VDA-package: Multicategory Vertex Discriminant Analysis

In VDA: VDA

Description

This package provides functions to optimize and execute Multicategory Vertex Discriminant Analysis, a method of supervised learning for an outcome with k predictor categories. Outcome classification is based on linear discrimination among the vertices of a regular simplex in a k-1-dimension Euclidean space, where each vertex represents a different category.

Details

Package:	VDA
Type:	Package
Version:	1.3
Date:	2013-Jul-05
License:	GPL-2
LazyLoad:	yes

Author(s)

Edward Grant, Xia Li, Kenneth Lange, Tong Tong Wu

Maintainer: Edward Grant [e-mail]

References

Lange, K. and Wu, T.T. (2008) An MM Algorithm for Multicategory Vertex Discriminant Analysis. Journal of Computational and Graphical Statistics, Volume 17, No 3, 527-544.

Examples

#load dataset from package
data(zoo)

#matrix containing all predictor vectors
x <- zoo[,2:17]

#outcome class vector
y <- zoo[,18]

#run VDA (ridge penalty)
out <- vda.r(x, y)

#Predict five cases based on VDA 
fivecases <- matrix(0,5,16)
fivecases[1,] <- c(1,0,0,1,0,0,0,1,1,1,0,0,4,0,1,0)
fivecases[2,] <- c(1,0,0,1,0,0,1,1,1,1,0,0,4,1,0,1)
fivecases[3,] <- c(0,1,1,0,1,0,0,0,1,1,0,0,2,1,1,0)
fivecases[4,] <- c(0,0,1,0,0,1,1,1,1,0,0,1,0,1,0,0)
fivecases[5,] <- c(0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0)
predict(out, fivecases)

#run vda.le (lasso and euclidean penalty)
outLE <- vda.le(x, y)

#Predict five cases based on VDA 
fivecases <- matrix(0,5,16)
fivecases[1,] <- c(1,0,0,1,0,0,0,1,1,1,0,0,4,0,1,0)
fivecases[2,] <- c(1,0,0,1,0,0,1,1,1,1,0,0,4,1,0,1)
fivecases[3,] <- c(0,1,1,0,1,0,0,0,1,1,0,0,2,1,1,0)
fivecases[4,] <- c(0,0,1,0,0,1,1,1,1,0,0,1,0,1,0,0)
fivecases[5,] <- c(0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0)
predict(outLE, fivecases)

Example output

Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
[1] 1 1 2 4 7
[1] 1 1 2 4 7

VDA documentation built on May 29, 2017, 6:32 p.m.