12.220 No ( 0.70000 0.30000 )
## 16) CompPrice < 110.5 5 0.000 No ( 1.00000 0.00000 ) *
## 17) CompPrice > 110.5 5 6.730 Yes ( 0.40000 0.60000 ) *
## 9) Income > 57 36 35.470 Yes ( 0.19444 0.80556 )
## 18) Population < 207.5 16 21.170 Yes ( 0.37500 0.62500 ) *
## 19) Population > 207.5 20 7.941 Yes ( 0.05000 0.95000 ) *
## 5) Price > 92.5 269 299.800 No ( 0.75465 0.24535 )
## 10) Advertising < 13.5 224 213.200 No ( 0.81696 0.18304 )
## 20) CompPrice < 124.5 96 44.890 No ( 0.93750 0.06250 )
## 40) Price < 106.5 38 33.150 No ( 0.84211 0.15789 )
## 80) Population < 177 12 16.300 No ( 0.58333 0.41667 )
## 160) Income < 60.5 6 0.000 No ( 1.00000 0.00000 ) *
## 161) Income > 60.5 6 5.407 Yes ( 0.16667 0.83333 ) *
## 81) Population > 177 26 8.477 No ( 0.96154 0.03846 ) *
## 41) Price > 106.5 58 0.000 No ( 1.00000 0.00000 ) *
## 21) CompPrice > 124.5 128 150.200 No ( 0.72656 0.27344 )
## 42) Price < 122.5 51 70.680 Yes ( 0.49020 0.50980 )
## 84) ShelveLoc: Bad 11 6.702 No ( 0.90909 0.09091 ) *
## 85) ShelveLoc: Medium 40 52.930 Yes ( 0.37500 0.62500 )
## 170) Price < 109.5 16 7.481 Yes ( 0.06250 0.93750 ) *
## 171) Price > 109.5 24 32.600 No ( 0.58333 0.41667 )
## 342) Age < 49.5 13 16.050 Yes ( 0.30769 0.69231 ) *
## 343) Age > 49.5 11 6.702 No ( 0.90909 0.09091 ) *
## 43) Price > 122.5 77 55.540 No ( 0.88312 0.11688 )
## 86) CompPrice < 147.5 58 17.400 No ( 0.96552 0.03448 ) *
## 87) CompPrice > 147.5 19 25.010 No ( 0.63158 0.36842 )
## 174) Price < 147 12 16.300 Yes ( 0.41667 0.58333 )
## 348) CompPrice < 152.5 7 5.742 Yes ( 0.14286 0.85714 ) *
## 349) CompPrice > 152.5 5 5.004 No ( 0.80000 0.20000 ) *
## 175) Price > 147 7 0.000 No ( 1.00000 0.00000 ) *
## 11) Advertising > 13.5 45 61.830 Yes ( 0.44444 0.55556 )
## 22) Age < 54.5 25 25.020 Yes ( 0.20000 0.80000 )
## 44) CompPrice < 130.5 14 18.250 Yes ( 0.35714 0.64286 )
## 88) Income < 100 9 12.370 No ( 0.55556 0.44444 ) *
## 89) Income > 100 5 0.000 Yes ( 0.00000 1.00000 ) *
## 45) CompPrice > 130.5 11 0.000 Yes ( 0.00000 1.00000 ) *
## 23) Age > 54.5 20 22.490 No ( 0.75000 0.25000 )
## 46) CompPrice < 122.5 10 0.000 No ( 1.00000 0.00000 ) *
## 47) CompPrice > 122.5 10 13.860 No ( 0.50000 0.50000 )
## 94) Price < 125 5 0.000 Yes ( 0.00000 1.00000 ) *
## 95) Price > 125 5 0.000 No ( 1.00000 0.00000 ) *
## 3) ShelveLoc: Good 85 90.330 Yes ( 0.22353 0.77647 )
## 6) Price < 135 68 49.260 Yes ( 0.11765 0.88235 )
## 12) US: No 17 22.070 Yes ( 0.35294 0.64706 )
## 24) Price < 109 8 0.000 Yes ( 0.00000 1.00000 ) *
## 25) Price > 109 9 11.460 No ( 0.66667 0.33333 ) *
## 13) US: Yes 51 16.880 Yes ( 0.03922 0.96078 ) *
## 7) Price > 135 17 22.070 No ( 0.64706 0.35294 )
## 14) Income < 46 6 0.000 No ( 1.00000 0.00000 ) *
## 15) Income > 46 11 15.160 Yes ( 0.45455 0.54545 ) *
set.seed(2)
train=sample(1:nrow(Carseats), 200)
Carseats.test=Carseats[-train,]
High.test=High[-train]
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 104 33
## Yes 13 50
(86+57)/200
## [1] 0.715
#用cv.tree()执行交叉验证确认最优的树复杂性
set.seed(3)
cv.carseats=cv.tree(tree.carseats,FUN=prune.misclass)#用分类错误率来剪枝
names(cv.carseats)
## [1] "size" "dev" "k" "method"
# "size" "dev" "k" "method"，k为成本复杂性参数值
cv.carseats
## $size
## [1] 21 19 14 9 8 5 3 2 1
##
## $dev
## [1] 74 76 81 81 75 77 78 85 81
##
## $k
## [1] -Inf 0.0 1.0 1.4 2.0 3.0 4.0 9.0 18.0
##
## $method
## [1] "misclass"
##
## attr(,"class")
## [1] "prune" "tree.sequence"
par(mfrow=c(1,2))
plot(cv.carseats$size,cv.carseats$dev,type="b")
plot(cv.carseats$k,cv.carseats$dev,type="b")
prune.carseats=prune.misclass(tree.carseats,best=9)
plot(prune.carseats)
text(prune.carseats,pretty=0)
