Help for package rpart

Priority:

recommended

Version:

4.1.24

Date:

2025-01-06

Description:

Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.

Title:

Recursive Partitioning and Regression Trees

Depends:

R (≥ 2.15.0), graphics, stats, grDevices

Suggests:

survival

License:

GPL-2 | GPL-3

LazyData:

yes

ByteCompile:

yes

NeedsCompilation:

yes

Author:

Terry Therneau [aut], Beth Atkinson [aut, cre], Brian Ripley [trl] (producer of the initial R port, maintainer 1999-2017)

Maintainer:

Beth Atkinson <atkinson@mayo.edu>

Repository:

CRAN

URL:

https://github.com/bethatkinson/rpart, https://cran.r-project.org/package=rpart

BugReports:

https://github.com/bethatkinson/rpart/issues

Packaged:

2025-01-06 13:26:22 UTC; ripley

Date/Publication:

2025-01-07 07:30:14 UTC

Automobile Data from 'Consumer Reports' 1990

Description

The car.test.frame data frame has 60 rows and 8 columns, giving data on makes of cars taken from the April, 1990 issue of Consumer Reports. This is part of a larger dataset, some columns of which are given in cu.summary.

Usage

car.test.frame

Format

This data frame contains the following columns:

Price: a numeric vector giving the list price in US dollars of a standard model
Country: of origin, a factor with levels ‘⁠France⁠’, ‘⁠Germany⁠’, ‘⁠Japan⁠’ , ‘⁠Japan/USA⁠’, ‘⁠Korea⁠’, ‘⁠Mexico⁠’, ‘⁠Sweden⁠’ and ‘⁠USA⁠’
Reliability: a numeric vector coded 1 to 5.
Mileage: fuel consumption miles per US gallon, as tested.
Type: a factor with levels Compact Large Medium Small Sporty Van
Weight: kerb weight in pounds.
Disp.: the engine capacity (displacement) in litres.
HP: the net horsepower of the vehicle.

Source

Consumer Reports, April, 1990, pp. 235–288 quoted in

John M. Chambers and Trevor J. Hastie eds. (1992) Statistical Models in S, Wadsworth and Brooks/Cole, Pacific Grove, CA, pp. 46–47.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
summary(z.auto)

Automobile Data from 'Consumer Reports' 1990

Description

Data on 111 cars, taken from pages 235–255, 281–285 and 287–288 of the April 1990 Consumer Reports Magazine.

Usage

data(car90)

Format

The data frame contains the following columns

Country: a factor giving the country in which the car was manufactured
Disp: engine displacement in cubic inches
Disp2: engine displacement in liters
Eng.Rev: engine revolutions per mile, or engine speed at 60 mph
Front.Hd: distance between the car's head-liner and the head of a 5 ft. 9 in. front seat passenger, in inches, as measured by CU
Frt.Leg.Room: maximum front leg room, in inches, as measured by CU
Frt.Shld: front shoulder room, in inches, as measured by CU
Gear.Ratio: the overall gear ratio, high gear, for manual transmission
Gear2: the overall gear ratio, high gear, for automatic transmission
HP: net horsepower
HP.revs: the red line—the maximum safe engine speed in rpm
Height: height of car, in inches, as supplied by manufacturer
Length: overall length, in inches, as supplied by manufacturer
Luggage: luggage space
Mileage: a numeric vector of gas mileage in miles/gallon as tested by CU; contains NAs.
Model2: alternate name, if the car was sold under two labels
Price: list price with standard equipment, in dollars
Rear.Hd: distance between the car's head-liner and the head of a 5 ft 9 in. rear seat passenger, in inches, as measured by CU
Rear.Seating: rear fore-and-aft seating room, in inches, as measured by CU
RearShld: rear shoulder room, in inches, as measured by CU
Reliability: an ordered factor with levels ‘⁠Much worse⁠’ < ‘⁠worse⁠’ < ‘⁠average⁠’ < ‘⁠better⁠’ < ‘⁠Much better⁠’: contains NAs.
Rim: factor giving the rim size
Sratio.m: Number of turns of the steering wheel required for a turn of 30 foot radius, manual steering
Sratio.p: Number of turns of the steering wheel required for a turn of 30 foot radius, power steering
Steering: steering type offered: manual, power, or both
Tank: fuel refill capacity in gallons
Tires: factor giving tire size
Trans1: manual transmission, a factor with levels ‘⁠⁠’, ‘⁠man.4⁠’, ‘⁠man.5⁠’ and ‘⁠man.6⁠’
Trans2: automatic transmission, a factor with levels ‘⁠⁠’, ‘⁠auto.3⁠’, ‘⁠auto.4⁠’, and ‘⁠auto.CVT⁠’. No car is missing both the manual and automatic transmission variables, but several had both as options
Turning: the radius of the turning circle in feet
Type: a factor giving the general type of car. The levels are: ‘⁠Small⁠’, ‘⁠Sporty⁠’, ‘⁠Compact⁠’, ‘⁠Medium⁠’, ‘⁠Large⁠’, ‘⁠Van⁠’
Weight: an order statistic giving the relative weights of the cars; 1 is the lightest and 111 is the heaviest
Wheel.base: length of wheelbase, in inches, as supplied by manufacturer
Width: width of car, in inches, as supplied by manufacturer

Source

This is derived (with permission) from the data set car.all in S-PLUS, but with some further clean up of variable names and definitions.

