#LOEHLE COLLATION
#this returns a list of length 18 in which each item is a table with two columns c("year","t")
	#bp s have been converted to year using 1950. For ocean sediments, this may or may not yield consistent results as authors weren't thinking in terms of the type of synchronoization discussed here

	proxy<-rep(list(NA),18)
	id<-c("GRIP","conroy","chesapeake","sargasso","caribbean","tsuolb", "shihua", "yang", "holmgren","demonocal","farmer","calvo","stott1","stott2","viau",
			"ge","kim","mangini")
	names(proxy)=id



#1) GRIP borehole  temperature (Dahl-Jensen et al., 1998); See Moberg Nature site supplementary material
#2) Conroy Lake pollen (Gajewski, 1988); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/pollen/recons/liadata.txt
#3) Chesapeake Bay Mg/Ca (Cronin et al., 2003); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/cronin2003/
#4) Sargasso Sea 18O (Keigwin, 1996); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/keigwin1996/
#5) Caribbean Sea 18O (Nyberg et al., 2002); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/nyberg2002/ converted to temperature on the Moberg article nature site suppl material
#6) Lake Tsuolbmajavri diatoms (Korhola et al., 2000); See Moberg Nature site supplementary material
#7) Shihua Cave layer thickness (Tan et al., 2003); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/speleothem/china/shihua_tan2003.txt use col 7 temp
#8.) China composite (Yang et al., 2002) which does use tree ring width for two out of the eight series that are averaged to get the composite, or 1.4% of the total data input to the mean computed below;ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/yang2002/china_temp.txt
#9) speleothem data from a South African cave (Holmgren et al., 1999); from author—email sent for archive link
#10) SST variations (warm season) off West Africa (deMenocal et al., 2000); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/demenocal2000/
#11) SST from the southeast Atlantic (Farmer et al., 2005); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/farmer2005/
#12) SST reconstruction in the Norwegian Sea (Calvo et al., 2002); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/pollen/recons/liadata.txt
#13-14) SST from two cores in the western tropical Pacific (Stott et al., 2004); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/stott2004/
#15) mean temperature for North America based on pollen profiles (Viau et al.,2006); http://www.lpc.uottawa.ca/data/reconstructions/index.html
#16) a phenology-based reconstruction from China (Ge et al., 2003); ftp://ftp.ncdc.noaa.gov/pub/data/paleo/historical/china/china_winter_temp.txt
#17) annual mean SST for northern Pacific site SSDP-102 (Latitude 34.9530, Longitude 128.8810) from Kim et al. (2004); http://doi.pangaea.de/10.1594/PANGAEA.438838 
#18) Spannagel Cave (Central Alps) stalagmite oxygen isotope data (Mangini et al., 2005).  ftp://ftp.ncdc.noaa.gov/pub/data/paleo/speleothem/europe/austria/spannagel2005.txtmean SST for northern Pacific site SSDP-102 (Latitude 34.9530, Longitude 128.8810) from


#1. GRIP BOREHOLE

    	#I have archived version emailed from Jones in July 2004 from Jones and Mann [2004]
	djgrip<-read.table("http://www.climate2003.com/data/moberg/djgrip.txt",skip=1)
		#from 1 to 2001	

	proxy[[1]]=djgrip
	names(proxy[[1]])=c("year","t")

#2. CONROY LAKE
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/pollen/recons/liadata.txt"
	#fred<-readLines(url)
	test<-read.table(url,skip=50,nrow=(118-50))
	test[,1]<-1975-test[,1]  #goes from 35 to 1968
	test<-test[nrow(test):1,1:2]
	range(test[,1])#[1]   35 1968
	proxy[[2]]=test
	names(proxy[[2]])=c("year","t")
		#also Hells Kitchen a candidate

#3 CHESAPEAKE BAY #from -183 to 1996 
	#used in Mann and Jones [2003]
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/cronin2003/cronin2003.txt"
	fred<-readLines(url)
	g<-read.fwf(url,skip=77,widths=c(9,10,11,10,10,10),fill=TRUE,nrow=530-77)
	dimnames(g)[[2]]<-c("Core","Depth","ModelYear","Mg/Ca","T.Est.","T.Est.Smooth") #from -183 to 1995.8
	g=g[!is.na(g[,1]),]
	g[order(g[,1],g[,2]),]
	proxy[[3]]=g
	proxy[[3]]=proxy[[3]][,c(3,6)]#snoothed t	
	names(proxy[[3]])=c("year","t")


