R/ClamMap2.r

In SurfClam/bio.surfclam:

#' ClamMap
#' @param area = 'custom' where xlim & ylim are specified or select from area list below
#' @param mapRes = coastline detail ('LR' = low resolution, 'MR' = medium resolution, 'HR' = high resolution, 'UR' = ultra resolution)
#' @param title = plot title
#' @param boundaries = for ploting specific management boundaries
#' @param isobath = plots bathymetry lines for specified depths from topex data 
#' @param bathcol = isobath line color, default is transparent blue
#' @param topolines = plots topographic lines for specified elevations from topex data 
#' @param bathcol = topolines line color, default is transparent brown
#' @param points.lst = points to overlay on map in PBSmapping format - list with 2 elements: 1st element is eventSet (EID, POS, X, Y), 2nd element is eventData (EID, pch, col, etc.) 
#' @param lines.lst = lines to overlay on map in PBSmapping format - list with 2 elements: 1st element is polySet (PID, SID, POS, X, Y), 2nd element is polyData (PID, SID, lty, col, etc.) 
#' @param poly.lst = polygons to overlay on map in PBSmapping format - list with 2 elements: 1st element is polySet (PID, SID, POS, X, Y), 2nd element is polyData (PID, SID, border, col, etc.) 
#' @param contours = plots overlaping polygons as contours (same format as poly.lst)
#' @param image.lst = image to overlay on map - list with 3 elements (x, y, z), 'bathymetry' produces image from bathymetry data 
#' @param color.fun = color function for image
#' @param zlim = zlim for image
#' @param grid = size of grid in degrees, default is no grid
#' @param stippling = adds stippling to land (purely for visual effect)
#' @param lol = adds water colored border to coastline (purely for visual effect)
#' @author Brad Hubley
#' @examples
#' ClamMap2(area='Ban')
#' @export

ClamMap2<-function(area='custom',ylim=c(40,52),xlim=c(-74,-47),mapRes='HR',land.col='wheat',title='',nafo=NULL,boundaries='clam',bathy.source='topex',isobaths=seq(100,1000,100),bathcol=rgb(0,0,1,0.1),topolines=NULL,topocol=rgb(0.8,0.5,0,0.2),points.lst=NULL,pt.cex=1,lines.lst=NULL,poly.lst=NULL,contours=NULL,image.lst=NULL,color.fun=tim.colors,zlim,grid=NULL,stippling=F,lol=F,labels=NULL,labcex=1.5,LT=T,plot.rivers=T,addSummerStrata=F,addsubareas=F,...){

	require(PBSmapping)|| stop("Install PBSmapping Package")
	require(fields)|| stop("Install fields Package")
	
	# Custom area
	if(area=='custom')	{ ylim=ylim; 			xlim=xlim			}
	
	## Area List
	if(area=='all')		{ ylim=c(42.5,48); 		xlim=c(-64,-47)	}
	if(area=='SS')		{ ylim=c(41,47); 		xlim=c(-68,-57)		}
	if(area=='ESS')		{ ylim=c(43,45.4); 		xlim=c(-62.5,-57.4)	}
	if(area=='WSS')		{ ylim=c(41,44); 		xlim=c(-67.3,-64)	}
	if(area=='BBn')		{ ylim=c(42.4,43); 		xlim=c(-66.6,-65.6)	}
	if(area=='BBs')		{ ylim=c(42.25,42.75); 	xlim=c(-66,-65.25)	}
	if(area=='BB')		{ xlim=c(-66.5,-65.25); ylim=c(42.25,43)	}
	if(area=='GB')		{ ylim=c(41.1,42.3); 	xlim=c(-67.3,-65.6)	}
	if(area=='GBb')		{ ylim=c(41.6,42.3); 	xlim=c(-66.7,-65.6)	}
	if(area=='Ger')		{ ylim=c(42.8,43.8); 	xlim=c(-67,-65)		}
	if(area=='Sab')		{ ylim=c(42.8,44.5); 	xlim=c(-62.5,-58.8)	}
	if(area=='West')	{ ylim=c(43,44.1); 		xlim=c(-62.2,-60.4)	}
	if(area=='Mid')		{ ylim=c(44.2,44.9);	xlim=c(-61.3,-60.1) }
	if(area=='Ban')		{ ylim=c(43.7,45.2); 	xlim=c(-60.5,-57)	}
	if(area=='SPB')		{ ylim=c(44.5,47.5);	xlim=c(-58,-55)		}
	if(area=='Grand')	{ ylim=c(43,46.5); 		xlim=c(-51.5,-48.5)		}
	if(area=='Grand2')	{ ylim=c(42.5,48); 		xlim=c(-55,-47)		}
	
	coast<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","gshhs",paste0("shoreline",mapRes,".csv")))
	rivers<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","gshhs",paste0("rivers",mapRes,".csv")))
	attr(coast,"projection")<-"LL"


	#par(...)
	plotMap(coast,xlim=xlim,ylim=ylim,border=NA,...)
	#addLines(rivers)
	
	if(lol)addPolys(coast,border=bathcol,lwd=6)
	
