##ABABNEH

   ##SHEEP MOUNTAIN
	url="d:/climate/data/tree/chronologies/r/northamerica"
	loc=file.path(url,"ca534.crn.tab")
	load(loc)
	ca534=ts(chron.crn[(1000:tsp(chron.crn)[2])-tsp(chron.crn)[1]+1],start=1000)
	ts.plot(ca534,xlim=c(1000,2000))

	loc=file.path(url,"ca046.crn.tab")
	load(loc);
	ca046=ts(chron.crn[(1000:tsp(chron.crn)[2])-tsp(chron.crn)[1]+1],start=1000)

	ts.plot(chron.crn,xlim=c(1000,2000),xaxs="i")


	plot(c(time(ca046)),ca046/1000,type="l",col="blue",xlim=c(1171,2007),xaxs="i",xlab="",ylab="Tree ring index",ylim=c(.2,2.4),yaxs="i",axes=FALSE)
	axis(side=1);box();axis(side=2,las=1,at=seq(0.2,2.4,.2))
	temp=(time(ca534)<=1980)
	lines(c(time(ca534))[temp],ca534[temp]/1000,col="black")
	lines(c(time(ca534))[!temp],ca534[!temp]/1000,col="grey80")
	lines(c(time(ca046)),ca046/1000,col="blue")

	abline(h=seq(0.4,2.2,.2),lty=3);abline(h=1)
	temp=(time(ca534)==1980)
	points(c(time(ca534))[temp],ca534[temp]/1000,pch=19,col="red",cex=1.4)
	temp=(time(ca046)==1970)
#	points(c(time(ca046))[temp],ca046[temp]/1000,pch=19,col="green",cex=1.4)



  ##THESIS
	url="d:/climate/data/hughes/ababneh_dissertation_fig4.txt"
	abab=read.table(url,skip=19,header=TRUE,sep="\t",fill=TRUE,nrow=832)
	abab=ts(abab[,4],start=abab[1,1])
	test=read.table(url,skip=19+835,sep="\t",header=TRUE,fill=TRUE)#,nrow=832)
	test=ts(test[,4],start=test[1,1])
	abab=ts.union(abab,test);dimnames(abab)[[2]]=c("abab","lamarche")

	
  ##COMPARE DIGITZED LAMARCHE TO ARCHIVED LAMARCHE	
	plot(c(time(abab)),abab[,"lamarche"],type="l",xlab="",ylab="")
	lines(c(time(ca046)),ca046/1000,col="red")


##ABABNEH SPLICE	
 ##THESIS
	url="d:/climate/data/hughes/ababneh_dissertation_fig4.txt"
	abab=read.table(url,skip=19,header=TRUE,sep="\t",fill=TRUE,nrow=832)
	abab=ts(abab[,4],start=abab[1,1]);tsp(abab) #1171 2002

	Z=ts.union(combine[,1]/1000,abab);tsp(Z) #200 2002
	Z=data.frame(Z); 
	names(Z)=c("ca534","abab"); 
	fm=lm(abab~ca534,data=Z[(1000:1750)-199,]) ;summary(fm)

	splice=ts( c(combine[(200:1170)-199,1]/1000,abab[(1171:1980)-1170]),start=200)
	combine[,1]=splice
	combine=extend.persist(combine)
	pca.abab=prcomp(combine,scale=TRUE)
	par(mar=c(3,3,3,1))
	barplot(-pca.abab$rotation[,1],names.arg=as.character(test1$id),ylim=c(0,1))
	  mtext(side=3,"Mann and Jones 2003 PC1 Weights: Updated",line=2,font=2)
	  box()
	  mtext(side=3,"Centered, Scaled, Ababneh Update",line=1,font=2)
	 	
	par(mar=c(3,3,2,1))
	plot(200:1980,scale(pca.mannomatic$u[,1]),col="red",type="l",ylab="",xlab="")
	lines(200:1980,scale(-pca.abab$x[,1]))
	title(main="Mann and Jones 2003 PC1s")

	nf=layout(array(1:2,dim=c(2,1)),heights=c(1.1,1.3))
	par(mar=c(0,3,2,1))
	plot(200:1980,scale(pca.mannomatic$u[,1]),type="l",ylab="",xlab="",axes=FALSE)
	axis(side=1,labels=FALSE);axis(side=2,las=1);box();abline(h=0,lty=2)
	  title("Comparison of Mann and Jones 2003-Style PC1s")
	  text(180,3.8,"Mannomatic with Graybill Version",pos=4,font=2)
	par(mar=c(3,3,0,1))
	plot(200:1980,scale(-pca.abab$x[,1]),type="l",ylab="",xlab="",axes=FALSE)
	axis(side=1);axis(side=2,las=1);box();abline(h=0,lty=2)
	  text(180,2.8,"Correlation PC1 with Ababneh Update",pos=4,font=2)