Examples

data(car90)
plot(car90$Price/1000, car90$Weight,
     xlab = "Price (thousands)", ylab = "Weight (lbs)")
mlowess <- function(x, y, ...) {
    keep <- !(is.na(x) | is.na(y))
    lowess(x[keep], y[keep], ...)
}
with(car90, lines(mlowess(Price/1000, Weight, f = 0.5)))

Automobile Data from 'Consumer Reports' 1990

Description

The cu.summary data frame has 117 rows and 5 columns, giving data on makes of cars taken from the April, 1990 issue of Consumer Reports.

Usage

cu.summary

Format

This data frame contains the following columns:

Price: a numeric vector giving the list price in US dollars of a standard model
Country: of origin, a factor with levels ‘⁠Brazil⁠’, ‘⁠England⁠’, ‘⁠France⁠’, ‘⁠Germany⁠’, ‘⁠Japan⁠’, ‘⁠Japan/USA⁠’, ‘⁠Korea⁠’, ‘⁠Mexico⁠’, ‘⁠Sweden⁠’ and ‘⁠USA⁠’
Reliability: an ordered factor with levels ‘⁠Much worse⁠’ < ‘⁠worse⁠’ < ‘⁠average⁠’ < ‘⁠better⁠’ < ‘⁠Much better⁠’
Mileage: fuel consumption miles per US gallon, as tested.
Type: a factor with levels Compact Large Medium Small Sporty Van

Source

Consumer Reports, April, 1990, pp. 235–288 quoted in

John M. Chambers and Trevor J. Hastie eds. (1992) Statistical Models in S, Wadsworth and Brooks/Cole, Pacific Grove, CA, pp. 46–47.

Examples

fit <- rpart(Price ~ Mileage + Type + Country, cu.summary)
par(xpd = TRUE)
plot(fit, compress = TRUE)
text(fit, use.n = TRUE)

Data on Children who have had Corrective Spinal Surgery

Description

The kyphosis data frame has 81 rows and 4 columns. representing data on children who have had corrective spinal surgery

Usage

kyphosis

Format

This data frame contains the following columns:

Kyphosis: a factor with levels absent present indicating if a kyphosis (a type of deformation) was present after the operation.
Age: in months
Number: the number of vertebrae involved
Start: the number of the first (topmost) vertebra operated on.

Source

John M. Chambers and Trevor J. Hastie eds. (1992) Statistical Models in S, Wadsworth and Brooks/Cole, Pacific Grove, CA.

Examples

fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
fit2 <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis,
              parms = list(prior = c(0.65, 0.35), split = "information"))
fit3 <- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
              control = rpart.control(cp = 0.05))
par(mfrow = c(1,2), xpd = TRUE)
plot(fit)
text(fit, use.n = TRUE)
plot(fit2)
text(fit2, use.n = TRUE)

Create Split Labels For an Rpart Object

Description

This function provides labels for the branches of an rpart tree.

Usage

## S3 method for class 'rpart'
labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)

Arguments

object

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

digits

the number of digits to be used for numeric values. All of the rpart functions that call labels explicitly set this value, with options("digits") as the default.

minlength

the minimum length for abbreviation of character or factor variables. If 0 no abbreviation is done; if 1 single English letters are used, first lower case than upper case (with a maximum of 52 levels). If the value is greater than , the abbreviate function is used, passed the minlength argument.

pretty

an argument included for compatibility with the original Splus tree package: pretty = 0 implies minlength = 0L, pretty = NULL implies minlength = 1L, and pretty = TRUE implies minlength = 4L.

collapse

logical. The returned set of labels is always of the same length as the number of nodes in the tree.

If collapse = TRUE (default), the returned value is a vector of labels for the branch leading into each node, with "root" as the label for the top node.

If FALSE, the returned value is a two column matrix of labels for the left and right branches leading out from each node, with "leaf" as the branch labels for terminal nodes.

...

optional arguments to abbreviate.

Value

Vector of split labels (collapse = TRUE) or matrix of left and right splits (collapse = FALSE) for the supplied rpart object. This function is called by printing methods for rpart and is not intended to be called directly by the users.

Mean-Variance Plot for an Rpart Object

Description

Creates a plot on the current graphics device of the deviance of the node divided by the number of observations at the node. Also returns the node number.

Usage

meanvar(tree, ...)

## S3 method for class 'rpart'
meanvar(tree, xlab = "ave(y)", ylab = "ave(deviance)", ...)

Arguments

tree

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

xlab

x-axis label for the plot.

ylab

y-axis label for the plot.

...

additional graphical parameters may be supplied as arguments to this function.

Value

an invisible list containing the following vectors is returned.

x

fitted value at terminal nodes (yval).

y

deviance of node divided by number of observations at node.

label

node number.

Side Effects

a plot is put on the current graphics device.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
meanvar(z.auto, log = 'xy')

Handles Missing Values in an Rpart Object

Description

Handles missing values in an "rpart" object.

Usage

na.rpart(x)

Arguments

x

a model frame.

Details

Default function that handles missing values when calling the function rpart.

It omits cases where part of the response is missing or all the explanatory variables are missing.

Follow Paths to Selected Nodes of an Rpart Object

Description

Returns a names list where each element contains the splits on the path from the root to the selected nodes.

Usage

path.rpart(tree, nodes, pretty = 0, print.it = TRUE)

Arguments

tree

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

nodes

an integer vector containing indices (node numbers) of all nodes for which paths are desired. If missing, user selects nodes as described below.

pretty

an integer denoting the extent to which factor levels in split labels will be abbreviated. A value of (0) signifies no abbreviation. A NULL, the default, signifies using elements of letters to represent the different factor levels.

print.it

Logical. Denotes whether paths will be printed out as nodes are interactively selected. Irrelevant if nodes argument is supplied.