#4. SARGASSO SEA 
	#used in Crowley and Lowery [2000] 
	loc<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/keigwin1996/fig3data"
	fred=readLines(loc)
	sarg.mod=read.table(loc,sep="\t",fill=TRUE,skip=4)
	names(sarg.mod)=c("year","SST","Sal_psu","dO18") 
	sarg.mod$bp=1950-sarg.mod$year
	sarg.mod=sarg.mod[!is.na(sarg.mod$year),]
	x=c(mean(sarg.mod$SST[1:20]),mean(sarg.mod$SST[21:41]));x # 22.94310 23.10305
	y=c(mean(sarg.mod$dO18[1:20]),mean(sarg.mod$dO18[21:41]));y #  -0.2885000 -0.3123810
	x=data.frame(cbind(c(1965,1985),x,y));names(x)=c("year","SST","dO18")
	x$dO18=x$dO18-.2 #DEsuser adjustment described by Keigwin

	loc="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/keigwin1996/fig4bdata"
	fred<-readLines(loc)
	g<-read.table(loc,skip=5,fill=TRUE) #from 25BP to 3125BP irregular
	dimnames(g)[[2]]<-c("bp","SST")##
	g$year=1950-g[,1]
	sarg.recon=g
	sarg.recon=rbind(x[,c("year","SST")],sarg.recon[,c("year","SST")])

	proxy[[4]]=sarg.recon
	names(proxy[[4]])=c("year","t")
	proxy[[4]]=proxy[[4]][!is.na(proxy[[4]]$t),]

#5. CARIBBEAN SEA 
	#not used so far in other studies #from 133 to 1950 irregular
	#two SST recons from cores PRP12 and PRB12
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/nyberg2002/nyberg2002.txt"
	fred<-readLines(url)
	g<-read.table(url,skip=93,nrow=119-93,fill=TRUE) #from 133 to 1950 irregular
	proxy[[5]]=g
	proxy[[5]]=proxy[[5]][,c(1,4)]
	names(proxy[[5]])=c("year","t")


#6. TSUOLBMAJAVRI
	url<-"d:/climate/data/erren/Korhola_fig4_points.txt"
	g<-read.table(url,skip=10,fill=TRUE) #from 11BP to 9425BP irregular
	g[,1]<-g[1]+1994.5
	range(g[,1]) #  -7534.661  1982.559
	names(g)=c("year","t") #check
	proxy[[6]]=g
	
	#We investigated the significant features in the temperature
	#reconstruction by means of the SiZer smoothing procedure
	#(Chaudhuri and Marron, 1999). Instead of focusing on a single
	#smooth, this approach utilizes a whole family of smooths, each
	#providing information about the underlying curve at a different
	#level of detail.



#7. beijing stalagmite reconstruction #665BC to 1985 -665 1985  1.0 #dim 2560 12
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/speleothem/china/shihua_tan2003.txt"
	test<-read.table(url,skip=113,fill=TRUE)
	names(test)=c("year","layer number","original thickness(um)","maximum error in um","sedimentary trend","detrended thickness um","reconstructed temperature","maximum error","anomaly","anomaly + error","anomaly - error" ,"max age error"  ) 
	proxy[[7]]<-test[,c(1,7)]
	names(proxy[[7]])=c("year","t")

#8. CHINA-yang #  0 1990  0.1
	#ALSO USED IN MJ03
	#this includes Thompson dO18 series - Dunde, Guliya
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/yang2002/china_temp.txt"
	g<-read.table(url,skip=73,fill=TRUE,header=TRUE,sep="\t") #goes from 0 to 1990 #in 10 year increments
	proxy[[8]]<-g[,c(1,2)]
	names(proxy[[8]])=c("year","t")
	

