R/bioMap.r
In BradHubley/SpatialHub: Survey Design and Spatial Analysis of Fisheries Data
Defines functions
bioMap
Documented in
bioMap
#' @title bioMap
#' @description a customizable mapping function that uses PBSmapping to plot fisheries data, bathymetry and mangement boundaries.
#' @param area = 'custom' where xlim & ylim are specified or select from area list below
#' @param ylim = y limits
#' @param xlim = x limits
#' @param mapRes = coastline detail ('LR' = low resolution, 'MR' = medium resolution, 'HR' = high resolution, 'UR' = ultra resolution)
#' @param land.col = colour for the land
#' @param nafo = undocumented
#' @param pt.cex = undocumented
#' @param labels = undocumented
#' @param labcex = undocumented
#' @param LT = undocumented
#' @param plot.rivers = undocumented
#' @param addsubareas = undocumented
#' @param subsetSurveyStrata = undocumented
#' @param addbasemap = undocumented
#' @param title = plot title
#' @param boundaries = for ploting specific management boundaries ("lobster", "scallop", "snowcrab", "SummerSurveyStrata", "GeorgesSurveyStrata", "AmericanSurveyStrata")
#' @param isobaths = plots bathymetry lines for specified depths from topex data
#' @param bathcol = isobath line color, default is transparent blue
#' @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)
#' @param ... = undocumented
#' @importFrom PBSmapping plotMap
#' @importFrom PBSmapping addPoints
#' @importFrom PBSmapping addLines
#' @importFrom PBSmapping addPolys
#' @importFrom PBSmapping addStipples
#' @importFrom PBSmapping addLabels
#' @importFrom PBSmapping calcCentroid
#' @importFrom PBSmapping makeGrid
#' @importFrom grDevices adjustcolor
#' @importFrom graphics box
#' @importFrom graphics image
#' @importFrom graphics text
#' @importFrom grDevices rgb
#' @importFrom utils read.csv
#' @author Brad Hubley
#' @examples
#' bioMap(area='lfa34')
#' @export
bioMap<-function(area='custom',ylim=c(40,52),xlim=c(-74,-47),mapRes='HR',land.col='wheat',title='',nafo=NULL,boundaries='LFAs',isobaths=seq(100,1000,100),bathcol=rgb(0,0,1,0.1),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,addsubareas=F,subsetSurveyStrata=NULL,addbasemap=F,...){
# Custom area
if(area=='custom') { ylim=ylim; xlim=xlim }
## Area List: preset map extents
if(area=='lfas') { ylim=c(42.5,48); xlim=c(-67.4,-57.8) }
if(area=='west') { ylim=c(42.5,46); xlim=c(-67.8,-64) }
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') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
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) }
if(area=='lfa27') { ylim=c(44.9,47.9); xlim=c(-61,-57.8) }
if(area=='lfa28') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='lfa29') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='lfa30') { ylim=c(44.6,45.9); xlim=c(-60.8,-59.6) }
if(area=='lfa31a') { ylim=c(44.4,45.7); xlim=c(-61.8,-60) }
if(area=='lfa31b') { ylim=c(44.1,45.3); xlim=c(-62.2,-60.5) }
if(area=='lfa32') { ylim=c(43.8,45); xlim=c(-63.5,-61.5) }
if(area=='lfa33') { ylim=c(42.5,44.8); xlim=c(-65.8,-62.2) }
if(area=='lfa34') { ylim=c(42.5,45); xlim=c(-67.8,-65) }
if(area=='lfa35') { ylim=c(44.5,46); xlim=c(-66,-63.2) }
if(area=='lfa36') { ylim=c(44.5,45.7); xlim=c(-67.2,-65) }
if(area=='lfa37') { ylim=c(44,45); xlim=c(-67.3,-66.4) }
if(area=='lfa38') { ylim=c(44,45); xlim=c(-67.3,-66.4) }
if(area=='lfa40') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
if(area=='lfa41') { ylim=c(41.1,44); xlim=c(-68,-63.5) }
if(area=='NENS') { xlim=c(-61,-58.2); ylim=c(45.9,47.5) }
if(area=='SENS') { xlim=c(-63.5,-57); ylim=c(42.5,46.1) }
if(area=='4X') { xlim=c(-67,-63.1); ylim=c(42.5,45) }
if(area=='23') { xlim=c(-60.5,-57); ylim=c(43,46.2) }
if(area=='24') { xlim=c(-63.5,-59); ylim=c(42.5,45.5) }
if(area=='not4X') { xlim=c(-63.5,-57); ylim=c(42.5,47.5) }
if(area=='halibut') { xlim=c(-68,-47); ylim=c(40,48) }
options(stringsAsFactors=F,warn=-1)
coast<-get(paste0("coast",mapRes))
rivers<-get(paste0("rivers",mapRes))
attr(coast,"projection")<-"LL"
attr(rivers,"projection")<-"LL"
plotMap(coast,xlim=xlim,ylim=ylim,border=NA,...)
