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Fig_1-ED_Fig 2 Revised.R
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Fig_1-ED_Fig 2 Revised.R
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wants <- c("rgeos", "rgdal", "maptools","RColorBrewer","raster","spdep")
has <- wants %in% rownames(installed.packages())
if(any(!has)) install.packages(wants[!has])
has <- wants %in% .packages()
for(p in wants[!has]) library(p,character.only = T)
add.alpha <- function(col, alpha=1){
if(missing(col))
stop("Please provide a vector of colours.")
apply(sapply(col, col2rgb)/255, 2,
function(x)
rgb(x[1], x[2], x[3], alpha=alpha))
}
normalise_ogm_set_b <- function(v,b, labels)
{
#na.v.i = which(v == -1.0)
#v = log(v)
v[is.infinite(v)] = NA
# v[v < 0] = NA
v.norm = as.integer(cut(v,breaks=b))
v.norm[is.na(v.norm)] = 0.0
# v.norm = (v.norm/max(v.norm))
# v.norm = v.norm * 10
return(list(v.norm,labels))
}
normalise_ogm_mines_set_b <- function(v,b, labels)
{
#na.v.i = which(v == -1.0)
#v = log(v)
v[is.infinite(v)] = NA
v.norm = as.integer(cut(v,breaks=b))
v.norm[is.na(v.norm)] = 0.0
v.norm = v.norm-1.0
return(list(v.norm,labels))
}
normalise_ogm <- function(v,b,density,log)
{
#na.v.i = which(v == -1.0)
#v = log(v)
v[is.infinite(v)] = NA
# v[v < 0] = NA
brks.v = quantile(v,probs = b,na.rm = T)
brks.v = unique(brks.v)
print(brks.v)
if(log)
{
label.brks = exp(brks.v)
}
else
{
label.brks = (brks.v)
}
if(density)
{
#temp = format(label.brks/cell.area,big.mark=",",trim=T,digits= 1,scientific=F)
labels = rep("",length(label.brks)-1)
for(i in 1:length(label.brks)-1)
{
labels[i] = paste(format(label.brks[i]/cell.area,big.mark=",",trim=T,digits= 2,scientific=F)
,"\n to \n",
format(label.brks[i+1]/cell.area,big.mark=",",trim=T,digits= 2,scientific=F))
}
}
else
{
#temp = format(label.brks,big.mark=",",trim=T, digits = 1,scientific=F)
labels = rep("",length(label.brks)-1)
for(i in 1:length(label.brks)-1)
{
labels[i] = paste(format(label.brks[i],big.mark=",",trim=T, digits = 2,scientific=F)
,"\n to \n",
format(label.brks[i+1],big.mark=",",trim=T, digits = 2,scientific=F))
}
}
#v.norm = as.integer(cut(v,breaks=brks.v))
v.norm = as.integer(cut(v,breaks=brks.v))
v.norm[is.na(v.norm)] = 0.0
# v.norm = (v.norm/max(v.norm))
# v.norm = v.norm * 10
return(list(v.norm,labels))
}
normalise_ogm_mines <- function(v,b,density,log)
{
#na.v.i = which(v == -1.0)
#v = log(v)
v[is.infinite(v)] = NA
# v[v < 0] = NA
brks.v = quantile(v,probs = b,na.rm = T)
brks.v = unique(brks.v)
print(brks.v)
if(log)
{
label.brks = exp(brks.v)
v = v + 1
}
else
{
label.brks = (brks.v)
}
if(density)
{
#temp = format(label.brks/cell.area,big.mark=",",trim=T,digits= 1,scientific=F)
labels = rep("",length(label.brks)-1)
for(i in 1:length(label.brks)-1)
{
labels[i] = paste(format(label.brks[i]/cell.area,big.mark=",",trim=T,digits= 2,scientific=F)
,"\n to \n",
format(label.brks[i+1]/cell.area,big.mark=",",trim=T,digits= 2,scientific=F))
}
}
else
{
#temp = format(label.brks,big.mark=",",trim=T, digits = 1,scientific=F)
labels = rep("",length(label.brks)-1)
for(i in 1:length(label.brks)-1)
{
labels[i] = paste(format(label.brks[i],big.mark=",",trim=T, digits = 2,scientific=F)
,"\n to \n",
format(label.brks[i+1],big.mark=",",trim=T, digits = 2,scientific=F))
}
}
#v.norm = as.integer(cut(v,breaks=brks.v))
v.norm = as.integer(cut(v,breaks=brks.v))
v.norm[is.na(v.norm)] = 0.0
v.norm = v.norm-1.0
