R/LobsterMap.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
Defines functions
LobsterMap
Documented in
LobsterMap
#' LobsterMap
#' @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
#' LobsterMap(area='34')
#' catchgrids <-lobGridPlot(subset(logsInSeason,SYEAR==2007,c("LFA","GRID_NUM","WEIGHT_KG")),lvls=c(100,50000,100000,200000,400000,600000,800000,1000000),FUN=sum,border=NA)
#' LobsterMap('all',poly.lst=catchgrids[1:2],title="2007 Lobster Catch")
#' ContLegend("bottomright",lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (t)",inset=0.02,cex=0.8,bg='white')
#' @export
LobsterMap<-function(area='custom',ylim=c(40,52),xlim=c(-74,-47),save=F, fname = 'LobsterMap',mapRes='HR',land.col='wheat',title='',nafo=NULL,boundaries='LFAs',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='lfa',labcex=1.5,LT=T,plot.rivers=T,
addGridGroups=F, addSummerStrata=F,polylstend=F, addsubareas=F,subsetSummerStrata=NULL, addGeorgesStrata=F, addAmericanStrata=F,addGrids=T,land.only=F,grid.labcex=1,special.labels=NULL,...){
options(stringsAsFactors=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(41.1,48); xlim=c(-67.8,-57.8) }
if(area=='27-38') { ylim=c(42.5,48); xlim=c(-67.4,-57.8) }
if(area=='27-33') { ylim=c(42.5,48); xlim=c(-66.6,-57.8) }
if(area=='27-32') { ylim=c(43.5,48); xlim=c(-63.6,-57.8) }
if(area=='27-32.Crop') { ylim=c(44,47.6); xlim=c(-63.6,-58.5) }
if(area=='34-38') { ylim=c(42.5,46); xlim=c(-67.8,-63.5) }
if(area=='35-36') { ylim=c(44.5,46); xlim=c(-67.2,-63.2) }
if(area=='west') { ylim=c(42.5,46); xlim=c(-67.8,-64) }
if(area=='27') { ylim=c(44.9,47.9); xlim=c(-61,-57.8) }
if(area=='27.Crop') { ylim=c(45.4,47.6); xlim=c(-61.1,-58.8) }
if(area=='28') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='29') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='30') { ylim=c(44.6,45.9); xlim=c(-60.8,-59.6) }
if(area=='30.Crop') { ylim=c(45.2,46); xlim=c(-61,-59.7) }
if(area=='31A') { ylim=c(44.4,45.7); xlim=c(-61.8,-60) }
if(area=='31A.Crop') { ylim=c(44.8,45.8); xlim=c(-61.6,-60.2) }
if(area=='31B') { ylim=c(44.1,45.3); xlim=c(-62.2,-60.5) }
if(area=='31B.Crop') { ylim=c(44.6,45.6); xlim=c(-62.35,-60.5) }
if(area=='32') { ylim=c(43.8,45); xlim=c(-63.5,-61.5) }
if(area=='32.Crop') { ylim=c(44.2,45.2); xlim=c(-63.5,-61.5) }
if(area=='33') { ylim=c(42.5,44.8); xlim=c(-65.8,-62.2) }
if(area=='34') { ylim=c(42.5,45); xlim=c(-67.8,-65) }
if(area=='35') { ylim=c(44.5,46); xlim=c(-66,-63.2) }
if(area=='36') { ylim=c(44.5,45.7); xlim=c(-67.2,-65) }
if(area=='37') { ylim=c(44.5,45.2); xlim=c(-67.2,-66) }
if(area=='38') { ylim=c(43.8,45); xlim=c(-67.5,-66.2) }
if(area=='40') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
if(area=='41') { ylim=c(41.1,44); xlim=c(-68,-63.5) }
if(area=='SWN') { ylim=c(42.5,45); xlim=c(-67.8,-62.2) }
if(area=='BoF') { ylim=c(43.75,46); xlim=c(-67.8,-63.2) }
if(area=='33-35') { ylim=c(42.5,46); xlim=c(-67.8,-63.2) }
if(area=='33-34') { ylim=c(42.5,45); xlim=c(-67.5,-62.2) }
if(area=='ENS') { ylim=c(43.8,45.7); xlim=c(-63.5,-59.8) }
coast<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","gshhs",paste0("shoreline","HR",".csv")))
rivers<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","gshhs",paste0("rivers",mapRes,".csv")))
attr(coast,"projection")<-"LL"
if(land.only){ addPolys(coast,col=land.col,...); return(1)}
# comment
if(save) {
print('pdf and png saved')
