R/printLOC.R

In plannapus/CONOP9companion: Tools for integrating biostratigraphic software CONOP9 in a statistical workflow

printLOC <-
function(CONOP, events="observed"){
	require(grDevices)
	require(scales)
	sectfile <- CONOP@Sectfile
	invisible(ifelse(events=="observed", obsdfile <- CONOP@Obsdfile, ifelse(events=="placed", obsdfile <- CONOP@Plcdfile, stop("The \'events\' argument should be \"observed\" (to use events as observed) or \"placed\" (to use events as placed by the optimization process)"))))
	composfile <- CONOP@Composfile
	for(SITE in 1:nrow(sectfile)){
		a <- rev(composfile[,4])
		b <- obsdfile[,SITE+2]
		type <- obsdfile[,2]
		abs(type)->type
		type[type>2] <- -1
		
		pdf(file=paste(sectfile[SITE,4],"_LOC.pdf",sep=""),width=10,height=10)
		layout(matrix(c(0,1,2,3),nrow=2,byrow=TRUE),width=c(3,20),height=c(3,20))
		
		par(mar=c(0,0,5,3))
		plot(0,0,type="n",xlim=range(a, na.rm=TRUE),ylim=c(0,10),xaxt="n",yaxt="n",yaxs="i",xaxs="i",xlab="",ylab="",bty="n")
		invisible(sapply(unique(a),function(x)lines(c(x,x),c(0,10), lty=1, col="black")))
		axis(3,at=pretty(range(a, na.rm=TRUE)),cex.axis=2)
		box()
		
		par(mar=c(5,5,0,0))
		plot(0,0,type="n",ylim=range(b, na.rm=TRUE),xlim=c(0,10),xaxt="n",yaxt="n",yaxs="i",xaxs="i",xlab="",ylab="",bty="n")
		invisible(sapply(unique(b)[!is.na(unique(b))],function(x)lines(c(0,10),c(x,x), lty=1, col="black")))
		axis(2,at=pretty(range(b, na.rm=TRUE)),las=2,cex.axis=2)
		box()
		
		par(mar=c(5,0,0,3))
		palette(c("red","blue"))
		
		plot(0,0,xaxs="i",yaxs="i",yaxt="n",xlab="",ylab="",xaxt="n",bty="o",
			 ylim=range(b,na.rm=TRUE),xlim=range(a, na.rm=TRUE),type="n")
		points(a, b, pch=23+type, bg=alpha(abs(type), 0.1), cex=3)
		title(sub=paste(sectfile[SITE,4]," vs Composite Section",sep=""),line=2,cex.sub=2)
		box()

		dev.off()
		}
	}