# R code developed by:
# International Research Institute for Climate and Society
# Columbia University in the City of New York, USA
# Last update: Jully 3, 2013
# --------------------------------------------------------------------------------
# Dependancies : (see each function for further details)
#		-- File "CDatasets2012.csv" containing the climatic data
# --------------------------------------------------------------------------------
# Results :
#		-- Plot the selected squared SRC contained in matrix AS with time
# --------------------------------------------------------------------------------
# Parameters :
#		-- AS a matrix containing all the SRC indices
#		-- p the total number of parameters of the model
#		-- names the names of the parameters of the model to be plotted (from one to p)
#		-- xlim, ylim the bounds of the plot
# --------------------------------------------------------------------------------
# Actions :
#		-- Load the data
#		-- Compute time and bounds
#		-- Compute the squared SRC with their confidence intervals for the parameters selected
#		-- Plot them
# --------------------------------------------------------------------------------

plotAllSquared<-function(AS,p,names,xlim,ylim) {

	Temp <- as.matrix(read.csv('/Users/paulb/Documents/Data/Kenya/CDatasets2012.csv',header = FALSE,sep = ";")) # We load this to be abble to name the x axis

	# Parameters of the Plot
	t<-nrow(AS)/p
	NPr<-length(names)
	#xlim<-c(1,t)
	#ylim<-c(0,0.1)
	Leg<-NULL;
	
	# Bounds of the plot
	plot.new()
	plot.window(xlim, ylim)
	axis(1, at=seq(1,t+1,by=t/200), labels=Temp[seq(1,t+1,by=t/200),1])#Un trait tout les 30
	axis(2, las=1, at=0.1*0:10)
	box()
	
	for (i in 1:NPr){
		# Select the lines corresponding to one parameter
		ASsub<-subset(AS, !regexpr(names[i],row.names(AS))==-1)
		
		# Find the values of the SRC and square them
		Values<-ASsub$original-ASsub$bias
		ValuesSq<-Values^2
		
		#Find the correct squred c.i. interval
		SubN<-ncol(ASsub);
		Min<-ASsub$"min. c.i."
		Max<-ASsub$"max. c.i."
		MinSq<-NULL
		MaxSq<-NULL
		for (j in 1:t) {
			a<-Min[j];
			b<-Max[j];
			if ((a<0) & (b<0)) {
				MinSq<-c(MinSq,b*b)
				MaxSq<-c(MaxSq,a*a)
			} else if ((a<0) & (b>0)) {
				MinSq<-c(MinSq,0)
				MaxSq<-c(MaxSq,max(a*a,b*b))
			} else {
				MinSq<-c(MinSq,a*a)
				MaxSq<-c(MaxSq,b*b)
			}
		}
		
		# Define the colors of the lines
		cols<-rainbow(2, s = 0.5, v = 0.8, start = i/p, end = i/p+5*i/(10*p), alpha = 1)
		Leg<-c(Leg,cols[1])
		
		# Plot the values and the c. i. 
		lines(ValuesSq, type="o", col=cols[1], pch=i)
		lines(MinSq, type="o", col=cols[2],pch=i)
		lines(MaxSq, type="o", col=cols[2],pch=i)
		#polygon(c(1:t,rev(1:t)),c(Min,rev(Max)),col=cols[3])
	}
	
	# Legend and labels
	title(main=paste("SRC squared variation in time for WCT"), col.main="red", font.main=4)
	title(xlab="Time", col.lab=rgb(0,0.5,0))
	title(ylab=paste("SRC squared"), col.lab=rgb(0,0.5,0)) 
	legend("topright", names, cex=0.8, col=Leg, pch=1:NPr, horiz=TRUE);

}