pdf(file.path(project.figuredirectory("bio.lobster"),paste0(fname,'.pdf')), width=6.5, height=5)
}
#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]])
if('density'%in%names(poly.lst[[2]]) & any(!is.na(poly.lst[[2]]$density))){
x=subset(poly.lst[[2]],!is.na(density))
addPolys(subset(poly.lst[[1]],SID==x$SID),density=x$density,angle=x$angle,col=x$linecol,border=x$border)
}
}
# NAFO
if(!is.null(nafo)){
nafo.xy<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","nafo.csv"))
if(nafo=='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$label=="5ZC"]<-"5ZEM"
addPolys(nafo.xy,border='grey',col=NULL)
addLabels(nafo.dat,col=rgb(0.5,0.5,0.5,0.5),cex=2)
}
#groundfish survey summer strata
if(addSummerStrata) {
a = file.path( project.datadirectory("bio.lobster"), "data","maps","summer_strata_labels.csv")
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = file.path( project.datadirectory("bio.lobster"), "data","maps","summerstrata.csv")
b = read.csv(b)
names(b) <- c('PID','X','Y')
if(!is.null(subsetSummerStrata)) {
b = b[which(b$PID %in% c(subsetSummerStrata)),]
}
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
attr(b,'projection') <- "LL"
addPolys(b,lty=1,border='blue',col=adjustcolor('white',alpha.f=1))
# addLabels(a,cex=0.6)
}
if(addGeorgesStrata) {
require('bio.polygons')
#b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
b = file.path( project.datadirectory("bio.lobster"), "data","maps",'GeorgesBankStrata.rdata')
load(b)
addPolys(out,lty=1,border='red',col=adjustcolor('white',alpha.f=1))
}
if(addAmericanStrata) {
b = importShapefile(file.path( project.datadirectory("bio.lobster"), "data","maps","BTS_Strata"), readDBF=F)
attr(b,'projection') <- "LL"
addPolys(b,lty=1,border='blue',col=adjustcolor('white',alpha.f=0))
}
#
if(addGridGroups){
io = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA_33_TO_ 38_GRID_GROUPS_NAD83.csv"))
addPolys(io)
}
# Boundries
if(boundaries=='LFAs'){
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys2.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
LFA41<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
subareas<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA2733subareas.csv"))
if(area=='31a')area<-311
if(area=='31b')area<-312
if(addsubareas)addPolys(subset(subareas,SID==1),lty=3)
# if(area=='41') addPolys(LFA41,border='blue')
lfa<-as.numeric(area)
if(lfa%in%LFAgrid$PID){
if(!is.na(lfa)){
grids<-subset(LFAgrid,PID==lfa)
#browser()
if(addGrids=='lfaonly')addPolys(grids,border=rgb(0,0,0,0.2),col=NULL)
if(any(grep('grid',labels))){
grids$label<-grids$SID
grids.dat<-merge(calcCentroid(grids),grids[c("PID","SID","label")])
addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.8),cex=1)
}
}
else {
addPolys(LFAgrid,border=rgb(0,0,0,0.2),col=NULL)
LFAgrid$label<-LFAgrid$SID
grids.dat<-merge(calcCentroid(LFAgrid),LFAgrid[c("PID","SID","label")])
}
}
#browser()
addPolys(LFAs, lwd=2,col=NULL)
if('lfa'%in% labels){
LFAgrid$label<-LFAgrid$PID
LFAgrid$label[LFAgrid$label==311]<-'31A'
LFAgrid$label[LFAgrid$label==312]<-'31B'
LFAgrid.dat<-merge(calcCentroid(LFAgrid,1),LFAgrid[c("PID","label")])
LFAgrid.dat <- subset(LFAgrid.dat,!duplicated(label))
il = which(LFAgrid.dat$label==36)
LFAgrid.dat$Y[il] = 45.02
il = which(LFAgrid.dat$label==35)
LFAgrid.dat$Y[il] = 45.23
LFAgrid.dat = as.data.frame(rbind(LFAgrid.dat,c(41,-66,41.9,41))) #add in lfa41 label
#addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
}
}
if(addGrids==T){