Details

The function has a required argument as an rpart object and a list of nodes as optional arguments. Omitting a list of nodes will cause the function to wait for the user to select nodes from the dendrogram. It will return a list, with one component for each node specified or selected. The component contains the sequence of splits leading to that node. In the graphical interaction, the individual paths are printed out as nodes are selected.

Value

A named (by node) list, each element of which contains all the splits on the path from the root to the specified or selected nodes.

Graphical Interaction

A dendrogram of the rpart object is expected to be visible on the graphics device, and a graphics input device (e.g. a mouse) is required. Clicking (the selection button) on a node selects that node. This process may be repeated any number of times. Clicking the exit button will stop the selection process and return the list of paths.

References

This function was modified from path.tree in S.

Examples

fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
print(fit)
path.rpart(fit, nodes = c(11, 22))

Plot an Rpart Object

Description

Plots an rpart object on the current graphics device.

Usage

## S3 method for class 'rpart'
plot(x, uniform = FALSE, branch = 1, compress = FALSE, nspace,
     margin = 0, minbranch = 0.3, branch.col = 1, branch.lty = 1, 
     branch.lwd = 1, ...)

Arguments

x

a fitted object of class "rpart", containing a classification, regression, or rate tree.

uniform

if TRUE, uniform vertical spacing of the nodes is used; this may be less cluttered when fitting a large plot onto a page. The default is to use a non-uniform spacing proportional to the error in the fit.

branch

controls the shape of the branches from parent to child node. Any number from 0 to 1 is allowed. A value of 1 gives square shouldered branches, a value of 0 give V shaped branches, with other values being intermediate.

compress

if FALSE, the leaf nodes will be at the horizontal plot coordinates of 1:nleaves. If TRUE, the routine attempts a more compact arrangement of the tree. The compaction algorithm assumes uniform=TRUE; surprisingly, the result is usually an improvement even when that is not the case.

nspace

the amount of extra space between a node with children and a leaf, as compared to the minimal space between leaves. Applies to compressed trees only. The default is the value of branch.

margin

an extra fraction of white space to leave around the borders of the tree. (Long labels sometimes get cut off by the default computation).

minbranch

set the minimum length for a branch to minbranch times the average branch length. This parameter is ignored if uniform=TRUE. Sometimes a split will give very little improvement, or even (in the classification case) no improvement at all. A tree with branch lengths strictly proportional to improvement leaves no room to squeeze in node labels.

branch.col

set the color of the branches.

branch.lty

set the line type of the branches.

branch.lwd

set the line width of the branches.

...

arguments to be passed to or from other methods.

Details

This function is a method for the generic function plot, for objects of class rpart. The y-coordinate of the top node of the tree will always be 1.

Value

The coordinates of the nodes are returned as a list, with components x and y.

Side Effects

An unlabeled plot is produced on the current graphics device: one being opened if needed.

In order to build up a plot in the usual S style, e.g., a separate text command for adding labels, some extra information about the plot needs be retained. This is kept in an environment in the package.

Examples

fit <- rpart(Price ~ Mileage + Type + Country, cu.summary)
par(xpd = TRUE)
plot(fit, compress = TRUE)
text(fit, use.n = TRUE)

Plot a Complexity Parameter Table for an Rpart Fit

Description

Gives a visual representation of the cross-validation results in an rpart object.

Usage

plotcp(x, minline = TRUE, lty = 3, col = 1,
       upper = c("size", "splits", "none"), ...)

Arguments

x

an object of class "rpart"

minline

whether a horizontal line is drawn 1SE above the minimum of the curve.

lty

line type for this line

col

colour for this line

upper

what is plotted on the top axis: the size of the tree (the number of leaves), the number of splits or nothing.

...

additional plotting parameters

Details

The set of possible cost-complexity prunings of a tree from a nested set. For the geometric means of the intervals of values of cp for which a pruning is optimal, a cross-validation has (usually) been done in the initial construction by rpart. The cptable in the fit contains the mean and standard deviation of the errors in the cross-validated prediction against each of the geometric means, and these are plotted by this function. A good choice of cp for pruning is often the leftmost value for which the mean lies below the horizontal line.

Value

None.

Side Effects

A plot is produced on the current graphical device.

PostScript Presentation Plot of an Rpart Object

Description

Generates a PostScript presentation plot of an rpart object.

Usage

post(tree, ...)

## S3 method for class 'rpart'
post(tree, title., 
     filename = paste(deparse(substitute(tree)), ".ps", sep = ""), 
     digits = getOption("digits") - 2, pretty = TRUE,
     use.n = TRUE, horizontal = TRUE, ...)

Arguments

tree

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

title.

a title which appears at the top of the plot. By default, the name of the rpart endpoint is printed out.

filename

ASCII file to contain the output. By default, the name of the file is the name of the object given by rpart (with the suffix .ps added). If filename = "", the plot appears on the current graphical device.

digits

number of significant digits to include in numerical data.

pretty

an integer denoting the extent to which factor levels will be abbreviated in the character strings defining the splits; (0) signifies no abbreviation of levels. A NULL signifies using elements of letters to represent the different factor levels. The default (TRUE) indicates the maximum possible abbreviation.

use.n

Logical. If TRUE (default), adds to the label ⁠#events level1/ #events level2/⁠ etc. for method class, ⁠n⁠ for method anova, and ⁠#events/n⁠ for methods poisson and exp).

horizontal

Logical. If TRUE (default), plot is horizontal. If FALSE, plot appears as landscape.

...

other arguments to the postscript function.

Details

The plot created uses the functions plot.rpart and text.rpart (with the fancy option). The settings were chosen because they looked good to us, but other options may be better, depending on the rpart object. Users are encouraged to write their own function containing favorite options.

