##REVIEW OF OSBORN AND BRIFFA [2006] FUNCTIONS

#TO EXTEND SERIES BY PERSISTENCE
	extend.persist<-function(tree) {
	extend.persist<-tree
	for (j in 1:ncol(tree) )  {
		test<-is.na(tree[,j])
		end1<-max ( c(1:nrow(tree)) [!test])
		test2<-( c(1:nrow(tree))>end1) & test
		extend.persist[test2,j]<-tree[end1,j]
		}
	extend.persist
	}
	
#JONES GRIDCELL ID FROM LAT AND LONG
	jones<-function(lat,long) {
	i<-18-floor(lat/5);
	j<- 36+ceiling(long/5);
	jones<-72*(i-1) + j
	jones
	}

#GAUSSIAN FILTER
	#see http://www.ltrr.arizona.edu/~dmeko/notes_8.pdf

	gaussian.filter.weights<-function(N,year) {
		#N number of points; year - is number of years
	sigma<-year/6
	i<-( (-(N-1)/2):((N-1)/2)   )  /sigma
	w<- ((2*pi)^-0.5) * exp(-0.5* i^2)
	gaussian.filter.weights<-w/sum(w)
	gaussian.filter.weights
	}

	truncated.gauss.weights<-function(year) {
	a<-gaussian.filter.weights(2*year+1,year)
	temp<-(a>0.05*max(a))
	a<-a[temp]
	a<-a/sum(a)
	truncated.gauss.weights<-a
	truncated.gauss.weights
	}
 
 #RETURN SMOOTHED SERIES 
  filter.combine.pad<-function(x,a,M=NA) {
	temp<-!is.na(x)  
   	year<-c(tsp(x)[1]:tsp(x)[2])[temp]
	w<-x[temp]
	N<-length(w)
	if(is.na(M)) M<-trunc (length(a)/2)+1
	w<-c (rep(mean(w[1:M]),M),w,rep(mean(w[(N-M+1):N]),M))
   	y<-filter(w,a,method="convolution",sides=2)
	y<-y[(M+1):(length(y)-M)]
	z<-ts (rep(NA,length(x)),start=tsp(x)[1],end=tsp(x)[2])
	z[temp]<-y
   	filter.combine.pad<-ts.union(x,z)
   	#filter.combine<-y[,2]
	filter.combine.pad
   	}

#MANNOMATIC DATA TRANSFORMATION
   sd.detrend<-function(x) {t<-c(1:length(x));fm<-lm(x~t);sd.detrend<-sd(fm$residuals);sd.detrend}

   mannomatic<-function(x,M=78) {
	N<-length(x)
	xstd<- (x- mean( x[(N-M):N]))/sd(x[(N-M):N])
	sdprox<-sd.detrend(xstd[(N-M):N]) 
	mannomatic<- xstd/sdprox
	mannomatic
	}

#FUNCTION TO LISTFILES AND REMOVE SUFFIXES
  strip<-function(h,n) {
	h<-unlist(strsplit(h, "\\."))
	h<-array(h,dim=c(n,length(h)/n))
	h<-t(h)
	strip<-h[,1]
	strip
	}

#CALCULATE ANNUAL AVERAGE FROM MONTHLY TIME SERIES
    annavg<-function(x) {
	n<-length(x)
	m<-n-12*floor(n/12)
	if(m>0) x<-c(x, rep(NA,12-m))
	years<-length(x)/12
	x<-array(x,dim=c(12,years))
	annavg<-apply(x,2,mean,na.rm=TRUE)
	return(annavg)
	}