--- a/cdf.r	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-# bin and average
-binaverage = function(x,nbin,rankORvalue){
-# use x[,1] to bin x[,2]
-	binned = list()
-	if (rankORvalue == 'value'){
-		mi = min(x[,1])
-		ma = max(x[,1])
-		bins = seq(mi,ma,length.out=nbin+1)
-		bins[1] = bins[1] - abs(mi)/100
-		bins[nbin+1] = bins[nbin+1] + abs(ma)/100
-		for (i in 1:nbin){
-			binned[[i]] = x[x[,1] >= bins[i] & x[,1] < bins[i+1],2]
-		}
-		bins[1] = bins[1] + abs(mi)/100
-		bins[nbin+1] = bins[nbin+1] - abs(ma)/100
-	} else {
-		x = x[order(x[,1]),]
-		step = round(nrow(x)/nbin)
-		bins = x[1,1]
-		for (i in 1:(nbin-1)){
-			binned[[i]] = x[((i-1)*step+1):(i*step),2]
-			bins = c(bins,x[i*step+1,1])
-		}
-		binned[[nbin]] = x[((nbin-1)*step+1):nrow(x),2]
-		bins[nbin+1] = x[nrow(x),1]
-	}
-# bin lavel
-	labels = character(0)
-	for (i in 1:nbin){
-		labels = c(labels,paste(format(bins[i],digits=2,nsmall=2),format(bins[i+1],digits=2,nsmall=2),sep='~'))	
-	}
-    list(binned=binned,bins=bins,labels=labels)
-}
-#res = binaverage(x,3,'rank')
-
-# CDF plot and KS.test
-mycdf = function(list,title,labels,legendposition,xlabel,legend_title){
-    L = length(list)
-    
-    # barplot for mean and std
-    avg = numeric(L)
-    err = numeric(L)
-    for (i in 1:L){
-        avg[i] = mean(list[[i]])
-        err[i] = sd(list[[i]])
-    }
-    #print(list[[1]])
-    #print(list[[2]])
-    #print(avg)
-    #print(err)
-	par(cex=1.5,mar=c(8,6,6,4))
-    xticks <- barplot(avg,names.arg=labels,las=2,ylab=xlabel,main='mean and standard deviation',xlab=legend_title,ylim=c(0,max(avg+err)))
-    arrows(xticks,avg+err, xticks, avg-err, angle=90, code=3, length=0.0)
-    
-	if (L>1){
-    # ks test
-	cat('\nKS test:\n')
-	cat('sample1\tsample2\tp-value\n')
-	cat('-------------------------------------------------\n')
-    for (i in 1:(L-1)){
-        for (j in (i+1):L){
-        cat(labels[i],'\t',labels[j],'\t')
-        ks = ks.test(list[[i]],list[[j]])
-        pv = max(2.2e-16,ks$p.value)
-	    pv = format(pv,digits=3,nsmall=2)
-		cat(pv,'\n')
-        }
-    }
-	cat('-------------------------------------------------\n')
-	}
-	if (L == 2){
-		title = paste(title,'\np=',pv,sep='')
-	}
-    # cdf plot
-    listx = list()
-    listy = list()
-    mi = 1e10
-    ma = 1e-10
-    for (i in 1:L){
-        mi = min(mi,list[[i]])
-        ma = max(ma,list[[i]])
-    }
-    for (i in 1:L){
-        listx[[i]] = c(mi,listx[i],ma)
-        listy[[i]] = c(0,listy[i],1)
-    }
-    for (i in 1:L){
-        mi = min(mi,list[[i]])
-        ma = max(ma,list[[i]])
-        listx[[i]] = sort(list[[i]])
-        listy[[i]] = c(1:length(list[[i]]))/length(list[[i]])          
-    }
-#par(xlog=(xlog=='xlog'))
-    plot(listx[[1]],listy[[1]],type='l',lty=1,lwd=2,col=2,main=title,xlab=xlabel,ylab='cumulative frequency')
-    for (i in 2:L){
-        lines(listx[[i]],listy[[i]],type='l',lty=i,lwd=2,col=i+1)
-    }
-    # legend
-    for (i in 1:L){
-        labels[i] = paste(labels[i],', n=',length(list[[i]]),sep='')
-    }
-    legend(legendposition,legend=labels,col=2:(L+1), lty=1:L,lwd=2, bty='n',title=legend_title)
-}