Jan-Philipp Kolb
3 August 2016
library(rpart)Grow a tree
fit <- rpart(Kyphosis ~ Age + Number + Start,
method="class", data=kyphosis)
printcp(fit) # display the results##
## Classification tree:
## rpart(formula = Kyphosis ~ Age + Number + Start, data = kyphosis,
## method = "class")
##
## Variables actually used in tree construction:
## [1] Age Start
##
## Root node error: 17/81 = 0.20988
##
## n= 81
##
## CP nsplit rel error xerror xstd
## 1 0.176471 0 1.00000 1.00000 0.21559
## 2 0.019608 1 0.82353 0.88235 0.20565
## 3 0.010000 4 0.76471 0.94118 0.21078
plotcp(fit) # visualize cross-validation results
summary(fit) # detailed summary of splits## Call:
## rpart(formula = Kyphosis ~ Age + Number + Start, data = kyphosis,
## method = "class")
## n= 81
##
## CP nsplit rel error xerror xstd
## 1 0.17647059 0 1.0000000 1.0000000 0.2155872
## 2 0.01960784 1 0.8235294 0.8823529 0.2056488
## 3 0.01000000 4 0.7647059 0.9411765 0.2107780
##
## Variable importance
## Start Age Number
## 64 24 12
##
## Node number 1: 81 observations, complexity param=0.1764706
## predicted class=absent expected loss=0.2098765 P(node) =1
## class counts: 64 17
## probabilities: 0.790 0.210
## left son=2 (62 obs) right son=3 (19 obs)
## Primary splits:
## Start < 8.5 to the right, improve=6.762330, (0 missing)
## Number < 5.5 to the left, improve=2.866795, (0 missing)
## Age < 39.5 to the left, improve=2.250212, (0 missing)
## Surrogate splits:
## Number < 6.5 to the left, agree=0.802, adj=0.158, (0 split)
##
## Node number 2: 62 observations, complexity param=0.01960784
## predicted class=absent expected loss=0.09677419 P(node) =0.7654321
## class counts: 56 6
## probabilities: 0.903 0.097
## left son=4 (29 obs) right son=5 (33 obs)
## Primary splits:
## Start < 14.5 to the right, improve=1.0205280, (0 missing)
## Age < 55 to the left, improve=0.6848635, (0 missing)
## Number < 4.5 to the left, improve=0.2975332, (0 missing)
## Surrogate splits:
## Number < 3.5 to the left, agree=0.645, adj=0.241, (0 split)
## Age < 16 to the left, agree=0.597, adj=0.138, (0 split)
##
## Node number 3: 19 observations
## predicted class=present expected loss=0.4210526 P(node) =0.2345679
## class counts: 8 11
## probabilities: 0.421 0.579
##
## Node number 4: 29 observations
## predicted class=absent expected loss=0 P(node) =0.3580247
## class counts: 29 0
## probabilities: 1.000 0.000
##
## Node number 5: 33 observations, complexity param=0.01960784
## predicted class=absent expected loss=0.1818182 P(node) =0.4074074
## class counts: 27 6
## probabilities: 0.818 0.182
## left son=10 (12 obs) right son=11 (21 obs)
## Primary splits:
## Age < 55 to the left, improve=1.2467530, (0 missing)
## Start < 12.5 to the right, improve=0.2887701, (0 missing)
## Number < 3.5 to the right, improve=0.1753247, (0 missing)
## Surrogate splits:
## Start < 9.5 to the left, agree=0.758, adj=0.333, (0 split)
## Number < 5.5 to the right, agree=0.697, adj=0.167, (0 split)
##
## Node number 10: 12 observations
## predicted class=absent expected loss=0 P(node) =0.1481481
## class counts: 12 0
## probabilities: 1.000 0.000
##
## Node number 11: 21 observations, complexity param=0.01960784
## predicted class=absent expected loss=0.2857143 P(node) =0.2592593
## class counts: 15 6
## probabilities: 0.714 0.286
## left son=22 (14 obs) right son=23 (7 obs)
## Primary splits:
## Age < 111 to the right, improve=1.71428600, (0 missing)
## Start < 12.5 to the right, improve=0.79365080, (0 missing)
## Number < 3.5 to the right, improve=0.07142857, (0 missing)
##
## Node number 22: 14 observations
## predicted class=absent expected loss=0.1428571 P(node) =0.1728395
## class counts: 12 2
## probabilities: 0.857 0.143
##
## Node number 23: 7 observations
## predicted class=present expected loss=0.4285714 P(node) =0.08641975
## class counts: 3 4
## probabilities: 0.429 0.571
# plot tree
plot(fit, uniform=TRUE,
main="Classification Tree for Kyphosis")
text(fit, use.n=TRUE, all=TRUE, cex=.8)
- CRAN Task View Machine & Statistical Learning