#addLines(rivers)
if(addbasemap){
addPolys(basemap, col="royalblue2", border="royalblue2")
addPolys(dm200, col="steelblue2", border="steelblue2")
addPolys(dm100, col="lightblue1", border="lightblue1")
}
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)) # KLUDGE!
for(i in unique(contours[[2]]$PID)){
addPolys(joinPolys(subset(contours[[1]],PID==i),junk,operation="DIFF"),polyProps=contours[[2]])
}
}
if(!is.null(poly.lst)){
addPolys(poly.lst[[1]],polyProps=poly.lst[[2]])
}
# Bathymetry
if(!is.null(isobaths)){
bath.lst<-list()
for(i in unique(ceiling(isobaths/1000))){
bath.lst[[i]]<-get(paste0("bathy.poly",i))
}
bathy.poly<-do.call(rbind,bath.lst)
bathy.poly<-subset(bathy.poly,Z%in%isobaths)
attr(bathy.poly,"projection") <- "LL"
addLines(bathy.poly,polyProps=data.frame(PID=unique(bathy.poly$PID),col=bathcol))
}
# NAFO
if(!is.null(nafo)){
if(nafo==TRUE){
#NAFO <- rgdal::readOGR("data/NAFODivisions/Divisions.shp")
sp::plot(NAFO,add=T,border='grey',col=NULL)
text(sp::coordinates(NAFO)[,1], sp::coordinates(NAFO)[,2],NAFO$ZONE,col=rgb(0.5,0.5,0.5,0.5),cex=1,...)
}else{
# nafo.xy<-read.csv(file.path( project.datadirectory("bio.polygons"), "data","Management_Areas","Fisheries","NAFO","nafo.csv"))
if(nafo[1]=='all')nafo<-unique(nafo.xy$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)
}
}
# Boundries
#groundfish survey strata
if('SummerSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) SummerStrata = subset(SummerStrata,PID %in% subsetSurveyStrata)
addPolys(SummerStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
if('GeorgesSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) GeorgesStrata = subset(GeorgesStrata,PID %in% subsetSurveyStrata)
addPolys(GeorgesStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
if('AmericanSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) AmericanStrata = subset(AmericanStrata,PID %in% subsetSurveyStrata)
addPolys(AmericanStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
# LFAs
if('lobster' %in% boundaries){
if(area=='31a')area<-311
if(area=='31b')area<-312
if(addsubareas)addPolys(subset(subareas,SID==1),lty=3)
lfa<-as.numeric(area)
if(lfa%in%LFAgrid$PID){
if(!is.na(lfa)){
grids<-subset(LFAgrid,PID==lfa)
#browser()
addPolys(grids,border=rgb(0,0,0,0.2),col=NULL)
if(labels=='grid'){
grids$label<-grids$SID
grids.dat<-merge(calcCentroid(grids),grids[c("PID","SID","label")])
#addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.8),cex=1)
}
}
else {
addPolys(LFAgrid,border=rgb(0,0,0,0.2),col=NULL)
}
}
#browser()
addPolys(LFAs)
if(labels=='lfa'){
LFAgrid$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('scallop' %in% boundaries){
addLines(SFA)
addPolys(SPA,col=NULL)
}
if('snowcrab' %in% boundaries){
text("CFA 23", x=-58.05, y=44.55, font=2, cex=1.0)
text("CFA 24", x=-60.9, y=43.75, font=2, cex=1.0)
text("CFA 4X", x=-64.2, y=43.25, font=2, cex=1.0)
text("N-ENS", x= -59.15, y=46.65, font=2, cex=1.0)
addLines(zones, col="darkgoldenrod1", lwd=2)
}
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='.')
# 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('lobster' %in% boundaries){
if('lfa'%in%labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.5),cex=labcex,font=2)
if('grid'%in%labels) addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=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]])
box(lwd=2)
title(main=title)
options(warn=0)
}
BradHubley/SpatialHub documentation built on April 6, 2024, 4:43 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions bioMap
Documented in bioMap
#' @title bioMap
#' @description a customizable mapping function that uses PBSmapping to plot fisheries data, bathymetry and mangement boundaries.