Side Effects

a plot of rpart is created using the postscript driver, or the current device if filename = "".

Examples

## Not run: 
z.auto <- rpart(Mileage ~ Weight, car.test.frame)
post(z.auto, file = "")   # display tree on active device
   # now construct postscript version on file "pretty.ps"
   # with no title
post(z.auto, file = "pretty.ps", title = " ")
z.hp <- rpart(Mileage ~ Weight + HP, car.test.frame)
post(z.hp)
## End(Not run)

Predictions from a Fitted Rpart Object

Description

Returns a vector of predicted responses from a fitted rpart object.

Usage

## S3 method for class 'rpart'
predict(object, newdata,
       type = c("vector", "prob", "class", "matrix"),
       na.action = na.pass, ...)

Arguments

object

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

newdata

data frame containing the values at which predictions are required. The predictors referred to in the right side of formula(object) must be present by name in newdata. If missing, the fitted values are returned.

type

character string denoting the type of predicted value returned. If the rpart object is a classification tree, then the default is to return prob predictions, a matrix whose columns are the probability of the first, second, etc. class. (This agrees with the default behavior of tree). Otherwise, a vector result is returned.

na.action

a function to determine what should be done with missing values in newdata. The default is to pass them down the tree using surrogates in the way selected when the model was built. Other possibilities are na.omit and na.fail.

...

further arguments passed to or from other methods.

Details

This function is a method for the generic function predict for class "rpart". It can be invoked by calling predict for an object of the appropriate class, or directly by calling predict.rpart regardless of the class of the object.

Value

A new object is obtained by dropping newdata down the object. For factor predictors, if an observation contains a level not used to grow the tree, it is left at the deepest possible node and frame$yval at the node is the prediction.

If type = "vector":
vector of predicted responses. For regression trees this is the mean response at the node, for Poisson trees it is the estimated response rate, and for classification trees it is the predicted class (as a number).

If type = "prob":
(for a classification tree) a matrix of class probabilities.

If type = "matrix":
a matrix of the full responses (frame$yval2 if this exists, otherwise frame$yval). For regression trees, this is the mean response, for Poisson trees it is the response rate and the number of events at that node in the fitted tree, and for classification trees it is the concatenation of at least the predicted class, the class counts at that node in the fitted tree, and the class probabilities (some versions of rpart may contain further columns).

If type = "class":
(for a classification tree) a factor of classifications based on the responses.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
predict(z.auto)

fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
predict(fit, type = "prob")   # class probabilities (default)
predict(fit, type = "vector") # level numbers
predict(fit, type = "class")  # factor
predict(fit, type = "matrix") # level number, class frequencies, probabilities

sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
fit <- rpart(Species ~ ., data = iris, subset = sub)
fit
table(predict(fit, iris[-sub,], type = "class"), iris[-sub, "Species"])

Print an Rpart Object

Description

This function prints an rpart object. It is a method for the generic function print of class "rpart".

Usage

## S3 method for class 'rpart'
print(x, minlength = 0, spaces = 2, cp, digits = getOption("digits"),
  nsmall = min(20, digits), ...)

Arguments

x

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

minlength

Controls the abbreviation of labels: see labels.rpart.

spaces

the number of spaces to indent nodes of increasing depth.

digits

the number of digits of numbers to print.

nsmall

the number of digits to the right of the decimal. See format.

cp

prune all nodes with a complexity less than cp from the printout. Ignored if unspecified.

...

arguments to be passed to or from other methods.

Details

This function is a method for the generic function print for class "rpart". It can be invoked by calling print for an object of the appropriate class, or directly by calling print.rpart regardless of the class of the object.

Side Effects

A semi-graphical layout of the contents of x$frame is printed. Indentation is used to convey the tree topology. Information for each node includes the node number, split, size, deviance, and fitted value. For the "class" method, the class probabilities are also printed.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
z.auto
## Not run: node), split, n, deviance, yval
      * denotes terminal node

 1) root 60 1354.58300 24.58333  
   2) Weight>=2567.5 45  361.20000 22.46667  
     4) Weight>=3087.5 22   61.31818 20.40909 *
     5) Weight<3087.5 23  117.65220 24.43478  
      10) Weight>=2747.5 15   60.40000 23.80000 *
      11) Weight<2747.5 8   39.87500 25.62500 *
   3) Weight<2567.5 15  186.93330 30.93333 *

## End(Not run)

Displays CP table for Fitted Rpart Object

Description

Displays the cp table for fitted rpart object.

Usage

printcp(x, digits = getOption("digits") - 2)

Arguments

x

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

digits

the number of digits of numbers to print.

Details

Prints a table of optimal prunings based on a complexity parameter.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
printcp(z.auto)
## Not run: 
Regression tree:
rpart(formula = Mileage ~ Weight, data = car.test.frame)

Variables actually used in tree construction:
[1] Weight

Root node error: 1354.6/60 = 22.576

        CP nsplit rel error  xerror     xstd 
1 0.595349      0   1.00000 1.03436 0.178526
2 0.134528      1   0.40465 0.60508 0.105217
3 0.012828      2   0.27012 0.45153 0.083330
4 0.010000      3   0.25729 0.44826 0.076998

## End(Not run)

Cost-complexity Pruning of an Rpart Object

Description

Determines a nested sequence of subtrees of the supplied rpart object by recursively snipping off the least important splits, based on the complexity parameter (cp).

Usage

prune(tree, ...)

## S3 method for class 'rpart'
prune(tree, cp, ...)

Arguments

tree

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

cp

Complexity parameter to which the rpart object will be trimmed.