tree.pred=predict(prune.carseats,Carseats.test,type="class")
table(tree.pred,High.test)
## High.test
## tree.pred No Yes
## No 97 25
## Yes 20 58
(94+60)/200
## [1] 0.77
prune.carseats=prune.misclass(tree.carseats,best=15)
plot(prune.carseats)
text(prune.carseats,pretty=0)
tree.pred=predict(prune.carseats,Carseats.test,type="class")
table(tree.pred,High.test)
## High.test
## tree.pred No Yes
## No 102 30
## Yes 15 53
(86+62)/200
## [1] 0.74
# Fitting Regression Trees 构建回归树
library(tree)
library(MASS)
set.seed(1)
train = sample(1:nrow(Boston), nrow(Boston)/2)
fix(Boston)
tree.boston=tree(medv~.,Boston,subset=train)
summary(tree.boston)
##
## Regression tree:
## tree(formula = medv ~ ., data = Boston, subset = train)
## Variables actually used in tree construction:
## [1] "rm" "lstat" "crim" "age"
## Number of terminal nodes: 7
## Residual mean deviance: 10.38 = 2555 / 246
## Distribution of residuals:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## -10.1800 -1.7770 -0.1775 0.0000 1.9230 16.5800
plot(tree.boston)
text(tree.boston,pretty=0)
cv.boston=cv.tree(tree.boston)
plot(cv.boston$size,cv.boston$dev,type='b')
prune.boston=prune.tree(tree.boston,best=5)#用prune.tree进行剪枝
plot(prune.boston)
text(prune.boston,pretty=0)
yhat=predict(tree.boston,newdata=Boston[-train,])
boston.test=Boston[-train,"medv"]
plot(yhat,boston.test)
abline(0,1)
mean((yhat-boston.test)^2)
## [1] 35.28688
# Bagging and Random Forests 袋装法与随机森林
library(randomForest)
## randomForest 4.6-14
## Type rfNews() to see new features/changes/bug fixes.
set.seed(1)
bag.boston=randomForest(medv~.,data=Boston,subset=train,mtry=13,importance=TRUE)
#参数mtry=13表示树上的每一个分裂点都考虑了所有的预测变量
bag.boston
##
## Call:
## randomForest(formula = medv ~ ., data = Boston, mtry = 13, importance = TRUE, subset = train)
## Type of random forest: regression
## Number of trees: 500
## No. of variables tried at each split: 13
##
## Mean of squared residuals: 11.39601
## % Var explained: 85.17
yhat.bag = predict(bag.boston,newdata=Boston[-train,])
plot(yhat.bag, boston.test)
abline(0,1)
mean((yhat.bag-boston.test)^2)
## [1] 23.59273
bag.boston=randomForest(medv~.,data=Boston,subset=train,mtry=13,ntree=25)
yhat.bag = predict(bag.boston,newdata=Boston[-train,])
mean((yhat.bag-boston.test)^2)
## [1] 23.66716
set.seed(1)
rf.boston=randomForest(medv~.,data=Boston,subset=train,mtry=6,importance=TRUE)
yhat.rf = predict(rf.boston,newdata=Boston[-train,])
mean((yhat.rf-boston.test)^2)
## [1] 19.62021
importance(rf.boston)# %IncMSE IncNodePurity 前者衡量准确性，后者衡量纯度
## %IncMSE IncNodePurity
## crim 16.697017 1076.08786
## zn 3.625784 88.35342
## indus 4.968621 609.53356
## chas 1.061432 52.21793
## nox 13.518179 709.87339
## rm 32.343305 7857.65451
## age 13.272498 612.21424
## dis 9.032477 714.94674
## rad 2.878434 95.80598
## tax 9.118801 364.92479
## ptratio 8.467062 823.93341
## black 7.579482 275.62272
## lstat 27.129817 6027.63740
varImpPlot(rf.boston)#变量重要性图
# Boosting 提升法
library(gbm)
## Loaded gbm 2.1.5
set.seed(1)
boost.boston=gbm(medv~.,data=Boston[train,],distribution="gaussian",n.trees=5000,interaction.depth=4)
#回归问题选择distribution="gaussian"，二分类问题选择bernoulli，interaction.depth=4限制了每棵树的深度
summary(boost.boston)#生成了变量相对影响图
par(mfrow=c(1,1))
plot(boost.boston,i="rm")#画出两个变量的偏相关图
plot(boost.boston,i="lstat")
yhat.boost=predict(boost.boston,newdata=Boston[-train,],n.trees=5000)
mean((yhat.boost-boston.test)^2)
## [1] 18.84709
boost.boston=gbm(medv~.,data=Boston[train,],distribution="gaussian",n.trees=5000,interaction.depth=4,shrinkage=0.2,verbose=F)
yhat.boost=predict(boost.boston,newdata=Boston[-train,],n.trees=5000)
mean((yhat.boost-boston.test)^2)
## [1] 18.33455