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
addPolys(LFAgrid,border=rgb(0,0,0,0.2),col=NULL)
addLines(LFAs, lwd=2) #Overlays Thicker lfa lines over grid lines
}
if(boundaries=='scallop'){
SFA<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","SFA.csv"))
addLines(SFA)
SPA<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","SPA.csv"))
addPolys(SPA,col=NULL)
}
# Bathymetry
sn<-ifelse(sum(isobaths/10)==sum(round(isobaths/10)),"",1)
if(!is.null(isobaths)){
bath.lst<-list()
for(i in unique(ceiling(isobaths/1000))){
load(file.path( project.datadirectory("bio.lobster"), "data","maps", bathy.source, paste0("bathy",sn,"Poly",i,".rdata")))
bath.lst[[i]]<-bathy.poly
}
bathy.poly<-do.call(rbind,bath.lst)
#browser()
bathy.poly<-subset(bathy.poly,Z%in%isobaths)
attr(bathy.poly,"projection") <- "LL"
addLines(bathy.poly,polyProps=data.frame(PID=unique(bathy.poly$PID),col=bathcol))
#browser()
}
#EEZ<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","EEZ.csv"))
#addLines(EEZ,lty=4,lwd=2)
if(area=="33") { #Changes label positions adjacent to LFA 33 for map
LFAgrid.dat$Y[LFAgrid.dat$PID %in% c(41, 40)] = 42.65
LFAgrid.dat$Y[LFAgrid.dat$PID=="34"] = 43.1
LFAgrid.dat$X[LFAgrid.dat$PID %in% c(34, 40)] = -65.5
LFAgrid.dat$X[LFAgrid.dat$PID=="41"] = -64
}
# plots land
if(LT){
addPolys(coast,col=land.col,...)
if(plot.rivers)addLines(rivers,...)
# add LFA labels
# if (area %in% c('27-38', 'all')) {labcex=0.9} #can copy / modify this line if you want label size to be associated with area chosen
if(area=='27-32') { #Can adjust size and colour of LFA labels based on "area of interest"
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col='white',cex=1.3*(labcex))
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col='firebrick3',cex=(labcex))
} else {
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
}
}
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.lobster"), "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$PID),col=topocol))
}
# plot points
if(!is.null(points.lst)){
addPoints(points.lst[[1]],polyProps=points.lst[[2]],cex=pt.cex)
}
# plot lines
if(!is.null(lines.lst)){
addLines(lines.lst[[1]],polyProps=lines.lst[[2]])
}
# add grid lines
if(!is.null(grid)){
x<-seq(floor(xlim[1]),ceiling(xlim[2]),grid)
y<-seq(floor(ylim[1]),ceiling(ylim[2]),grid)
gridlines<-makeGrid(x,y,byrow=TRUE,addSID=TRUE,projection="LL",zone=NULL)
addLines(gridlines,col='grey80',lwd=1)
}
if('grid'%in%labels) {
LFAgrid$label<-LFAgrid$SID
grids.dat<-merge(calcCentroid(LFAgrid),LFAgrid[c("PID","SID","label")])
#if (area %in% grids.dat$PID){
#grids.dat=subset(grids.dat, PID==area)}
addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=grid.labcex)
}
if('subarea'%in%labels) addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=labcex)
if(is.list(labels)) addLabels(labels[[1]],polyProps=labels[[2]])
if(polylstend==T & !is.null(poly.lst)){
addPolys(poly.lst[[1]],polyProps=poly.lst[[2]])
if(is.null(special.labels)) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
if(!is.null(special.labels)) {
re = subset(LFAgrid.dat,!duplicated(label))
re = merge(re,special.labels,by.y='LFA',by.x='PID')
re$label = re$labs
addLabels(re,col=rgb(0,0,0,0.8),cex=labcex)
}
}
box(lwd=2)
title(main=title)
if(save){
dev.off()
pdf2png(file.path(project.figuredirectory("bio.lobster"),fname))
}
}
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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Defines functions LobsterMap
