##TEMPERATURE CORRELATION
   #this calculates statlist with 6 items in list 

 #Mann PRoxy Data and Info 
  method="online"
   if (method=="offline") {load("d:/climate/data/mann08/mann.tab")
	load("d:/climate/data/mann08/mannorig.tab")
	load("d:/climate/data/mann08/idorig.tab")
 	names(mannorig)=idorig$idorig
	load("d:/climate/data/mann08/details.tab")
	source("d:/climate/scripts/mann.2008/instrumental.txt")} else {
	url="http://www.climateaudit.org/data/mann.2008"
	download.file(file.path(url,"mann.tab"),"temp.dat",mode="wb");load("temp.dat")
	download.file(file.path(url,"mannorig.tab"),"temp.dat",mode="wb");load("temp.dat")
	download.file(file.path(url,"details.tab"),"temp.dat",mode="wb");load("temp.dat")
	download.file(file.path(url,"idorig.tab"),"temp.dat",mode="wb");load("temp.dat")
	names(mannorig)=idorig$idorig
	source("http://www.climateaudit.org/scripts/mann.2008/instrumental.txt")}


	#notes: details.tab here incorporates lat-longs from rtable. 

 ##FUNCTIONS
	g=function(X) ts(X[,2],start=X[1,1])
	use0="pairwise.complete.obs"
	absmax= function(x) if(sum(!is.na(x))>0) unique(x[(abs(x)==max(abs(x),na.rm=T))&!is.na(abs(x))])[1] else NA
	library(gplots)
	source("http://www.climateaudit.org/scripts/utilities.txt")


#################
##CALCULATE CORRELATIONS FOR VARIETY OF CASES
  #gridcell and next-nearest for both infilled and original; si and rtable


  statlist=rep(list(NA),6)
  names(statlist)[1:6]=c("grid_infill","grid_orig","next_infill","next_orig","si","rtable")

  #1.  GRIDCELL AND INFILLED
      stat=array(NA,dim=c(1209,6))
	for(k in 1:1209) {
	 test=match(info$jones[!is.na(info$mann)],details$jones[k]);temp=!is.na(test)	
	if(sum(temp) ==1){	
          index=info$mannid[!is.na(info$mann)][temp];index
	   x=ts.union(inst[,paste(index)],g(mann[[k]]) )
	   temp1=(time(x)>=1850)&(time(x)<=1995)
	   temp2=(time(x)>=1850)&(time(x)<=1949)
	   temp3=(time(x)>=1896)&(time(x)<=1995)
	  stat[k,1:3]=round(c(	cor(x[temp1,],use=use0)[1,2]	,cor(x[temp2,],use=use0)[1,2]	,cor(x[temp3,],use=use0)[1,2] ),3)
       }}
    	statlist[["grid_infill"]]=stat[,1:3]	

  #2.  GRIDCELL AND ORIGINAL
	for(k in 1:1209) {
	 test=match(info$jones[!is.na(info$mann)],details$jones[k]);temp=!is.na(test)	
	if(sum(temp) ==1){	
          index=info$mannid[!is.na(info$mann)][temp];index
	   x=ts.union(inst[,paste(index)],g(mannorig[[details$old[k]]]) )
	   temp1=(time(x)>=1850)&(time(x)<=1995)
	   temp2=(time(x)>=1850)&(time(x)<=1949)
	   temp3=(time(x)>=1896)&(time(x)<=1995)
	  stat[k,4:6]=round(c(	cor(x[temp1,],use=use0)[1,2]	,cor(x[temp2,],use=use0)[1,2]	,cor(x[temp3,],use=use0)[1,2] ),3)
       }}
	statlist[["grid_orig"]]=stat[,4:6]

  #3. NEXTNEAREST AND INFILLED
	statnext=array(NA,dim=c(1209,6) )
	
	for(k in 1:387) {
	 #test=match(info$jones[!is.na(info$mann)],details$jones[k]+details$nextnearest[k]);temp=!is.na(test)	
 	test=match(info$jones[!is.na(info$mann)],c(details$next1[k],details$next2[k]) );temp=!is.na(test)	
	if(sum(temp) > 1){	
          index=info$mannid[!is.na(info$mann)][temp];index
   	  x=ts.union(inst[,paste(index)],g(mann[[k]]) )
	   temp1=(time(x)>=1850)&(time(x)<=1995)
	   temp2=(time(x)>=1850)&(time(x)<=1949)
	   temp3=(time(x)>=1896)&(time(x)<=1995)
	  statnext[k,1:6]=round(c( cor(x[temp1,],use=use0)[1:2,3]	,cor(x[temp2,],use=use0)[1:2,3]	,cor(x[temp3,],use=use0)[1:2,3] ),3)
       }}
	statlist[["next_infill"]]=statnext[,1:3]

 #4. NEXTNEAREST AND ORIGINAL
	for(k in 1:1209) {
	test=match(info$jones[!is.na(info$mann)],c(details$next1[k],details$next2[k]) );temp=!is.na(test)	
	if(sum(temp) >11){	
          index=info$mannid[!is.na(info$mann)][temp];index
  	  x=ts.union(inst[,paste(index)],g(mannorig[[details$old[k]]]) )
 	   temp1=(time(x)>=1850)&(time(x)<=1995)
	   temp2=(time(x)>=1850)&(time(x)<=1949)
	   temp3=(time(x)>=1896)&(time(x)<=1995)
	  statnext[k,1:6]=round(c( cor(x[temp1,],use=use0)[1:2,3]	,cor(x[temp2,],use=use0)[1:2,3]	,cor(x[temp3,],use=use0)[1:2,3] ),3)
         }}

	statlist[["next_orig"]]=statnext[,4:6]

 #5. MANN SI
	statlist[["si"]]=details[,c("r1850_1995","r1896_1995","r1850_1949")]  #collated from SD1        

 #6. MANN RTABLE
	statlist[["rtable"]]=details[,c("rtable.r1850_1995", "rtable.r1850_1995lf","rtable.r1896_1995","rtable.r1896_1995lf"  )]  
		#collated from rtable