##SCRIPT TO READ MANN DATA AND STORE AS R-TABLES
   # an updated collation script is used for MM05	
   # downloads and collates the following. Save commands are commented out, but can be easily restored.

	#temperature eigenvectors 	- eof.tab
	#temperature PCs		- pc.tab
	#temperature eigenvalues	- lambda.tab
	#MBH gridpoints			- grid2.tab	
	#PCa weights			- pca.weights.tab
	#5 reconstructed temperature PCs- rpc.tab
	#NH reconstruction		- nhmann.tab
	#reconstruction weights		- weights1.txt
	#gridcell standard deviations	- grid2 
	#MBH cells with no CRU values 	- nil	
		#calculated from Jones data
	#gridcell st dev from CRU	- mann.scale
		#calcualted from Jones data

##COLLATION OF MBH DATA  
  ## EOFs
  #load 16 EOFs dim 16x1082
     #this is also at Corrigendum SI  #Sept 2004
	url<-"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS"
	eof<-array(rep(NA,16*1082),dim=c(1082,16))
	id<-c("01","02","03","04","05","06","07","08","09","10","11","12","13","14","15","16")
	for ( k in 1: 16 ) {
		loc<-file.path(url,paste("eof",id[k],".out",sep=""))	
		eof[,k]<-read.table(loc)[,2]
		}	
	dimnames(eof)[[2]]<-paste("PC",id)

  ###PCs
  #note: although PC decomposition is on monthly data from 1902-1993, this is annual data
  # zeroed to 1902-1980 (matching regression against proxies)
  # some care has to be taken here
  #this is also at Corrigendum SI
	loc1<-c(paste("0",1:9,sep=""),paste("1",0:6,sep=""))
	loc<-file.path("ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS",paste("pc",loc1,".out",sep=""))
	pc<-NULL;
	for (m in 1:16)  {
		g<-read.table(loc[m])
		stemp<-g[,2]
		pc<-cbind(pc,stemp);
		}
	dimnames(pc)[[2]]<-paste("PC",loc1)

  ##EIGENVALUES
	#also at Corrigendum SI
	#col1-eigenvector; col2 - standard deviation; col 3- % of total variance; col4 - cumulative pct of total variance 
	loc1<-"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/tpca-eigenvals.out";
	lambda<-scan(file=loc1,n=1082*4,skip=0);
	lambda<-t(array(lambda,dim=c(4,1082)));


  ##GRIDPOINTS - SAVE AS TABLE WITH JONES GRID BOXES
	loc1<-"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/gridpoints.loc"
	grid2<-read.table(file=loc1) ##the dimension is 1082x5 and is read as a data.frame

	##this corresponds to Mann's 1082 locations
	#col1 is long index 1,...72 from Greenwich going east; col 2 lat index 1,..36 going N to S; col 3 is grid-box long centre; col 4 is grid-box lat centre;
	#the Mann lat index is the sames as the Jones lat index;
	#this script puts Jones long index in col 5

	for (i in 1:1082) {
		latgp<-grid2[i,2];longgp<-grid2[i,1];
		if (longgp>36) longgp<-grid2[i,1]-36 else longgp<-grid2[i,1]+36;#converts Mann long-gp to Jones long-gp
		grid2[i,5]<-72*(latgp-1)+longgp;###saves series # for reference to Jones data
		} # this is inelegant but I couldn't find mod-function in R
	#save(grid2,file="c:/climate/data/mann/gridpoints.tab")


  ##PCA WEIGHTS
	loc1<-"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/pca-weights.out";
	pcaweights<-scan(file=loc1,n=128*2,skip=0);
	pcaweights<-t(array(pcaweights,dim=c(2,128)));
	#save(pcaweights,file="c:/climate/data/mann/pcaweights.tab")

  ###RECONSTRUCTED PC FROM 1400 TO 1980 (VARYING FIRST YEARS)
	loc<-c("ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/rpc01.dat",
		"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/rpc02.dat",
		"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/rpc03.dat",
		"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/rpc04.dat",
		"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/EIGENVECTORS/rpc05.dat")

	rpcyear1<-c(1400,1450,1750,1760,1450)
	n<-1981-rpcyear1;
	k<-rpcyear1-1399;
	rpc<-c(rep(NA,581*5));
	rpc<-array(rpc,dim=c(5,581));
	dim(rpc);

	for (m in 1:5)  {
		skip1<-1;
		s<-scan(file=loc[m],n=581*2,skip=skip1);
		s<-array(s,dim=c(2,n[m]));
		rpc[m,k[m]+0:(n[m]-1)]<-s[2,];
		}
	rpc<-t(rpc);
	rpc<-ts(rpc,start=1400,end=1980);##possible conversion to ts format
	locf<-"c:/climate/data/mann/rpc.tab";
	#save(rpc,file=locf);

  ###NH MEAN 1400-1995
	#note: in earlier download this was only to 1995.
	loc1<-"ftp://eclogite.geo.umass.edu/pub/mann/MANNETAL98/nhmean.dat";
	nhmann<-read.table(loc1,skip=1,fill=TRUE)
	b<-c("year","NH.RECON","NH.RAW","-1.sigma","-2.sigma","+1.sigma","+2.sigma")
	dimnames(nhmann)[[2]]<-b
		##col1-year; col2- NH reconstruction; col3-NH -raw; col4- minus 1 sigma; col5- minus 2 sigma; col6- plus 1 sigma; col7 -plus 2 sigma
	nhmann[582:599,c(2,4,5,6,7)]<-NA
	nhmann[1:502,3]<-NA
	locf<-"c:/climate/data/mann/nhmann.tab";
	#save(nhmann,file=locf);

  ###WEIGHTS IN RECONSTRUCTION
	#these match wieghts in original email and provide public location. Impossible to tell that these weights are used and not mentioned in Corrigendum: Apr 06
	#g<-read.table("ftp://holocene.evsc.virginia.edu/pub/MBH98/PCS/multiproxy.inf")
	#temp<-(g[,1]<0); weights1<-g[!temp,1]
		#blocked for me

	weights1<-scan("http://www.climate2003.com/data/MM03/weights.txt",skip=1)

  ##GRIDPOINT STANDARD DEVIATIONS
	#these were not archived originally and original temperature data not then available
	#so CRU data from  summer 2003 was downloaded and standard deviations calculated
		#see read.jones.txt for this
	#4 cells had NO data and logical vector keeps track of this
 	mann.scale<-c(read.table("c:/climate/data/mann/mann.scale.txt"))
	nil<-c(read.table("c:/climate/data/mann/nil.txt"))
		#these are 4 cells with NO values in updated CRU