#' @param area = 'custom' where xlim & ylim are specified or select from area list below
#' @param ylim = y limits
#' @param xlim = x limits
#' @param mapRes = coastline detail ('LR' = low resolution, 'MR' = medium resolution, 'HR' = high resolution, 'UR' = ultra resolution)
#' @param land.col = colour for the land
#' @param nafo = undocumented
#' @param pt.cex = undocumented
#' @param labels = undocumented
#' @param labcex = undocumented
#' @param LT = undocumented
#' @param plot.rivers = undocumented
#' @param addsubareas = undocumented
#' @param subsetSurveyStrata = undocumented
#' @param addbasemap = undocumented
#' @param title = plot title
#' @param boundaries = for ploting specific management boundaries ("lobster", "scallop", "snowcrab", "SummerSurveyStrata", "GeorgesSurveyStrata", "AmericanSurveyStrata")
#' @param isobaths = plots bathymetry lines for specified depths from topex data
#' @param bathcol = isobath line color, default is transparent blue
#' @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)
#' @param ... = undocumented
#' @importFrom PBSmapping plotMap
#' @importFrom PBSmapping addPoints
#' @importFrom PBSmapping addLines
#' @importFrom PBSmapping addPolys
#' @importFrom PBSmapping addStipples
#' @importFrom PBSmapping addLabels
#' @importFrom PBSmapping calcCentroid
#' @importFrom PBSmapping makeGrid
#' @importFrom grDevices adjustcolor
#' @importFrom graphics box
#' @importFrom graphics image
#' @importFrom graphics text
#' @importFrom grDevices rgb
#' @importFrom utils read.csv
#' @author Brad Hubley
#' @examples
#' bioMap(area='lfa34')
#' @export
bioMap<-function(area='custom',ylim=c(40,52),xlim=c(-74,-47),mapRes='HR',land.col='wheat',title='',nafo=NULL,boundaries='LFAs',isobaths=seq(100,1000,100),bathcol=rgb(0,0,1,0.1),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,addsubareas=F,subsetSurveyStrata=NULL,addbasemap=F,...){
# Custom area
if(area=='custom') { ylim=ylim; xlim=xlim }
## Area List: preset map extents
if(area=='lfas') { ylim=c(42.5,48); xlim=c(-67.4,-57.8) }
if(area=='west') { ylim=c(42.5,46); xlim=c(-67.8,-64) }
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') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
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) }
if(area=='lfa27') { ylim=c(44.9,47.9); xlim=c(-61,-57.8) }
if(area=='lfa28') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='lfa29') { ylim=c(45.3,46); xlim=c(-61.6,-60.3) }
if(area=='lfa30') { ylim=c(44.6,45.9); xlim=c(-60.8,-59.6) }
if(area=='lfa31a') { ylim=c(44.4,45.7); xlim=c(-61.8,-60) }
if(area=='lfa31b') { ylim=c(44.1,45.3); xlim=c(-62.2,-60.5) }
if(area=='lfa32') { ylim=c(43.8,45); xlim=c(-63.5,-61.5) }
if(area=='lfa33') { ylim=c(42.5,44.8); xlim=c(-65.8,-62.2) }
if(area=='lfa34') { ylim=c(42.5,45); xlim=c(-67.8,-65) }
if(area=='lfa35') { ylim=c(44.5,46); xlim=c(-66,-63.2) }
if(area=='lfa36') { ylim=c(44.5,45.7); xlim=c(-67.2,-65) }
if(area=='lfa37') { ylim=c(44,45); xlim=c(-67.3,-66.4) }
if(area=='lfa38') { ylim=c(44,45); xlim=c(-67.3,-66.4) }
if(area=='lfa40') { ylim=c(42.25,43); xlim=c(-66.5,-65.25)}
if(area=='lfa41') { ylim=c(41.1,44); xlim=c(-68,-63.5) }
if(area=='NENS') { xlim=c(-61,-58.2); ylim=c(45.9,47.5) }
if(area=='SENS') { xlim=c(-63.5,-57); ylim=c(42.5,46.1) }
if(area=='4X') { xlim=c(-67,-63.1); ylim=c(42.5,45) }
if(area=='23') { xlim=c(-60.5,-57); ylim=c(43,46.2) }
if(area=='24') { xlim=c(-63.5,-59); ylim=c(42.5,45.5) }
if(area=='not4X') { xlim=c(-63.5,-57); ylim=c(42.5,47.5) }
if(area=='halibut') { xlim=c(-68,-47); ylim=c(40,48) }
options(stringsAsFactors=F,warn=-1)
coast<-get(paste0("coast",mapRes))
rivers<-get(paste0("rivers",mapRes))
attr(coast,"projection")<-"LL"
attr(rivers,"projection")<-"LL"
plotMap(coast,xlim=xlim,ylim=ylim,border=NA,...)