Documented in LobsterMap
#' LobsterMap
#' @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
#' LobsterMap(area='34')
#' catchgrids <-lobGridPlot(subset(logsInSeason,SYEAR==2007,c("LFA","GRID_NUM","WEIGHT_KG")),lvls=c(100,50000,100000,200000,400000,600000,800000,1000000),FUN=sum,border=NA)
#' LobsterMap('all',poly.lst=catchgrids[1:2],title="2007 Lobster Catch")
#' ContLegend("bottomright",lvls=catchgrids$lvls/1000,Cont.data=catchgrids,title="Catch (t)",inset=0.02,cex=0.8,bg='white')
#' @export
LobsterMap<-function(area='custom',ylim=c(40,52),xlim=c(-74,-47),save=F, fname = 'LobsterMap',mapRes='HR',land.col='wheat',title='',nafo=NULL,boundaries='LFAs',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='lfa',labcex=1.5,LT=T,plot.rivers=T,
addGridGroups=F, addSummerStrata=F,polylstend=F, addsubareas=F,subsetSummerStrata=NULL, addGeorgesStrata=F, addAmericanStrata=F,addGrids=T,land.only=F,grid.labcex=1,special.labels=NULL,...){
options(stringsAsFactors=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(41.1,48); xlim=c(-67.8,-57.8) }
if(area=='27-38') { ylim=c(42.5,48); xlim=c(-67.4,-57.8) }
if(area=='27-33') { ylim=c(42.5,48); xlim=c(-66.6,-57.8) }
if(area=='27-32') { ylim=c(43.5,48); xlim=c(-63.6,-57.8) }
if(area=='27-32.Crop') { ylim=c(44,47.6); xlim=c(-63.6,-58.5) }
if(area=='34-38') { ylim=c(42.5,46); xlim=c(-67.8,-63.5) }
if(area=='35-36') { ylim=c(44.5,46); xlim=c(-67.2,-63.2) }
if(area=='west') { ylim=c(42.5,46); xlim=c(-67.8,-64) }
if(area=='27') { ylim=c(44.9,47.9); xlim=c(-61,-57.8) }
if(area=='27.Crop') { ylim=c(45.4,47.6); xlim=c(-61.1,-58.8) }
if(area=='28') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='29') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='30') { ylim=c(44.6,45.9); xlim=c(-60.8,-59.6) }
if(area=='30.Crop') { ylim=c(45.2,46); xlim=c(-61,-59.7) }
if(area=='31A') { ylim=c(44.4,45.7); xlim=c(-61.8,-60) }
if(area=='31A.Crop') { ylim=c(44.8,45.8); xlim=c(-61.6,-60.2) }
if(area=='31B') { ylim=c(44.1,45.3); xlim=c(-62.2,-60.5) }
if(area=='31B.Crop') { ylim=c(44.6,45.6); xlim=c(-62.35,-60.5) }
if(area=='32') { ylim=c(43.8,45); xlim=c(-63.5,-61.5) }
if(area=='32.Crop') { ylim=c(44.2,45.2); xlim=c(-63.5,-61.5) }
if(area=='33') { ylim=c(42.5,44.8); xlim=c(-65.8,-62.2) }
if(area=='34') { ylim=c(42.5,45); xlim=c(-67.8,-65) }
if(area=='35') { ylim=c(44.5,46); xlim=c(-66,-63.2) }
if(area=='36') { ylim=c(44.5,45.7); xlim=c(-67.2,-65) }
if(area=='37') { ylim=c(44.5,45.2); xlim=c(-67.2,-66) }
if(area=='38') { ylim=c(43.8,45); xlim=c(-67.5,-66.2) }
if(area=='40') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
if(area=='41') { ylim=c(41.1,44); xlim=c(-68,-63.5) }
if(area=='SWN') { ylim=c(42.5,45); xlim=c(-67.8,-62.2) }
if(area=='BoF') { ylim=c(43.75,46); xlim=c(-67.8,-63.2) }
if(area=='33-35') { ylim=c(42.5,46); xlim=c(-67.8,-63.2) }
if(area=='33-34') { ylim=c(42.5,45); xlim=c(-67.5,-62.2) }
if(area=='ENS') { ylim=c(43.8,45.7); xlim=c(-63.5,-59.8) }
coast<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","gshhs",paste0("shoreline","HR",".csv")))
rivers<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","gshhs",paste0("rivers",mapRes,".csv")))
attr(coast,"projection")<-"LL"
if(land.only){ addPolys(coast,col=land.col,...); return(1)}
# comment
if(save) {
print('pdf and png saved')
pdf(file.path(project.figuredirectory("bio.lobster"),paste0(fname,'.pdf')), width=6.5, height=5)
}