#9 homgren
	#[102] "      mm       Calendar yr   T7 delta C13  T7 delta O18"        
	url="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/speleothem/africa/cold_air_cave.txt"
	test=read.fwf(url,skip=102,widths=c(10,15,15,15),nrow=582-102)
	proxy[[9]]<-test
	proxy[[9]]<-proxy[[9]][,c(2,4)]
	names(proxy[[9]])=c("year","proxy")

		#[102] "      mm       Calendar yr   T7 delta C13  T7 delta O18"                             
		#[103] "      1            1996       -5.187736     -2.905723"                               
		#[104] "      5            1975       -5.186736     -2.897723"                               


#10 demonacal 
	url="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/demenocal2000/658_sst.txt"
	fred<-readLines(url)
	test=read.table(url,skip=94,header=TRUE,sep="\t",fill=TRUE,nrow=40)
	test$year=1950-test[,1]
	test$t=apply(test[,3:4],1,mean)
	proxy[[10]]<-test[,c("year","t")]
		
	

#11. Famer 
#depth   cal age   Mg/Ca     temperature
#(cm)       (yr)   mmol/mol  (degC)
#  5.5        0     2.11     14.0
#  6.5       66     2.17     14.2
	url="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/farmer2005/farmer2005.txt"
	test=read.fwf(url,skip=70,widths=c(6,9,10,10),nrow=292-70)
	names(test)=c("depth","bp","mg","t")
	test$year=1950-test$bp
	proxy[[11]]<-test[,c("year","t")]


#12 calvo
#http://doi.pangaea.de/10.1594/PANGAEA.438810

	url="http://doi.pangaea.de/10.1594/PANGAEA.438810?format=html"
	fred=readLines(url)
	temp=(substr(fred,1,8)=="<tr><td>")
	n=nchar(fred[temp])
	fred= substr(fred[temp],9,n-10)
	fred=gsub("</td><td>","\t",fred)
	write.table(fred,"temp.dat",quote=FALSE,row.names=FALSE,col.names=FALSE)
	x=read.table("temp.dat",sep="\t",fill=TRUE)
	names(x)=c("depth","bp","t")
	x$year=1950-1000*x$bp

	url="http://doi.pangaea.de/10.1594/PANGAEA.510801?format=html"
	fred=readLines(url)
	temp=(substr(fred,1,8)=="<tr><td>")
	n=nchar(fred[temp])
	fred= substr(fred[temp],9,n-10)
	fred=gsub("</td><td>","\t",fred)
	write.table(fred,"temp.dat",quote=FALSE,row.names=FALSE,col.names=FALSE)
	y=read.table("temp.dat",sep="\t",fill=TRUE)
	names(y)[1:3]=c("depth","bp","t");y$year=1950-1000*y$bp

	proxy[[12]]=rbind(y[,c("year","t")],x[c("year","t")])



	#. MD95-2011 JM97-948/2A also alkenone 438810
	#With a sample spacing of 0.5 cm in core JM97-948/2A and 1.0 cm in core MD95-2011, the resulting mean temporal
	#resolution is 3.4 years and 8.4 years, respectively.
	# https://bora.uib.no/bitstream/1956/385/2/2001PA000654.pdf
	#During MD101, core MD95-2011 (66.97
N, 7.64
E, 1048 meter water depth, and a
	#length of 17.49 meter) was recovered using a giant piston corer (CALYPSO). Due to overpenetration of the giant
	#piston corer, a box core, JM97-948/2A, was later used at
	#the same position to sample the surface sediments lost during the piston coring.	
	#2003 PAleo Late Holocene surface ocean conditions of the Norwegian Sea (Vøring Plateau)  Carin Andersson,1 Bjørg Risebrobakken,2 Eystein Jansen,1,2,3 and Svein Olaf Dahl4
	#O18 Risebrobakken, B; Jansen, E; Andersson, C et al. (2003): High-resolution study of Holocene paleoclimatic and paleoceanographic changes in the Nordic Seas, Paleoceanography