...

further arguments passed to or from other methods.

Value

A new rpart object that is trimmed to the value cp.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
zp <- prune(z.auto, cp = 0.1)
plot(zp) #plot smaller rpart object

Residuals From a Fitted Rpart Object

Description

Method for residuals for an rpart object.

Usage

## S3 method for class 'rpart'
residuals(object, type = c("usual", "pearson", "deviance"), ...)

Arguments

object

fitted model object of class "rpart".

type

Indicates the type of residual desired.

For regression or anova trees all three residual definitions reduce to y - fitted. This is the residual returned for user method trees as well.

For classification trees the usual residuals are the misclassification losses L(actual, predicted) where L is the loss matrix. With default losses this residual is 0/1 for correct/incorrect classification. The pearson residual is (1-fitted)/sqrt(fitted(1-fitted)) and the deviance residual is sqrt(minus twice logarithm of fitted).

For poisson and exp (or survival) trees, the usual residual is the observed - expected number of events. The pearson and deviance residuals are as defined in McCullagh and Nelder.

...

further arguments passed to or from other methods.

Value

Vector of residuals of type type from a fitted rpart object.

References

McCullagh P. and Nelder, J. A. (1989) Generalized Linear Models. London: Chapman and Hall.

Examples

fit <- rpart(skips ~ Opening + Solder + Mask + PadType + Panel,
             data = solder.balance, method = "anova")
summary(residuals(fit))
plot(predict(fit),residuals(fit))

Recursive Partitioning and Regression Trees

Description

Fit a rpart model

Usage

rpart(formula, data, weights, subset, na.action = na.rpart, method,
      model = FALSE, x = FALSE, y = TRUE, parms, control, cost, ...)

Arguments

formula

a formula, with a response but no interaction terms. If this is a data frame, it is taken as the model frame (see model.frame).

data

an optional data frame in which to interpret the variables named in the formula.

weights

optional case weights.

subset

optional expression saying that only a subset of the rows of the data should be used in the fit.

na.action

the default action deletes all observations for which y is missing, but keeps those in which one or more predictors are missing.

method

one of "anova", "poisson", "class" or "exp". If method is missing then the routine tries to make an intelligent guess. If y is a survival object, then method = "exp" is assumed, if y has 2 columns then method = "poisson" is assumed, if y is a factor then method = "class" is assumed, otherwise method = "anova" is assumed. It is wisest to specify the method directly, especially as more criteria may added to the function in future.

Alternatively, method can be a list of functions named init, split and eval. Examples are given in the file ‘tests/usersplits.R’ in the sources, and in the vignettes ‘User Written Split Functions’.

model

if logical: keep a copy of the model frame in the result? If the input value for model is a model frame (likely from an earlier call to the rpart function), then this frame is used rather than constructing new data.

x

keep a copy of the x matrix in the result.

y

keep a copy of the dependent variable in the result. If missing and model is supplied this defaults to FALSE.

parms

optional parameters for the splitting function.
Anova splitting has no parameters.
Poisson splitting has a single parameter, the coefficient of variation of the prior distribution on the rates. The default value is 1.
Exponential splitting has the same parameter as Poisson.
For classification splitting, the list can contain any of: the vector of prior probabilities (component prior), the loss matrix (component loss) or the splitting index (component split). The priors must be positive and sum to 1. The loss matrix must have zeros on the diagonal and positive off-diagonal elements. The splitting index can be gini or information. The default priors are proportional to the data counts, the losses default to 1, and the split defaults to gini.

control

a list of options that control details of the rpart algorithm. See rpart.control.

cost

a vector of non-negative costs, one for each variable in the model. Defaults to one for all variables. These are scalings to be applied when considering splits, so the improvement on splitting on a variable is divided by its cost in deciding which split to choose.

...

arguments to rpart.control may also be specified in the call to rpart. They are checked against the list of valid arguments.

Details

This differs from the tree function in S mainly in its handling of surrogate variables. In most details it follows Breiman et. al (1984) quite closely. R package tree provides a re-implementation of tree.

Value

An object of class rpart. See rpart.object.

References

Breiman L., Friedman J. H., Olshen R. A., and Stone, C. J. (1984) Classification and Regression Trees. Wadsworth.

Examples

fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
fit2 <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis,
              parms = list(prior = c(.65,.35), split = "information"))
fit3 <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis,
              control = rpart.control(cp = 0.05))
par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped
plot(fit)
text(fit, use.n = TRUE)
plot(fit2)
text(fit2, use.n = TRUE)

Internal Functions

Description

Internal functions, only used by packages rpart and ipred.

Usage

pred.rpart(fit, x)
rpart.anova(y, offset, parms, wt)
rpart.class(y, offset, parms, wt)
rpart.matrix(frame)
rpart.poisson(y, offset, parms, wt)
rpartco(tree, parms)

Arguments

fit

a tree fitted by rpart.

x

a matrix of predictors.

y

the responses.

offset

an offset, or NULL.

parms

a list of parameters, usually empty.

wt

case weights.

frame

model frame (from call to rpart)

tree

a tree fitted by rpart.

Value

For rpartco the x,y plotting coordinates of the nodes.

rpart.anova, rpart.class and rpart.poisson return a list with components

y

(adjusting for offset if necessary),

parms

as input,

numresp

the number of responses,

summary

a function to be invoked by summary.rpart,

text

a function to be invoked by text.rpart.

Control for Rpart Fits

Description

Various parameters that control aspects of the rpart fit.

Usage

rpart.control(minsplit = 20, minbucket = round(minsplit/3), cp = 0.01, 
              maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,
              surrogatestyle = 0, maxdepth = 30, ...)