#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]])
if('density'%in%names(poly.lst[[2]]) & any(!is.na(poly.lst[[2]]$density))){
x=subset(poly.lst[[2]],!is.na(density))
addPolys(subset(poly.lst[[1]],SID==x$SID),density=x$density,angle=x$angle,col=x$linecol,border=x$border)
}
}
# NAFO
if(!is.null(nafo)){
nafo.xy<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","nafo.csv"))
if(nafo=='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$label=="5ZC"]<-"5ZEM"
addPolys(nafo.xy,border='grey',col=NULL)
addLabels(nafo.dat,col=rgb(0.5,0.5,0.5,0.5),cex=2)
}
#groundfish survey summer strata
if(addSummerStrata) {
a = file.path( project.datadirectory("bio.lobster"), "data","maps","summer_strata_labels.csv")
a = read.csv(a,header=T)
names(a)[4] <- 'label'
b = file.path( project.datadirectory("bio.lobster"), "data","maps","summerstrata.csv")
b = read.csv(b)
names(b) <- c('PID','X','Y')
if(!is.null(subsetSummerStrata)) {
b = b[which(b$PID %in% c(subsetSummerStrata)),]
}
b = within(b,{POS <- ave(PID,list(PID),FUN=seq_along)})
attr(b,'projection') <- "LL"
addPolys(b,lty=1,border='blue',col=adjustcolor('white',alpha.f=1))
# addLabels(a,cex=0.6)
}
if(addGeorgesStrata) {
require('bio.polygons')
#b = file.path(project.datadirectory('bio.polygons'),'data','Science','PED','GeorgesBankStrata.rdata')
b = file.path( project.datadirectory("bio.lobster"), "data","maps",'GeorgesBankStrata.rdata')
load(b)
addPolys(out,lty=1,border='red',col=adjustcolor('white',alpha.f=1))
}
if(addAmericanStrata) {
b = importShapefile(file.path( project.datadirectory("bio.lobster"), "data","maps","BTS_Strata"), readDBF=F)
attr(b,'projection') <- "LL"
addPolys(b,lty=1,border='blue',col=adjustcolor('white',alpha.f=0))
}
#
if(addGridGroups){
io = read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA_33_TO_ 38_GRID_GROUPS_NAD83.csv"))
addPolys(io)
}
# Boundries
if(boundaries=='LFAs'){
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys2.csv"))
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
LFA41<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA41Offareas.csv"))
subareas<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFA2733subareas.csv"))
if(area=='31a')area<-311
if(area=='31b')area<-312
if(addsubareas)addPolys(subset(subareas,SID==1),lty=3)
# if(area=='41') addPolys(LFA41,border='blue')
lfa<-as.numeric(area)
if(lfa%in%LFAgrid$PID){
if(!is.na(lfa)){
grids<-subset(LFAgrid,PID==lfa)
#browser()
if(addGrids=='lfaonly')addPolys(grids,border=rgb(0,0,0,0.2),col=NULL)
if(any(grep('grid',labels))){
grids$label<-grids$SID
grids.dat<-merge(calcCentroid(grids),grids[c("PID","SID","label")])
addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.8),cex=1)
}
}
else {
addPolys(LFAgrid,border=rgb(0,0,0,0.2),col=NULL)
LFAgrid$label<-LFAgrid$SID
grids.dat<-merge(calcCentroid(LFAgrid),LFAgrid[c("PID","SID","label")])
}
}
#browser()
addPolys(LFAs, lwd=2,col=NULL)
if('lfa'%in% labels){
LFAgrid$label<-LFAgrid$PID
LFAgrid$label[LFAgrid$label==311]<-'31A'
LFAgrid$label[LFAgrid$label==312]<-'31B'
LFAgrid.dat<-merge(calcCentroid(LFAgrid,1),LFAgrid[c("PID","label")])
LFAgrid.dat <- subset(LFAgrid.dat,!duplicated(label))
il = which(LFAgrid.dat$label==36)
LFAgrid.dat$Y[il] = 45.02
il = which(LFAgrid.dat$label==35)
LFAgrid.dat$Y[il] = 45.23
LFAgrid.dat = as.data.frame(rbind(LFAgrid.dat,c(41,-66,41.9,41))) #add in lfa41 label
#addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
}
}
if(addGrids==T){
LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
addPolys(LFAgrid,border=rgb(0,0,0,0.2),col=NULL)
addLines(LFAs, lwd=2) #Overlays Thicker lfa lines over grid lines
}
if(boundaries=='scallop'){
SFA<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","SFA.csv"))
addLines(SFA)
SPA<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","SPA.csv"))
addPolys(SPA,col=NULL)
}
# Bathymetry
sn<-ifelse(sum(isobaths/10)==sum(round(isobaths/10)),"",1)
if(!is.null(isobaths)){
bath.lst<-list()
for(i in unique(ceiling(isobaths/1000))){
load(file.path( project.datadirectory("bio.lobster"), "data","maps", bathy.source, paste0("bathy",sn,"Poly",i,".rdata")))
bath.lst[[i]]<-bathy.poly
}
bathy.poly<-do.call(rbind,bath.lst)
#browser()
bathy.poly<-subset(bathy.poly,Z%in%isobaths)
attr(bathy.poly,"projection") <- "LL"
addLines(bathy.poly,polyProps=data.frame(PID=unique(bathy.poly$PID),col=bathcol))
#browser()
}
#EEZ<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","EEZ.csv"))
#addLines(EEZ,lty=4,lwd=2)
if(area=="33") { #Changes label positions adjacent to LFA 33 for map
LFAgrid.dat$Y[LFAgrid.dat$PID %in% c(41, 40)] = 42.65
LFAgrid.dat$Y[LFAgrid.dat$PID=="34"] = 43.1
LFAgrid.dat$X[LFAgrid.dat$PID %in% c(34, 40)] = -65.5
LFAgrid.dat$X[LFAgrid.dat$PID=="41"] = -64
}
# plots land
if(LT){
addPolys(coast,col=land.col,...)
if(plot.rivers)addLines(rivers,...)
# add LFA labels
# if (area %in% c('27-38', 'all')) {labcex=0.9} #can copy / modify this line if you want label size to be associated with area chosen
if(area=='27-32') { #Can adjust size and colour of LFA labels based on "area of interest"
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col='white',cex=1.3*(labcex))
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col='firebrick3',cex=(labcex))
} else {
if(boundaries=='LFAs') if('lfa'%in% labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
}
}
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.lobster"), "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$PID),col=topocol))
}
# plot points
if(!is.null(points.lst)){
addPoints(points.lst[[1]],polyProps=points.lst[[2]],cex=pt.cex)
}
# plot lines
if(!is.null(lines.lst)){
addLines(lines.lst[[1]],polyProps=lines.lst[[2]])
}
# add grid lines
if(!is.null(grid)){
x<-seq(floor(xlim[1]),ceiling(xlim[2]),grid)
y<-seq(floor(ylim[1]),ceiling(ylim[2]),grid)
gridlines<-makeGrid(x,y,byrow=TRUE,addSID=TRUE,projection="LL",zone=NULL)
addLines(gridlines,col='grey80',lwd=1)
}
if('grid'%in%labels) {
LFAgrid$label<-LFAgrid$SID
grids.dat<-merge(calcCentroid(LFAgrid),LFAgrid[c("PID","SID","label")])
#if (area %in% grids.dat$PID){
#grids.dat=subset(grids.dat, PID==area)}
addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=grid.labcex)
}
if('subarea'%in%labels) addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=labcex)
if(is.list(labels)) addLabels(labels[[1]],polyProps=labels[[2]])
if(polylstend==T & !is.null(poly.lst)){
addPolys(poly.lst[[1]],polyProps=poly.lst[[2]])
if(is.null(special.labels)) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.8),cex=labcex)
if(!is.null(special.labels)) {
re = subset(LFAgrid.dat,!duplicated(label))
re = merge(re,special.labels,by.y='LFA',by.x='PID')
re$label = re$labs
addLabels(re,col=rgb(0,0,0,0.8),cex=labcex)
}
}
box(lwd=2)
title(main=title)
if(save){
dev.off()
pdf2png(file.path(project.figuredirectory("bio.lobster"),fname))
}
}
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