# v.norm = (v.norm/max(v.norm))
# v.norm = v.norm * 10
return(list(v.norm,labels))
}
w.wout.infrastructure.boxplot<-function(inds, o, b, add,x1,x2,xlims,ylims,ticks,add.signif)
{
no.infr.i <- which((master[inds,ogm.cols[[o]]]) == 0 & master[inds,bd.cols[[b]]] > 0)
no.infr.quants <- quantile(master[inds[no.infr.i],bd.cols[[b]]],probs = c(0.025,0.975),na.rm=T)
bp = boxplot(master[inds[no.infr.i],bd.cols[[b]]],
range=0,log="y",add=add, at = x1,
ylims = ylims, xlims = xlims,yaxt=ticks,
col = "#e3d7b6",cex.axis=0.7,lwd=1, plot=F)
bp$stats[c(1,5),1] = no.infr.quants
bxp(bp,
range=0,log="y",add=add, at = x1,
ylims = ylims, xlims = xlims,axes=F,
boxfill = "#e3d7b6",cex.axis=0.7,lwd=1, show.names=T)
w.infr.i<-which(master[inds,ogm.cols[[o]]] > 0 & master[inds,bd.cols[[b]]] > 0)
w.infr.quants <- quantile(master[inds[w.infr.i],bd.cols[[b]]],probs = c(0.025,0.975),na.rm=T)
median.1 = median(master[inds[no.infr.i],bd.cols[[b]]])
median.2 = median(master[inds[w.infr.i],bd.cols[[b]]])
col = ifelse(median.2 < median.1,"dark red","black")
bp<-boxplot(master[inds[w.infr.i],bd.cols[[b]]],
range = 0,log="y",add=T, at = x2,
ylims = ylims,xlims = xlims,yaxt=ticks,border = col,
col="#968b69",cex.axis=0.7,lwd=1, plot=F)
bp$stats[c(1,5),1] = w.infr.quants
bxp(bp,range = 0,log="y",add=T, at = x2,
ylims = ylims,xlims = xlims,axes=F,boxcol = col,
boxfill="#968b69",border=col,cex.axis=0.7,lwd=1, show.names=T)
ret<-NA
if(add.signif && length(no.infr.i) > 0 && length(w.infr.i) > 0 &&
sum(is.na(master[inds[no.infr.i],bd.cols[[b]]]) < length(no.infr.i)) &&
sum(is.na(master[inds[w.infr.i],bd.cols[[b]]]) < length(w.infr.i)))
{
# ret<-wilcox.test(master[inds[no.infr.i],bd.cols[[b]]],master[inds[w.infr.i],bd.cols[[b]]])$p.value
df.mod = data.frame(c(master[inds[no.infr.i],bd.cols[[b]]],
master[inds[w.infr.i],bd.cols[[b]]]))
names(df.mod) = "bd"
df.mod$label = c(rep(1,length(no.infr.i)),rep(2,length(w.infr.i)))
df.mod$Longitude = c(master$Longitude[inds[no.infr.i]],master$Longitude[inds[w.infr.i]])
df.mod$Latitude = c(master$Latitude[inds[no.infr.i]],master$Latitude[inds[w.infr.i]])
n.zeroes = 1
n = 0
while(n.zeroes > 0 && n < 1E6)
{
n = n + 2000
print(paste("Finding min distance: ",n))
neighbourhood = dnearneigh(cbind(df.mod$Longitude,df.mod$Latitude),0,n,longlat = T)
n.zeroes = sum(unlist(lapply(neighbourhood,function (x) x[1])) == 0)
}
n.min = n
n2 = nb2listw(neighbourhood,glist = NULL, style = "W",zero.policy = T)
m1= lm(bd ~ label, df.mod)
m2 = errorsarlm(bd ~ label, data = df.mod, zero.policy = T, n2)
moran1 = moran.test(residuals(m1),n2)
moran2 = moran.test(residuals(m2),n2)
ret = list(m1 = m1,
m2 = m2,
moran1 = moran1,
moran2 = moran2)
}
if(b == 1) sig.scalar = 1.2
if(b == 3) sig.scalar = 1.3
if(add.signif && !is.na(ret))
{
signif.val = summary(ret$m2)[[46]][2,4]
text(x1+0.5,ylims[2]*sig.scalar,as.character(symnum(signif.val, corr=FALSE,
cutpoints = c(0, .001,.01,.05, .1, 1),
symbols = c("***","**","*","."," "))),
cex=1.2,
col = col)
}
return(ret)
}
w.any.realm.wout.infrastructure.boxplot<-function(inds, o, b, add,x1,x2,xlims,ylims,ticks,add.signif)
{
no.infr.i <- which((master[inds,ogm.cols[[o]]]) == 0 & master[inds,bd.cols[[b]]] > 0)
no.infr.quants <- quantile(master[inds[no.infr.i],bd.cols[[b]]],probs = c(0.025,0.975),na.rm=T)
bp = boxplot(master[inds[no.infr.i],bd.cols[[b]]],
range=0,log="y",add=add, at = x1,
ylims = ylims, xlims = xlims,yaxt=ticks,
col = "#e3d7b6",cex.axis=0.7,lwd=1, plot=F)