#13) SST from two cores in the western tropical Pacific (Stott et al., 2004); MD98_2181 MD98_2176
	#9. STOTT 2004 MD81  MD76  MD70
#[1] " Depth      Age    ave. ruber Mg/Ca  SST  ave. ruber d18O      d18Ow"  
#[2] "  (cm)    (yr BP)     (mmol/mol)     (°C)     (‰ VPDB)        (‰ SMOW)"
# [82] "    1      13.84         5.21       29.10"                                               
# [83] "    3      40.65                               -2.81"                                    
# [84] "    7      90.90         5.01       28.66      -2.57            0.23"                    
# [85] "   11      136.87                              -2.50"                                    
 
	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/stott2004/stott2004.txt"
	md81<-read.fwf(url,widths=c(6,12,12,12,11,15),fill=TRUE,nrow=408-81,skip=81)
	names(md81)<-c("depth","bp","mg.ca","t","ruber.dO18","dO18w")
	md81$year=1950-md81$bp

	md76<-read.fwf(url,widths=c(6,12,12,12,11,15),fill=TRUE,nrow=665-416,skip=416)
	names(md76)<-c("depth","bp","mg.ca","t","ruber.dO18","dO18w")
	md76$year=1950-md76$bp

	proxy[[13]]=md81[,c("year","t")]
	proxy[[14]]=md76[,c("year","t")]


#15) mean temperature for North America based on pollen profiles (Viau et al.,2006);
	url="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/pollen/recons/northamerica/viau2006namerica-temp.txt"
	test=read.table(url,skip=75,nrow=25,fill=TRUE)
	test$year=1950-100*test[,1];names(test)[2]="t"
	proxy[[15]]=test[,c("year","t")]

#16) a phenology-based reconstruction from China (Ge et al., 2003);
		fred=readLines(url)
 [91] "Period(AD)     T.Anom.      3 pt. Avg.    Error "                                 
 [92] "      15          0.2           -             1"                                  
 [93] "      45         -0.2       0.03333333      1.1"                                  

	url="ftp://ftp.ncdc.noaa.gov/pub/data/paleo/historical/china/china_winter_temp.txt"
	test=read.fwf(url,skip=91,widths=c(10,13),nrow=158-91 )
	names(test)=c("year","t")
	proxy[[16]]=test


#17) annual mean SST for northern Pacific site SSDP-102 (Latitude 34.9530, Longitude 128.8810) from Kim et al. (2004); and
#13 SSDP-I02	34.95	128.88	40	13 (1–35) 	61 	This study
	#http://doi.pangaea.de/10.1594/PANGAEA.438838
	#SSDP-102  * Latitude: 34.9530 * Longitude: 128.8810 * Elevation: -40.0 m 
		#Depth [m] Age [kyr BP] SST (1-12) [deg C] 
		#0.02 0.01 21.8 

	url="http://doi.pangaea.de/10.1594/PANGAEA.438838?format=html"
	fred=readLines(url)
	temp=(substr(fred,1,8)=="<tr><td>")
	n=nchar(fred[temp])
	fred= substr(fred[temp],9,n-10)
	fred=gsub("</td><td>","\t",fred)
	write.table(fred,"temp.dat",quote=FALSE,row.names=FALSE,col.names=FALSE)
	x=read.table("temp.dat",sep="\t",fill=TRUE)
	names(x)=c("depth","bp","t")
	x$year=1950-1000*x$bp
	proxy[[17]]=x[,c("year","t")]


#187) Spannagel Cave (Central Alps) stalagmite oxygen isotope data (Mangini et al., 2005).
 # SPANNAGEL, AUSTRIA MANGINI to 1935
  	url<-"ftp://ftp.ncdc.noaa.gov/pub/data/paleo/speleothem/europe/austria/spannagel2005.txt"
		    #SPA 12 only
	test<-read.table(url,skip=56,header=TRUE,fill=TRUE)
	proxy[[18]]=test[,c(2,4)]	;names(proxy[[18]])=c("year","t")


	save(proxy,file="d:/climate/scripts/loehle/proxy.tab")

	names(proxy[[9]])=c("year","t") #this is ad hoc merely for plotting 
	par(mfrow=c(5,4))
	for (i in 1:18) { plot(proxy[[i]]$year,proxy[[i]]$t,type="l",xlab="",ylab="",xlim=c(0,2000),main=paste(id[i]))}