	# Image
	if(!is.null(image.lst)){
		if(missing(zlim))zlim<-range(image.lst$z,na.rm=T)
		image(image.lst,add=T,col=color.fun(100),zlim=zlim)
	}

	# plot polygons
	if(!is.null(contours)){
		contours[[2]]<-subset(contours[[2]],PID%in%contours[[1]]$PID)
		junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40))
		for(i in unique(contours[[2]]$PID)){
			addPolys(joinPolys(subset(contours[[1]],PID==i),junk,operation="DIFF"),polyProps=contours[[2]])
		}
	}
	if(!is.null(poly.lst)){
		addPolys(poly.lst[[1]],polyProps=poly.lst[[2]])
	}
	
	
	# Bathymetry
		sn<-ifelse(sum(isobaths/10)==sum(round(isobaths/10)),"",1)
		#browser()
		if(!is.null(isobaths)){
			bath.lst<-list()
			for(i in unique(ceiling(isobaths/1000))){
	 			load(file.path( project.datadirectory("bio.surfclam"), "data","maps", bathy.source, paste0("bathy",sn,"Poly",i,".rdata")))
	 			bath.lst[[i]]<-bathy.poly
	 		}
 			bathy.poly<-do.call(rbind,bath.lst)
 		#browser()
			bathy.poly<-subset(bathy.poly,Z%in%isobaths)
			attr(bathy.poly,"projection") <- "LL"
			addLines(bathy.poly,polyProps=data.frame(PID=unique(bathy.poly$PID),col=bathcol))
			#browser()
		}
	
	# NAFO
	if(!is.null(nafo)){
		
        nafo.xy<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","nafo.csv"))
        if(nafo[1]=='all')nafo<-unique(nafo.xy$label)
        nafo.sel<-subset(nafo.xy,label%in%nafo)
        nafo.dat<-merge(calcCentroid(nafo.sel),nafo.sel[c("PID","label")])[!duplicated(nafo.sel[c("PID","label")]),]
        nafo.dat$label[nafo.dat$label=="5ZC"]<-"5ZEM"
        
		addPolys(nafo.xy,border='grey',col=NULL)
		addLabels(nafo.dat,col=rgb(0.5,0.5,0.5,0.5),cex=2)
	}
	
	
#groundfish survey summer strata	
	if(addSummerStrata) {
			  loadfunctions('polygons')
			  a = find.ecomod.gis('summer_strata_labels',return.one.match=F)
			  a = read.csv(a,header=T)
			  names(a)[4] <- 'label'
			  b = find.ecomod.gis('strat.gf',return.one.match=F)
			  b = read.table(b)
			  names(b) <- c('X','Y','PID')
			  b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
			  addPolys(b,lty=1,border='black',col=NULL)
			 # addLabels(a,cex=0.6)
			}
  # Boundries
	
	if(boundaries=='clam'){
		

	}

	if(boundaries=='scallop'){
		SFA<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","SFA.csv"))
		addLines(SFA)
		SPA<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","SPA.csv"))
		addPolys(SPA,col=NULL)
	}
		
	EEZ<-read.csv(file.path( project.datadirectory("bio.surfclam"), "data","maps","EEZ.csv"))
	addLines(EEZ,lty=4,lwd=2)
	
	# plots land
	if(LT){
		addPolys(coast,col=land.col,...)
		if(plot.rivers)addLines(rivers,...)
	}
	
	if(stippling)addStipples (coast, pch='.')
	
	# Topography
	
		if(!is.null(topolines)){
			topo.lst<-list()
			for(i in unique(ceiling(topolines/1000))){
	 			load(file.path( project.datadirectory("bio.surfclam"), "data", "maps","topex",paste0("topoPoly",i,".rdata")))
	 			topo.lst[[i]]<-topo.poly
	 		}
 			topo.poly<-do.call(rbind,topo.lst)
 			topo.poly<-subset(topo.poly,Z%in%topolines)
			attr(topo.poly,"projection") <- "LL"
			addLines(topo.poly,polyProps=data.frame(PID=unique(topo.poly$PID),col=topocol))
		}
	


	# plot points
	if(!is.null(points.lst)){
		addPoints(points.lst[[1]],polyProps=points.lst[[2]],cex=pt.cex)
	}

	# plot lines
	if(!is.null(lines.lst)){
		addLines(lines.lst[[1]],polyProps=lines.lst[[2]])
	}
	
	# add grid lines
	if(!is.null(grid)){
		x<-seq(floor(xlim[1]),ceiling(xlim[2]),grid)
		y<-seq(floor(ylim[1]),ceiling(ylim[2]),grid)
		gridlines<-makeGrid(x,y,byrow=TRUE,addSID=TRUE,projection="LL",zone=NULL)
		addLines(gridlines,col='grey80',lwd=1)
	}
	
	if(is.list(labels)) addLabels(labels[[1]],polyProps=labels[[2]])


	box(lwd=2)
	

	title(main=title)
	

}