bp$stats[c(1,5),1] = no.infr.quants
bxp(bp,
range=0,log="y",add=add, at = x1,
ylims = ylims, xlims = xlims,axes=F,
boxfill = "#e3d7b6",cex.axis=0.7,lwd=1, show.names=T)
w.infr.i<-which(master[,ogm.cols[[o]]] > 0 & master[,bd.cols[[b]]] > 0)
w.infr.quants <- quantile(master[w.infr.i,bd.cols[[b]]],probs = c(0.025,0.975),na.rm=T)
median.1 = median(master[inds[no.infr.i],bd.cols[[b]]])
median.2 = median(master[w.infr.i,bd.cols[[b]]])
col = ifelse(median.2 < median.1,"dark red","black")
bp<-boxplot(master[w.infr.i,bd.cols[[b]]],
range = 0,log="y",add=T, at = x2,
ylims = ylims,xlims = xlims,yaxt=ticks,border = col,
col="#968b69",cex.axis=0.7,lwd=1, plot=F)
bp$stats[c(1,5),1] = w.infr.quants
bxp(bp,range = 0,log="y",add=T, at = x2,
ylims = ylims,xlims = xlims,axes=F,boxcol = col,
boxfill="#968b69",border=col,cex.axis=0.7,lwd=1, show.names=T)
ret<-NA
if(length(no.infr.i) > 0 && length(w.infr.i) > 0 &&
sum(is.na(master[inds[no.infr.i],bd.cols[[b]]]) < length(no.infr.i)) &&
sum(is.na(master[w.infr.i,bd.cols[[b]]]) < length(w.infr.i)))
{
ret<-wilcox.test(master[inds[no.infr.i],bd.cols[[b]]],master[w.infr.i,bd.cols[[b]]])$p.value
}
if(b == 1) sig.scalar = 1.2
if(b == 3) sig.scalar = 1.3
if(add.signif && !is.na(ret)) text(x1+0.5,ylims[2]*sig.scalar,as.character(symnum(ret, corr=FALSE,
cutpoints = c(0, .001,.01,.05, .1, 1),
symbols = c("***","**","*","."," "))),
cex=1.2,
col = col)
return(ret)
}
#Specify the input directory
indsn="C:/Users/mikeha/Work/Fossil Fuels and biodiversity/"
wgs1984.proj <- CRS("+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0")
moll.proj <- CRS("+proj=moll +datum=WGS84")
WL <- readShapePoly("C:/Users/mikeha/Work/Spatial data/natural-earth-vector-master/natural-earth-vector-master/10m_physical/ne_10m_land.shp")#download from 'naturalearth.com'
proj4string(WL) <- wgs1984.proj
WL.moll <- spTransform(WL, moll.proj)
world<-readShapeSpatial("C:/Users/mikeha/Dropbox/World countries/outline_clip")
proj4string(world) = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
#comb.shp.name = "BD_Realm_OGM_Realm_Continent_no_dup"
comb.shp.name = "BD_Realm_OGM_Realm_Continent_no_dup_all_well_count_conc_1"
comb = readShapeSpatial(paste(indsn,"Combined/",comb.shp.name,sep=""),
repair=T,delete_null_obj=T, force_ring = F)
proj4string(comb) = "+proj=moll +datum=WGS84"
# Don't transform plot as equal area projection
# comb = spTransform(comb,CRS(proj4string(world)))
# proj4string(comb) = proj4string(world)
# Transform the world outline
world = spTransform(world,CRS(proj4string(comb)))
proj4string(world) = proj4string(comb)
shp.un.regions = readShapeSpatial("c:/Users/mikeha/Work/Fossil Fuels and Biodiversity/UNEP regions/UNEP_regions_multi.shp",
repair=T,delete_null_obj=T, force_ring = F)
proj4string(shp.un.regions) = CRS("+init=epsg:4326")
shp.un.regions = spTransform(shp.un.regions,CRS("+proj=moll +ellps=WGS84"))
shp.un.countries = readShapeSpatial("c:/Users/mikeha/Work/Fossil Fuels and Biodiversity/UNEP regions/EEZv8_UNEP_Countries.shp",
repair=T,delete_null_obj=T, force_ring = F)
proj4string(shp.un.countries) = CRS("+init=epsg:4326")
shp.un.countries = spTransform(shp.un.countries,CRS("+proj=moll +ellps=WGS84"))
outdir = "C:/Users/mikeha/Google Drive/Fossil Fuels and biodiversity/Figures/"
wgs1984.proj <- CRS("+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0")
comb.wgs = spTransform(comb,wgs1984.proj)
comb.wgs.pts = gCentroid(comb.wgs,byid=T)
