example-css.R
In GMD: Generalized Minimum Distance of distributions

## load library
require("GMD")

## simulate data around 12 points in Euclidean space
pointv <- data.frame(x=c(1,2,2,4,4,5,5,6,7,8,9,9),y=c(1,2,8,2,4,4,5,9,9,8,1,9))
set.seed(2012)
mydata <- c()
for (i in 1:nrow(pointv)){
  mydata <- rbind(mydata,cbind(rnorm(10,pointv[i,1],0.1),rnorm(10,pointv[i,2],0.1)))
}
mydata <- data.frame(mydata); colnames(mydata) <- c("x","y")
plot(mydata,type="p",pch=21, main="Simulated data")

## determine a "good" k using elbow
dist.obj <- dist(mydata[,1:2])
hclust.obj <- hclust(dist.obj)
css.obj <- css.hclust(dist.obj,hclust.obj)
elbow.obj <- elbow.batch(css.obj)
print(elbow.obj)

## make partition given the "good" k
k <- elbow.obj$k; cutree.obj <- cutree(hclust.obj,k=k)
mydata$cluster <- cutree.obj

## draw a elbow plot and label the data
dev.new(width=12, height=6)
par(mfcol=c(1,2),mar=c(4,5,3,3),omi=c(0.75,0,0,0))
plot(mydata$x,mydata$y,pch=as.character(mydata$cluster),col=mydata$cluster,cex=0.75,
     main="Clusters of simulated data")
plot.elbow(css.obj,elbow.obj,if.plot.new=FALSE)

## clustering with more relaxed thresholds (, resulting a smaller "good" k)
elbow.obj2 <- elbow.batch(css.obj,ev.thres=0.90,inc.thres=0.05)
mydata$cluster2 <- cutree(hclust.obj,k=elbow.obj2$k)

dev.new(width=12, height=6)
par(mfcol=c(1,2), mar=c(4,5,3,3),omi=c(0.75,0,0,0))
plot(mydata$x,mydata$y,pch=as.character(mydata$cluster2),col=mydata$cluster2,cex=0.75,
     main="Clusters of simulated data")
plot.elbow(css.obj,elbow.obj2,if.plot.new=FALSE)