R/plotproxy.all.R

In ClamR: Time Series Modeling for Climate Change Proxies

plotproxy.all<-function(gout, ylab1="", ylab2="",xlab="", main="",
xlim=NULL, ylim1=NULL, ylim2=NULL, legposition="topleft",
YAXstyle=0, pbox=TRUE,
legnames  = c('Phs', 'Pos', 'Amp', 'Prd')  )
{

#########   plots all the wilkinson curves on the same graph
    if(missing(ylab1)) ylab1 = expression(delta*"18O(% VPDB)")
    if(missing(ylab2)) ylab2 = "Growth distance (mm)"
    if(missing(xlab)) xlab = "Distance from Margin (mm)"
	if(missing(main)) main=""

 	
    JOUT = gout$JOUT
    JMAT  = matrix(ncol=5, nrow=length(JOUT))
    for(i in 1:length(JOUT))
	{
        JMAT[i,] = c(JOUT[[i]]$par[1:4], JOUT[[i]]$mid)
	}
	
    colnames(JMAT) <- c('Phs', 'Pos', 'Amp', 'Prd', 'mid')
	
    if(missing(legnames))
	{
		legnames  = c('Phs', 'Pos', 'Amp', 'Prd')	
    }
		
 
	if (YAXstyle==0)
	{
	mai = par("mai")
    mai[4] = mai[2]
	par(mai=mai)

        G = apply(JMAT, 2, range)
	ex = range(JMAT[,5])
	why = range(G[1:2,1])
        if(missing(xlim) | is.null(xlim))   xlim = range(ex)
        if(missing(ylim1)| is.null(ylim1) ) ylim1=range(why)
        if(missing(ylim2) | is.null(ylim2) ) ylim2=range(why)
        
    plot(ex, why , type='n', xlab="mm", ylab="", main="", axes=FALSE, ann=FALSE, xlim=xlim)
    axis(1)
    title(xlab='mm')
	
	if(pbox) { box() }
		

		
		for(j in 1:4)
		{
		
        	ay = JMAT[,j]
        	by = RESCALE(ay, G[1,1], G[2, 1] ,  G[1,j], G[2, j]  )
        	points(JMAT[,5] , by, col=j, pch=j)
        	lines(JMAT[,5] , by, col=j)
		}
	
	u = par("usr")
	
	uax = u[1:2]
	nudge = .1
	for (j in 1:4)
		{
			ipos = uax[1]
			if(j==1 || j==4) 
			{
			ipos = uax[2]
			iside=4
			}
			if(j==2 || j==3)
			{
			iside=2
			}
			ay=JMAT[,j]
			axy = pretty[ay]
			baxy = RESCALE (axy, G[1,1], G[2,1], G[1,j], G[2,j])
			axis(iside, at=baxy, labels=axy, pos=ipos,  col.lab=j, col.ticks=j)
		}
	
	}
#####  Now set up the axis
		
    if(YAXstyle==1)
	{
		
		plot(JMAT[,5], JMAT[,2], xlim=xlim, ylim=ylim1, type="o",col=4,  pch=19, xlab=xlab, ylab=ylab1)
		points(JMAT[,5], JMAT[,3],  type="o", col=4,  pch=21)
		axis(2,col=4)
		par(new=T)
		plot(JMAT[,5], JMAT[,1], xlim=xlim, ylim=ylim2, type="o", col=2, pch=15, xlab="", ylab="", axes=F)
		points(JMAT[,5], JMAT[,4], type="o", col=2,  pch=22)
		axis(4,col=2)
		mtext(ylab2, side=4,line=11)

	}
	
    legend(legposition , legend=legnames, pch=c(15,19,21,22), col=c(2,4,4,2) , bg='white', xpd=TRUE )
	
	
}