comb$Latitude = coordinates(comb.wgs.pts)[,2]
comb$Longitude = coordinates(comb.wgs.pts)[,1]
#master<-read.csv(paste(indsn,"Combined/",comb.shp.name,".csv",sep=""))
master<-comb@data
master$InvArea[which(master$InvArea < 0.0)] = 0.0
#Convert from per m2 to per 1000 km2
master$InvArea = master$InvArea * 1E9
hs.inds = which(master$Realm_1 == 0)
terr.inds = which(master$Realm_1 == 1)
eez.inds = which(master$Realm_1 == 2)
ant.inds = which(master$Realm_1 == 3)
mar.inds<-c(hs.inds,eez.inds)
continents = as.character(unique(master$CONTINENT))
continents = continents[!(continents == " ") & !(continents == "Antarctica")]
continents.inds = sapply(continents,function(x) which(master$CONTINENT == x & master$Realm_1 == 1))
#Realm labels
realm.labels = c("Terrestrial","High Seas","EEZ","Antarctica","Global")
#Find the columns corresponding to each category of ogm data
ogm.colnames = c("Count_","Count_1","Count_2","sum_counts","sum_length")
ogm.labels= c("Wells","Coal mines","Refineries","Wells,mines & refineries",
"Pipeline length","Field area ","Fut. field area")
#add colume for well, refineries and pipelines
master$w_r_p_m = rowSums(master[,c("Count_","Count_2", "sum_length","prdcoalcnt")])
ogm.colnames = c(ogm.colnames,"w_r_p_m")
ogm.cols = sapply(ogm.colnames, function(x) which(colnames(master) == x))
master$w_r_p = rowSums(master[,c("Count_","Count_2", "sum_length")])
ogm.colnames = c(ogm.colnames,"w_r_p")
ogm.cols = sapply(ogm.colnames, function(x) which(colnames(master) == x))
ogm.colnames = c(ogm.colnames,"prdcoalcnt")
ogm.cols = sapply(ogm.colnames, function(x) which(colnames(master) == x))
ogm.colnames = c(ogm.colnames,"validblkar")
ogm.cols = sapply(ogm.colnames, function(x) which(colnames(master) == x))
bd.colnames = c("SpCount","SumInvArea","InvArea","MaxInvArea","MinInvArea")
bd.labels = c("Assessed Spp. richness", "Sum RR","Assessed Spp. mean range rarity", "Max RR", "Min RR")
bd.cols = sapply(bd.colnames, function(x) which(colnames(master) == x))
wilcox.test.outputs<-array(NA, dim=c(length(ogm.colnames),length(bd.colnames),12))
# Construct map of the bd in question -------------------------------------
cell.area = 50*50 #km2
def.breaks <- seq(0,1,length.out = 10)
def.breaks <-c(0,0.5,0.75,0.9,0.95,0.96,0.97,0.98,0.99,1.0)
wells = comb@data$Count_
wells.breaks = c(0.99,30,1000,3000,8000,68000)
wells.labels = c("1\n to \n<30","30\n to \n<1,000","1,000\n to \n<3,000","3,000\n to \n<8,000",">8,000")
wells.norm = normalise_ogm_set_b(wells,wells.breaks, wells.labels)
#def.breaks <- seq(0,1,length.out = 20)
refineries = log(comb@data$Count_2)
refineries.norm = normalise_ogm(refineries,def.breaks,F,T)
pipes = (comb@data$sum_length)
pipes.breaks = c(1E-3,200,700,1000,2000,8500)
pipes.labels = c(">0\n to \n<200","200\n to \n<700","700\n to \n<1,000","1,000\n to \n<2,000",">2,000")
pipes.norm = normalise_ogm_set_b(pipes, pipes.breaks, pipes.labels)
exploited.fields = comb@data$Sum_Area
exploited.fields[which(exploited.fields > 2500.0)] = 2500.0
# exploited.fields = log(exploited.fields)
fields.breaks = c(1E-3,50,250,700,1500,2600)
fields.labels = c(">0\n to \n<50","50\n to \n<250","250\n to \n<700","700\n to \n<1,500",">1,500")
exploited.fields.norm = normalise_ogm_set_b(exploited.fields, fields.breaks,fields.labels)
unexploited.fields = comb@data$Sum_Area_1
unexploited.fields[which(unexploited.fields > 2500.0)] = 2500.0