#addLines(rivers)
if(addbasemap){
addPolys(basemap, col="royalblue2", border="royalblue2")
addPolys(dm200, col="steelblue2", border="steelblue2")
addPolys(dm100, col="lightblue1", border="lightblue1")
}
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]]$PID)
junk<-data.frame(PID=1,POS=1:4,X=c(162,161,161,162),Y=c(-41,-41,-40,-40)) # KLUDGE!
for(i in unique(contours[[2]]$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
if(!is.null(isobaths)){
bath.lst<-list()
for(i in unique(ceiling(isobaths/1000))){
bath.lst[[i]]<-get(paste0("bathy.poly",i))
}
bathy.poly<-do.call(rbind,bath.lst)
bathy.poly<-subset(bathy.poly,Z%in%isobaths)
attr(bathy.poly,"projection") <- "LL"
addLines(bathy.poly,polyProps=data.frame(PID=unique(bathy.poly$PID),col=bathcol))
}
# NAFO
if(!is.null(nafo)){
if(nafo==TRUE){
#NAFO <- rgdal::readOGR("data/NAFODivisions/Divisions.shp")
sp::plot(NAFO,add=T,border='grey',col=NULL)
text(sp::coordinates(NAFO)[,1], sp::coordinates(NAFO)[,2],NAFO$ZONE,col=rgb(0.5,0.5,0.5,0.5),cex=1,...)
}else{
# nafo.xy<-read.csv(file.path( project.datadirectory("bio.polygons"), "data","Management_Areas","Fisheries","NAFO","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$label=="5ZC"]<-"5ZEM"
addPolys(nafo.xy,border='grey',col=NULL)
addLabels(nafo.dat,col=rgb(0.5,0.5,0.5,0.5),cex=2)
}
}
# Boundries
#groundfish survey strata
if('SummerSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) SummerStrata = subset(SummerStrata,PID %in% subsetSurveyStrata)
addPolys(SummerStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
if('GeorgesSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) GeorgesStrata = subset(GeorgesStrata,PID %in% subsetSurveyStrata)
addPolys(GeorgesStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
if('AmericanSurveyStrata' %in% boundaries) {
if(!is.null(subsetSurveyStrata)) AmericanStrata = subset(AmericanStrata,PID %in% subsetSurveyStrata)
addPolys(AmericanStrata,lty=1,border='lightblue',col=adjustcolor('blue',alpha.f=0.15))
}
# LFAs
if('lobster' %in% boundaries){
if(area=='31a')area<-311
if(area=='31b')area<-312
if(addsubareas)addPolys(subset(subareas,SID==1),lty=3)
lfa<-as.numeric(area)
if(lfa%in%LFAgrid$PID){
if(!is.na(lfa)){
grids<-subset(LFAgrid,PID==lfa)
#browser()
addPolys(grids,border=rgb(0,0,0,0.2),col=NULL)
if(labels=='grid'){
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)
}
}
#browser()
addPolys(LFAs)
if(labels=='lfa'){
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('scallop' %in% boundaries){
addLines(SFA)
addPolys(SPA,col=NULL)
}
if('snowcrab' %in% boundaries){
text("CFA 23", x=-58.05, y=44.55, font=2, cex=1.0)
text("CFA 24", x=-60.9, y=43.75, font=2, cex=1.0)
text("CFA 4X", x=-64.2, y=43.25, font=2, cex=1.0)
text("N-ENS", x= -59.15, y=46.65, font=2, cex=1.0)
addLines(zones, col="darkgoldenrod1", lwd=2)
}
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='.')
# 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('lobster' %in% boundaries){
if('lfa'%in%labels) addLabels(subset(LFAgrid.dat,!duplicated(label)),col=rgb(0,0,0,0.5),cex=labcex,font=2)
if('grid'%in%labels) addLabels(subset(grids.dat,!duplicated(label)),col=rgb(0.5,0.5,0.5,0.5),cex=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]])
box(lwd=2)
title(main=title)
options(warn=0)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.