Arguments

minsplit

the minimum number of observations that must exist in a node in order for a split to be attempted.

minbucket

the minimum number of observations in any terminal <leaf> node. If only one of minbucket or minsplit is specified, the code either sets minsplit to minbucket*3 or minbucket to minsplit/3, as appropriate.

cp

complexity parameter. Any split that does not decrease the overall lack of fit by a factor of cp is not attempted. For instance, with anova splitting, this means that the overall R-squared must increase by cp at each step. The main role of this parameter is to save computing time by pruning off splits that are obviously not worthwhile. Essentially,the user informs the program that any split which does not improve the fit by cp will likely be pruned off by cross-validation, and that hence the program need not pursue it.

maxcompete

the number of competitor splits retained in the output. It is useful to know not just which split was chosen, but which variable came in second, third, etc.

maxsurrogate

the number of surrogate splits retained in the output. If this is set to zero the compute time will be reduced, since approximately half of the computational time (other than setup) is used in the search for surrogate splits.

usesurrogate

how to use surrogates in the splitting process. 0 means display only; an observation with a missing value for the primary split rule is not sent further down the tree. 1 means use surrogates, in order, to split subjects missing the primary variable; if all surrogates are missing the observation is not split. For value 2 ,if all surrogates are missing, then send the observation in the majority direction. A value of 0 corresponds to the action of tree, and 2 to the recommendations of Breiman et.al (1984).

xval

number of cross-validations.

surrogatestyle

controls the selection of a best surrogate. If set to 0 (default) the program uses the total number of correct classification for a potential surrogate variable, if set to 1 it uses the percent correct, calculated over the non-missing values of the surrogate. The first option more severely penalizes covariates with a large number of missing values.

maxdepth

Set the maximum depth of any node of the final tree, with the root node counted as depth 0. Maximum value 30 (as node numbers have to be stored in 32-bit signed integer types).

...

mop up other arguments.

Value

A list containing the options.

Initialization function for exponential fitting

Description

This function does the initialization step for rpart, when the response is a survival object. It rescales the data so as to have an exponential baseline hazard and then uses Poisson methods. This function would rarely if ever be called directly by a user.

Usage

rpart.exp(y, offset, parms, wt)

Arguments

y

the response, which will be of class Surv

offset

optional offset

parms

parameters controlling the fit. This is a list with components shrink and method. The first is the prior for the coefficient of variation of the predictions. The second is either "deviance" or "sqrt" and is the measure used for cross-validation. If values are missing the defaults are used, which are "deviance" for the method, and a shrinkage of 1.0 for the deviance method and 0 for the square root.

wt

case weights, if present

Value

a list with the necessary initialization components

Author(s)

Terry Therneau

Recursive Partitioning and Regression Trees Object

Description

These are objects representing fitted rpart trees.

Value

frame

data frame with one row for each node in the tree. The row.names of frame contain the (unique) node numbers that follow a binary ordering indexed by node depth. Columns of frame include var, a factor giving the names of the variables used in the split at each node (leaf nodes are denoted by the level "<leaf>"), n, the number of observations reaching the node, wt, the sum of case weights for observations reaching the node, dev, the deviance of the node, yval, the fitted value of the response at the node, and splits, a two column matrix of left and right split labels for each node. Also included in the frame are complexity, the complexity parameter at which this split will collapse, ncompete, the number of competitor splits recorded, and nsurrogate, the number of surrogate splits recorded.

Extra response information which may be present is in yval2, which contains the number of events at the node (poisson tree), or a matrix containing the fitted class, the class counts for each node, the class probabilities and the ‘node probability’ (classification trees).

where

an integer vector of the same length as the number of observations in the root node, containing the row number of frame corresponding to the leaf node that each observation falls into.

call

an image of the call that produced the object, but with the arguments all named and with the actual formula included as the formula argument. To re-evaluate the call, say update(tree).

terms

an object of class c("terms", "formula") (see terms.object) summarizing the formula. Used by various methods, but typically not of direct relevance to users.

splits

a numeric matrix describing the splits: only present if there are any. The row label is the name of the split variable, and columns are count, the number of observations (which are not missing and are of positive weight) sent left or right by the split (for competitor splits this is the number that would have been sent left or right had this split been used, for surrogate splits it is the number missing the primary split variable which were decided using this surrogate), ncat, the number of categories or levels for the variable (+/-1 for a continuous variable), improve, which is the improvement in deviance given by this split, or, for surrogates, the concordance of the surrogate with the primary, and index, the numeric split point. The last column adj gives the adjusted concordance for surrogate splits. For a factor, the index column contains the row number of the csplit matrix. For a continuous variable, the sign of ncat determines whether the subset x < cutpoint or x > cutpoint is sent to the left.

csplit

an integer matrix. (Only present only if at least one of the split variables is a factor or ordered factor.) There is a row for each such split, and the number of columns is the largest number of levels in the factors. Which row is given by the index column of the splits matrix. The columns record 1 if that level of the factor goes to the left, 3 if it goes to the right, and 2 if that level is not present at this node of the tree (or not defined for the factor).

method

character string: the method used to grow the tree. One of "class", "exp", "poisson", "anova" or "user" (if splitting functions were supplied).

cptable

a matrix of information on the optimal prunings based on a complexity parameter.

variable.importance

a named numeric vector giving the importance of each variable. (Only present if there are any splits.) When printed by summary.rpart these are rescaled to add to 100.

numresp

integer number of responses; the number of levels for a factor response.

parms, control

a record of the arguments supplied, which defaults filled in.

functions

the summary, print and text functions for method used.

ordered

a named logical vector recording for each variable if it was an ordered factor.

na.action

(where relevant) information returned by model.frame on the special handling of NAs derived from the na.action argument.