# unexploited.fields = log(unexploited.fields)
unexploited.fields.norm = normalise_ogm_set_b(unexploited.fields, fields.breaks, fields.labels)
valid.blocks = comb@data$validblkar
# valid.blocks = log(valid.blocks)
blocks.breaks = c(1E-3,500,1000,1500,2000,2500)
blocks.labels = c(">0\n to \n<500","500\n to \n<1,000","1,000\n to \n<1,500","1,500\n to \n<2,000",">2,000")
valid.blocks.norm = normalise_ogm_set_b(valid.blocks, blocks.breaks,blocks.labels)
bid.blocks = comb@data$bidblkarea
#bid.blocks[which(bid.blocks > 2500.0)] = 2500.0
# bid.blocks = log(bid.blocks)
bid.blocks.norm = normalise_ogm_set_b(bid.blocks, blocks.breaks,blocks.labels)
prd.mines = comb@data$prdcoalcnt
# prd.mines = log(prd.mines)
mines.breaks = c(0,1,2,4,6,8,18)
mines.labels = c("1\n to \n<2","2\n to \n<4","4\n to \n<6","6\n to \n<8",">8")
prd.mines.norm = normalise_ogm_set_b(prd.mines,mines.breaks,mines.labels)
exp.mines = comb@data$explcoalcn
# exp.mines = log(exp.mines)
exp.mines.norm = normalise_ogm_set_b(exp.mines, mines.breaks,mines.labels)
sr.breaks <-c(0,1,25,50,100,350,600,850,1100,1350,1600)
sr.labels<-c("1\n to \n<25","25\n to \n<50","50\n to \n<100","100\n to \n<350","350\n to \n<600","600\n to \n<850","850\n to \n<1,100","1,100","1,100\n to \n<1,350",">1,350")
sr.breaks <-c(0.9,10,20,30,45,
60,100,250,500,
750,1000,2000)
sr.labels<-c("1\n to \n<10",
"10\n to \n<20",
"20\n to \n<30",
"30\n to \n<45",
"45\n to \n<60",
"60\n to \n<100",
"100\n to \n<250",
"250\n to \n<500",
"500\n to \n<750",
"750\n to \n<1,000",
">1,000")
n.breaks = 100
sr = (comb@data$SpCount)
sr.breaks = c(seq(0,1100,length.out = n.breaks-1),range(sr)[2])
sr.norm = normalise_ogm_set_b(sr, sr.breaks,sr.labels)
rr.breaks<-c(0,1E-9,1E-5,1E-4,2.5E-4,5E-4,7.5E-4,1E-3,1E-2,1E-1,1E9)
rr.labels<-c(">0\n to \n<0.00001",
"0.00001\n to \n<0.0001",
"0.0001\n to \n<0.00025",
"0.00025\n to \n<0.0005",
"0.0005\n to \n<0.00075",
"0.00075\n to \n<0.001",
"0.001\n to \n<0.01",
"0.01\n to \n<0.1",
">0.1")
rr = 1E9*comb@data$InvArea
rr = log(rr)
rr[is.infinite(rr)] = NA
rr.up.val = -2.5
rr.breaks = c((seq(range(rr,na.rm = T)[1],rr.up.val, length.out = n.breaks-1)),
range(rr,na.rm = T)[2])
# rr.breaks = c(head(seq(range(rr,na.rm = T)[1],0,length.out = n.breaks-20),n.breaks-21),
# seq(0,range(rr,na.rm=T)[2], length.out = 20))
#rr.breaks = quantile(rr, na.rm=T,probs = seq(0,1,length.out = n.breaks))
rr.norm = normalise_ogm_mines_set_b(rr,rr.breaks,rr.labels)
# Read in map of oceans - for background
bound.shp.name = 'cntry_eez_merge_iso3_moll_mar_bgeom.shp'
bound = readShapeSpatial(paste(indsn,"GIS/",bound.shp.name,sep=""),
repair=T,delete_null_obj=T, force_ring = F)
proj4string(bound) = "+proj=moll +datum=WGS84"
#Read in map of EEZs
eez.shp.name = "World_EEZ_Moll_DS.shp"
eez = readShapeSpatial(paste(indsn,"GIS/",eez.shp.name,sep=""),
repair=T,delete_null_obj=T, force_ring = F)
proj4string(eez) = "+proj=moll +ellps=WGS84"
legend.x.scale = 0.35
# Plot Species Richness and Range rarity as two panel plot------------------------------- ------------------------------
#plot.bg.colours = c('#2c6223','#045580','#04806d')
height.cm = 18
width.cm = 14
#png(paste(outdir,"WellsPipes_moll_bg_eez_grey.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
pdf(file = paste(outdir,"SR_meanRR_moll_grey-fine.pdf",sep=""),width=width.cm/2.54,height=height.cm/2.54)
par(oma=c(0,0,0,0))
par(mar=c(0,0,0,0))
par(xpd=NA)
par(cex=1)
layout(matrix(c(1,2,3,4),nrow = 4), heights = c(0.45,0.05,0.45,0.05))
