rpart to graphNEL Converter

Description

Creates an object of class graphNEL from one of class rpart.

Usage

rpart2gNEL(tr, remap=function(x) x, nsep="\n")

Arguments

Details

Not explicitly used in the book, but the basis for a certain graph illustrating application of rpart. The newer coin/party packages have more interesting rendering approaches based on graphviz.

grabSplitV is a utility function for acquiring the variable names, remapAff will remap affymetrix probe names to gene symbols for use in the remap parameter.

Value

a graphNEL-class instance with nodes constructed to convey information on the data tree fit

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

See Also

rpart, graphNEL-class

Examples

library(rpart)
example(rpart)
ff = rpart2gNEL(fit2)
ff
nodes(ff)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(RbcBook1)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: graph
Loading required package: rpart
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RbcBook1/rpart2gNEL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rpart2gNEL
> ### Title: rpart to graphNEL Converter
> ### Aliases: rpart2gNEL rpart2gNEL grabSplitV remapAff
> ### Keywords: models
> 
> ### ** Examples
> 
> library(rpart)
> example(rpart)

rpart> fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)

rpart> fit2 <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis,
rpart+               parms = list(prior = c(.65,.35), split = "information"))

rpart> fit3 <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis,
rpart+               control = rpart.control(cp = 0.05))

rpart> par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped

rpart> plot(fit)

rpart> text(fit, use.n = TRUE)

rpart> plot(fit2)

rpart> text(fit2, use.n = TRUE)
> ff = rpart2gNEL(fit2)
> ff
A graphNEL graph with directed edges
Number of Nodes = 5 
Number of Edges = 4 
> nodes(ff)
[1] "absent\n(64:17)"  "absent\n(44:2)"   "present\n(20:15)"
[4] "absent\n(9:1)"    "present\n(11:14)"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>