There may be attributes "xlevels" and "levels" recording the levels of any factor splitting variables and of a factor response respectively.

Optional components include the model frame (model), the matrix of predictors (x) and the response variable (y) used to construct the rpart object.

Structure

The following components must be included in a legitimate rpart object.

Plots the Approximate R-Square for the Different Splits

Description

Produces 2 plots. The first plots the r-square (apparent and apparent - from cross-validation) versus the number of splits. The second plots the Relative Error(cross-validation) +/- 1-SE from cross-validation versus the number of splits.

Usage

rsq.rpart(x)

Arguments

x

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

Side Effects

Two plots are produced.

Note

The labels are only appropriate for the "anova" method.

Examples

z.auto <- rpart(Mileage ~ Weight, car.test.frame)
rsq.rpart(z.auto)

Snip Subtrees of an Rpart Object

Description

Creates a "snipped" rpart object, containing the nodes that remain after selected subtrees have been snipped off. The user can snip nodes using the toss argument, or interactively by clicking the mouse button on specified nodes within the graphics window.

Usage

snip.rpart(x, toss)

Arguments

x

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

toss

an integer vector containing indices (node numbers) of all subtrees to be snipped off. If missing, user selects branches to snip off as described below.

Details

A dendrogram of rpart is expected to be visible on the graphics device, and a graphics input device (e.g., a mouse) is required. Clicking (the selection button) on a node displays the node number, sample size, response y-value, and Error (dev). Clicking a second time on the same node snips that subtree off and visually erases the subtree. This process may be repeated an number of times. Warnings result from selecting the root or leaf nodes. Clicking the exit button will stop the snipping process and return the resulting rpart object.

See the documentation for the specific graphics device for details on graphical input techniques.

Value

A rpart object containing the nodes that remain after specified or selected subtrees have been snipped off.

Warning

Visually erasing the plot is done by over-plotting with the background colour. This will do nothing if the background is transparent (often true for screen devices).

Examples

## dataset not in R
## Not run: 
z.survey <- rpart(market.survey) # grow the rpart object
plot(z.survey) # plot the tree
z.survey2 <- snip.rpart(z.survey, toss = 2) # trim subtree at node 2
plot(z.survey2) # plot new tree

# can also interactively select the node using the mouse in the
# graphics window

## End(Not run)

Soldering of Components on Printed-Circuit Boards

Description

The solder.balance data frame has 720 rows and 6 columns, representing a balanced subset of a designed experiment varying 5 factors on the soldering of components on printed-circuit boards.

The solder data frame is the full version of the data with 900 rows. It is located in both the rpart and the survival packages.

Usage

solder

Format

This data frame contains the following columns:

Opening: a factor with levels ‘⁠L⁠’, ‘⁠M⁠’ and ‘⁠S⁠’ indicating the amount of clearance around the mounting pad.
Solder: a factor with levels ‘⁠Thick⁠’ and ‘⁠Thin⁠’ giving the thickness of the solder used.
Mask: a factor with levels ‘⁠A1.5⁠’, ‘⁠A3⁠’, ‘⁠B3⁠’ and ‘⁠B6⁠’ indicating the type and thickness of mask used.
PadType: a factor with levels ‘⁠D4⁠’, ‘⁠D6⁠’, ‘⁠D7⁠’, ‘⁠L4⁠’, ‘⁠L6⁠’, ‘⁠L7⁠’, ‘⁠L8⁠’, ‘⁠L9⁠’, ‘⁠W4⁠’ and ‘⁠W9⁠’ giving the size and geometry of the mounting pad.
Panel: 1:3 indicating the panel on a board being tested.
skips: a numeric vector giving the number of visible solder skips.

Source

John M. Chambers and Trevor J. Hastie eds. (1992) Statistical Models in S, Wadsworth and Brooks/Cole, Pacific Grove, CA.

Examples

fit <- rpart(skips ~ Opening + Solder + Mask + PadType + Panel,
             data = solder.balance, method = "anova")
summary(residuals(fit))
plot(predict(fit), residuals(fit))

Stage C Prostate Cancer

Description

A set of 146 patients with stage C prostate cancer, from a study exploring the prognostic value of flow cytometry.

Usage

data(stagec)

Format

A data frame with 146 observations on the following 8 variables.

pgtime: Time to progression or last follow-up (years)
pgstat: 1 = progression observed, 0 = censored
age: age in years
eet: early endocrine therapy, 1 = no, 2 = yes
g2: percent of cells in G2 phase, as found by flow cytometry
grade: grade of the tumor, Farrow system
gleason: grade of the tumor, Gleason system
ploidy: the ploidy status of the tumor, from flow cytometry. Values are ‘⁠diploid⁠’, ‘⁠tetraploid⁠’, and ‘⁠aneuploid⁠’

Details

A tumor is called diploid (normal complement of dividing cells) if the fraction of cells in G2 phase was determined to be 13% or less. Aneuploid cells have a measurable fraction with a chromosome count that is neither 24 nor 48, for these the G2 percent is difficult or impossible to measure.

Examples

require(survival)
rpart(Surv(pgtime, pgstat) ~ ., stagec)

Summarize a Fitted Rpart Object

Description

Returns a detailed listing of a fitted rpart object.

Usage

## S3 method for class 'rpart'
summary(object, cp = 0, digits = getOption("digits"), file, ...)

Arguments

object

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

digits

Number of significant digits to be used in the result.

cp

trim nodes with a complexity of less than cp from the listing.

file

write the output to a given file name. (Full listings of a tree are often quite long).