plot.norm = sr.norm
features.to.plot = which(plot.norm[[1]] > 0)
#features.to.plot = which(sr > 1100)
#plot(eez,border = "black", add = T)
plot(WL.moll,lwd=0.05,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
cols <- c(colorRampPalette(rev(brewer.pal(8,"RdYlBu")))(n.breaks-1),"#7a0177")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot]+1, border = NA, add=T)
plot(WL.moll, add=T, col = NA, border= "black",lwd=0.05)
mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
# t=legend(bbox(bound)[1,1]*0.8,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
# title="Assessed species richness",
# xpd=T,horiz=T,
# fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
# x.intersp = 0.02,
# adj=c(-2,2))
#
# text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
# plot.norm[[2]],
# pos=1,
# cex=0.5)
par(mar=c(2,3,0,3))
x.lim = c(0,1300)#
y.lim = c(0,1)
width <- (1300)/(n.breaks-1)
x_step <- seq(0, 1300, width)
plot(NA, axes=F, xlab="",ylab="",xlim = x.lim, ylim = y.lim)
sapply(seq_len(n.breaks-1),
function(i) {
rect(x_step[i], 0, x_step[i]+width, 1, col=i, border=NA)
})
rect(x_step[n.breaks-1], 0, x_step[n.breaks-1]+100, 1, col=n.breaks, border=NA)
axis(1,at=seq(0,1400,200),labels = c(seq(0,1200,200),'>1100'), tick = F, line=-1,cex.axis=0.7)
mtext(side = 1, "Assessed species richness", line = 1, cex = 0.8)
par(mar=c(0,0,0,0))
plot.norm = rr.norm
features.to.plot = which(plot.norm[[1]] > 0)
#features.to.plot = which(rr > rr.up.val)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
cols <- c(colorRampPalette(rev(brewer.pal(8,"RdYlBu")))(n.breaks-1),"#7a0177")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot]+2, border = NA, add=T)
plot(WL.moll, add=T, col = NA, border= "black",lwd=0.1)
mtext("b",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
#
# t=legend(bbox(bound)[1,1]*0.65,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
# title="Assessed range rarity",
# xpd=T,horiz=T,
# fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
# x.intersp = 0.08,
# adj=c(-2,2))
#
# text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
# plot.norm[[2]],
# pos=1,
# cex=0.5)
par(mar=c(2,3,0,3))
x.lim = c(min(rr.breaks, na.rm = T),rr.up.val + 1)
y.lim = c(0,1)
width <- (rr.up.val - min(rr.breaks, na.rm = T))/(n.breaks-2)
x_step <- seq(min(rr.breaks, na.rm = T), rr.up.val, width)
plot(NA, axes=F, xlab="",ylab="",xlim = x.lim, ylim = y.lim)
sapply(seq_len(n.breaks-1),
function(i) {
rect(x_step[i], 0, x_step[i]+width, 1, col=i, border=NA)
})
rect(x_step[n.breaks-1], 0, x_step[n.breaks-1]+1, 1, col=n.breaks, border=NA)
axis(1,at=seq(-12,x.lim[2],1),labels = c(seq(-12,rr.up.val,1),paste0('>',rr.up.val)),tick = F, line=-1,cex.axis=0.7)#
mtext(side = 1, "Assessed range rarity", line = 1, cex = 0.8)
#axis(1,at=rr.breaks,tick = F, line=-1,cex.axis=0.8)
dev.off()
# Plot wells and pipelines as two panel plot------------------------------- ------------------------------
#plot.bg.colours = c('#2c6223','#045580','#04806d')
height.cm = 18
width.cm = 14
#png(paste(outdir,"WellsPipes_moll_bg_eez_grey.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
pdf(file = paste(outdir,"WellsPipes_moll_bg_eez_grey.pdf",sep=""),width=width.cm/2.54,height=height.cm/2.54)
par(oma=c(0,0,0,0))
par(mar=c(4,0,0,0))
par(xpd=NA)
par(cex=1)
layout(matrix(c(1,2),nrow = 2))
plot.norm = wells.norm
