R/syas.R

In paleoMAS: Paleoecological Analysis

syas <-
function(x,y,z,fossil,age,delta,percen,method="canberra",
	quant=0.05,plot=TRUE,window=3,detrend=FALSE,crossv,
	maximum=0.99,classes=200,colors=c("red","blue"),line=TRUE,
	ylabel="Age",xlabel="Parameter")
{
{
	ak<-z[colnames(y),]
	syn.as<-synthetic(x,y,z,delta,plot=FALSE,percen=percen)
	distances<-fossil.dist(syn.as,fossil,method=method)
	values<-fossil.values(distances,age,quant=quant,
		detrend=detrend,crossv=crossv)
	if(plot==TRUE){
		dis<-distances[-1,]
		ifelse(dis>quantile(dis,prob=maximum),quantile(dis,
			prob=maximum),dis)->dis1
		dis2<-matrix(as.integer(cut(dis1,seq(min(dis1),max(dis1),
			l=classes),include.lowest=TRUE)),dim(dis1))
		colorRampPalette(colors)(classes)->palette
		image(x=distances[1,],y=values[,1],scale(t(dis2)),
			col=palette,ylab=ylabel,xlab=xlabel)
		if(line==TRUE){	
			if(detrend==FALSE){
				lines(values[,c(2,1)],type="l")
				}
			else{
				lines(values[,c(3,1)],type="l")
				}
			}
	}
results<-list(syn.as,values)
names(results)<-c("syn.as","values")
return(results)
}
}