...

arguments to be passed to or from other methods.

Details

This function is a method for the generic function summary for class "rpart". It can be invoked by calling summary for an object of the appropriate class, or directly by calling summary.rpart regardless of the class of the object.

It prints the call, the table shown by printcp, the variable importance (summing to 100) and details for each node (the details depending on the type of tree).

Examples

## a regression tree
z.auto <- rpart(Mileage ~ Weight, car.test.frame)
summary(z.auto)

## a classification tree with multiple variables and surrogate splits.
summary(rpart(Kyphosis ~ Age + Number + Start, data = kyphosis))

Place Text on a Dendrogram Plot

Description

Labels the current plot of the tree dendrogram with text.

Usage

## S3 method for class 'rpart'
text(x, splits = TRUE, label, FUN = text, all = FALSE,
     pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,
     fancy = FALSE, fwidth = 0.8, fheight = 0.8, bg = par("bg"),
     minlength = 1L, ...)

Arguments

x

fitted model object of class "rpart". This is assumed to be the result of some function that produces an object with the same named components as that returned by the rpart function.

splits

logical flag. If TRUE (default), then the splits in the tree are labeled with the criterion for the split.

label

For compatibility with rpart2, ignored in this version (with a warning).

FUN

the name of a labeling function, e.g. text.

all

Logical. If TRUE, all nodes are labeled, otherwise just terminal nodes.

minlength

the length to use for factor labels. A value of 1 causes them to be printed as ‘a’, ‘b’, ..... Larger values use abbreviations of the label names. See the labels.rpart function for details.

pretty

an alternative to the minlength argument, see labels.rpart.

digits

number of significant digits to include in numerical labels.

use.n

Logical. If TRUE, adds to label ⁠(#events level1/ #events level2/⁠ etc. for class, n for anova, and ⁠#events/n⁠ for poisson and exp).

fancy

Logical. If TRUE, nodes are represented by ellipses (interior nodes) and rectangles (leaves) and labeled by yval. The edges connecting the nodes are labeled by left and right splits.

fwidth

Relates to option fancy and the width of the ellipses and rectangles. If fwidth < 1 then it is a scaling factor (default = 0.8). If fwidth > 1 then it represents the number of character widths (for current graphical device) to use.

fheight

Relates to option fancy and the height of the ellipses and rectangles. If fheight <1 then it is a scaling factor (default = 0.8). If fheight > 1 then it represents the number of character heights (for current graphical device) to use.

bg

The color used to paint the background to annotations if fancy = TRUE.

...

Graphical parameters may also be supplied as arguments to this function (see par). As labels often extend outside the plot region it can be helpful to specify xpd = TRUE.

Side Effects

the current plot of a tree dendrogram is labeled.

Examples

freen.tr <- rpart(y ~ ., freeny)
par(xpd = TRUE)
plot(freen.tr)
text(freen.tr, use.n = TRUE, all = TRUE)

Return Cross-Validated Predictions

Description

Gives the predicted values for an rpart fit, under cross validation, for a set of complexity parameter values.

Usage

xpred.rpart(fit, xval = 10, cp, return.all = FALSE)

Arguments

fit

a object of class "rpart".

xval

number of cross-validation groups. This may also be an explicit list of integers that define the cross-validation groups.

cp

the desired list of complexity values. By default it is taken from the cptable component of the fit.

return.all

if FALSE return only the first element of the prediction

Details

Complexity penalties are actually ranges, not values. If the cp values found in the table were .36, .28, and .13, for instance, this means that the first row of the table holds for all complexity penalties in the range [.36, 1], the second row for cp in the range [.28, .36) and the third row for [.13,.28). By default, the geometric mean of each interval is used for cross validation.

Value

A matrix with one row for each observation and one column for each complexity value. If return.all is TRUE and the prediction for each node is a vector, then the result will be an array containing all of the predictions. When the response is categorical, for instance, the result contains the predicted class followed by the class probabilities of the selected terminal node; result[1,,] will be the matrix of predicted classes, result[2,,] the matrix of class 1 probabilities, etc.

Examples

fit <- rpart(Mileage ~ Weight, car.test.frame)
xmat <- xpred.rpart(fit)
xerr <- (xmat - car.test.frame$Mileage)^2
apply(xerr, 2, sum)   # cross-validated error estimate

# approx same result as rel. error from printcp(fit)
apply(xerr, 2, sum)/var(car.test.frame$Mileage) 
printcp(fit)

Automobile Data from 'Consumer Reports' 1990

Description

Usage

Format

Source

See Also

Examples

Automobile Data from 'Consumer Reports' 1990

Description

Usage

Format

Source

See Also

Examples

Automobile Data from 'Consumer Reports' 1990

Description

Usage

Format

Source

See Also

Examples

Data on Children who have had Corrective Spinal Surgery

Description

Usage

Format

Source

Examples

Create Split Labels For an Rpart Object

Description

Usage

Arguments

Value

See Also

Mean-Variance Plot for an Rpart Object

Description

Usage

Arguments

Value

Side Effects

See Also

Examples

Handles Missing Values in an Rpart Object

Description

Usage

Arguments

Details

Follow Paths to Selected Nodes of an Rpart Object

Description

Usage

Arguments

Details

Value

Graphical Interaction

References

See Also

Examples

Plot an Rpart Object

Description

Usage

Arguments

Details

Value

Side Effects

See Also

Examples

Plot a Complexity Parameter Table for an Rpart Fit

Description

Usage

Arguments

Details

Value

Side Effects

See Also

PostScript Presentation Plot of an Rpart Object

Description

Usage

Arguments

Details

Side Effects

See Also