# comb@data$wells.norm = wells.norm[[1]]
#
# comb.wgs84 = spTransform(comb,wgs1984.proj)
# world.wgs84 = spTransform(world,wgs1984.proj)
#
# r <- raster(ncol=360, nrow=160)
# extent(r) <- extent(comb.wgs84)
# wells.raster = rasterize(x = comb.wgs84,y = r,field = "wells.norm", fun = 'mean')
features.to.plot = which(plot.norm[[1]] > 0 & comb$Realm_1 > 0)
#plot(eez,border = "black", add = T)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*legend.x.scale,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Wells (2500 km"^{-2},")",sep="")),
xpd=T,horiz=T,
fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
x.intersp = 0.08,
adj=c(-2,2))
text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
plot.norm[[2]],
pos=1,
cex=0.5)
plot.norm = pipes.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
mtext("b",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*legend.x.scale,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Pipeline length (km 2500 km"^{-2},")",sep="")),
xpd=T,horiz=T,
fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
x.intersp = 0.08,
adj=c(-2,2))
text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
plot.norm[[2]],
pos=1,
cex=0.5)
dev.off()
# Plot exploited and unexploited field areas as two panel plot ------------------------------
plot.bg.colours = c('#2c6223','#045580')
height.cm = 18
width.cm = 15
#png(paste(outdir,"Ex_Unexp_fields_moll_bg_eez_grey.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
pdf(file = paste(outdir,"Ex_Unexp_fields_moll_bg_eez_grey.pdf",sep=""),width=width.cm/2.54,height=height.cm/2.54)
par(oma=c(0,0,0,0))
par(mar=c(0,0,0,0))
par(xpd=NA)
par(cex=1)
layout(matrix(c(1,2,3),nrow = 3), heights = c(0.45,0.45,0.1))
plot.norm = exploited.fields.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
# t=legend(bbox(bound)[1,1]*0.6,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
# title=expression(paste("Exploited fields (km"^{-2}," 250 km"^{-2},")",sep="")),
# xpd=T,horiz=T,
# fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
# x.intersp = 0.08,
# adj=c(-2,2))
#
# text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
# plot.norm[[2]],
# pos=1,
# cex=0.5)
plot.norm = unexploited.fields.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
mtext("b",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*legend.x.scale,bbox(bound)[2,1]*1.05,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Fields (km"^{-2}," 2500 km"^{-2},")",sep="")),
xpd=NA,horiz=T,
fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1.5,
x.intersp = 0.08,
adj=c(-2,2))
text(t$text$x-(700000),t$text$y-(0.06*abs(t$text$y)),
plot.norm[[2]],
pos=1,
cex=0.8)
dev.off()
# Plot valid and bidding block areas as two panel plot ------------------------------
plot.bg.colours = c('#2c6223','#045580')
height.cm = 18
width.cm = 15
#png(paste(outdir,"Val_bid_blocks_moll_bg_no_data_eez_grey.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
pdf(file = paste(outdir,"Val_bid_blocks_moll_bg_no_data_eez_grey.pdf",sep=""),width=width.cm/2.54,height=height.cm/2.54)
par(oma=c(0,0,0,0))
par(mar=c(0,0,0,0))
par(xpd=NA)
par(cex=1)
layout(matrix(c(1,2,3),nrow = 3), heights = c(0.45,0.45,0.1))
plot.norm = valid.blocks.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
plot(shp.un.countries,col="white",add=T,border=NA)
#plot(shp.un.countries,border = NA,density = 20, add=T)
mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
