# The MIT License
# Copyright (c) 2007 The GGobi Foundation
# http://www.ggobi.org/book/code-license.txt


# Read data
d.olive<-read.csv("olive.csv",row.names=1)
d.olive.sub <- subset(d.olive,
   select=c(region,palmitic:eicosenoic))
d.flea<-read.csv("flea.csv")

# load libraries
#library(MASS)
library(rggobi)

# Fit the model
olive.lda <- lda(region~., d.olive.sub)
pregion<-predict(olive.lda,d.olive.sub)$class
table(d.olive[,1],pregion)
plot(predict(olive.lda, d.olive.sub)$x)
gd <- ggobi(cbind(d.olive, pregion))[1]
glyph_color(gd) <- c(rep(6,323), rep(5,98), rep(1,151))

# Compute and view variance-covariance ellipses
d.flea.varcov<-rbind(f.var.ellipse(d.flea[d.flea[,1]=="Concinna",-1]),
  f.var.ellipse(d.flea[d.flea[,1]=="Heikert.",-1]),
  f.var.ellipse(d.flea[d.flea[,1]=="Heptapot.",-1]))
colnames(d.flea.varcov)<-colnames(d.flea[,-1])
d.flea.varcov<-rbind(d.flea[,-1],d.flea.varcov)
gd <- ggobi(d.flea.varcov)[1]
glyph_color(gd)<-c(rep(6,21),rep(5,22),rep(1,31),rep(6,100),rep(1,100),rep(5,100))
glyph_type(gd)<-c(rep(3,74),rep(6,300))
glyph_size(gd)<-c(rep(5,74),rep(2,300))