# function to draw screeplots of cumulative
# eigenvalues in classical metric scaling

CMDscreeplot<-function(mydata,raw=T,abs=T,maxcomp=10) {
n=min(dim(mydata))-1
x<-cmdscale(as.matrix(mydata),k=n,eig=TRUE)

#x<-cmdscale(as.matrix(mydata))


k<-min(n,maxcomp)
w<-c(0:k)

if (raw==T) y<-x$eig


if (raw==F & abs==T) y<-abs(x$eig)
if(raw==F & abs==F) y<- x$eig*x$eig
y<-c(0,y)
z<-100*cumsum(y)/sum(y)

if (raw==T) { 
plot(w,z[1:(k+1)],type="l",xlab="number of dimensions",
 cex.main=1.5, lwd=3, col="red",
 ylim=c(0,100),
 ylab="cumulative percentage of total eigenvlaues",
  main="Scree plot of eigenvalues",
 xaxt="n", yaxt="n") 
}

if (raw==F & abs==T) { plot(w,z[1:(k+1)],type="l",xlab="number of dimensions",
 cex.main=1.5, lwd=3, col="red",
 ylim=c(0,100),
 ylab="cumulative percentage of total absolutes eigenvalues",
  main="Scree plot of absolute values of eigenvalues",
 xaxt="n", yaxt="n") }
 
if (raw==F & abs==F) { plot(w,z[1:(k+1)],type="l",xlab="number of dimensions",
 cex.main=1.5, lwd=3, col="red",
 ylim=c(0,100),
 ylab="cumulative percentage of total variance",
  main="Scree plot of squared eigenvalues",
 xaxt="n", yaxt="n") }
 
axis(1,at=w,lwd=2)
axis(2,at=c(0,20,40,60,80,100),lwd=2)
abline(a=100,b=0,lwd=2,lty="dashed",col="orange")
text(w,z[1:(k+1)],labels=w,cex=0.8,adj=c(1.2,-.1),col="blue")
}


# Examples of calls to it are
#default choice using raw eigenvalues and maximum of ten
CMDscreeplot(towns)
# same as 
CMDscreeplot(towns,raw=TRUE,maxcomp=10) 
#
# plot using absolute values of eigenvalues
CMDscreeplot(towns,raw=FALSE,abs=TRUE,maxcomp=10) 
#same as 
CMDscreeplot(towns,raw=FALSE,maxcomp=10) 
#
# plot using squared eigenvalues
CMDscreeplot(towns,raw=FALSE,abs=FALSE,maxcomp=10) 
#