# t=legend(bbox(bound)[1,1]*0.5,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
# title=expression(paste("Valid blocks (km"^{-2}," 2500 km"^{-2},")",sep="")),
# xpd=T,horiz=T,
# fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
# x.intersp = 0.08,
# adj=c(-2,2))
#
# text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
# plot.norm[[2]],
# pos=1,
# cex=0.5)
plot.norm = bid.blocks.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.5,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
plot(shp.un.countries,col="white",add=T,border=NA)
#plot(shp.un.countries,border = NA,density = 20, add=T)
mtext("b",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*legend.x.scale,bbox(bound)[2,1]*1.05,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Blocks (km"^{-2}," 2500 km"^{-2},")",sep="")),
xpd=NA,horiz=T,
fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1.5,
x.intersp = 0.08,
adj=c(-2,2))
text(t$text$x-(700000),t$text$y-(0.06*abs(t$text$y)),
plot.norm[[2]],
pos=1,
cex=0.8)
dev.off()
# Plot producing and exploration mines as two panel plot------------------------------- ------------------------------
plot.bg.colours = c('#2c6223','#045580')
height.cm = 18
width.cm = 15
#png(paste(outdir,"Prod_expl_mines_moll_bg_pts_eez.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
pdf(file = paste(outdir,"Prod_expl_mines_moll_bg_pts_eez.pdf",sep=""),width=width.cm/2.54,height=height.cm/2.54)
par(oma=c(0,0,0,0))
par(mar=c(0,0,0,0))
par(xpd=NA)
par(cex=1)
layout(matrix(c(1,2,3),nrow = 3), heights=c(0.45,0.45,0.1))
plot.norm = prd.mines.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.1,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
cols = add.alpha(cols,0.6)
palette(cols)
pts.to.plot = gCentroid(comb[features.to.plot,],byid = T)
plot(pts.to.plot,col = plot.norm[[1]][features.to.plot], border = NA, add=T,pch=16,cex=0.8)
#plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
# mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
#
# t=legend(bbox(bound)[1,1]*0.7,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
# title=expression(paste("Producing mines (2500 km"^{-2},")",sep="")),
# xpd=T,horiz=T,
# fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1,
# x.intersp = 0.08,
# adj=c(-2,2))
#
# text(t$text$x-(400000),t$text$y-(0.01*abs(t$text$y)),
# plot.norm[[2]],
# pos=1,
# cex=0.5)
plot.norm = exp.mines.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(WL.moll,lwd=0.1,col = "lightgrey", border = "black")#add=T
plot(bound,lwd=0.5,col = NA,border = "black", add=T)
cols = col2rgb(rev(brewer.pal(length(plot.norm[[2]]),"RdYlBu")))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
cols = add.alpha(cols,0.6)
palette(cols)
pts.to.plot = gCentroid(comb[features.to.plot,],byid = T)
plot(pts.to.plot,col = plot.norm[[1]][features.to.plot], border = NA, add=T,pch=16,cex=0.8)
# plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
mtext("b",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*legend.x.scale,bbox(bound)[2,1]*1.05,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Mines (2500 km"^{-2},")",sep="")),
xpd=NA,horiz=T,
fill=seq(1:length(plot.norm[[2]])),bty="n", cex=1.5,
x.intersp = 0.08,
adj=c(-2,2))
text(t$text$x-(700000),t$text$y-(0.06*abs(t$text$y)),
plot.norm[[2]],
pos=1,
cex=0.8)
dev.off()
# Plot map of refineries --------------------------------------------------
height.cm = 9
width.cm = 14
png(paste(outdir,"Refineries.png",sep=""),width=width.cm,height=height.cm,units="cm",res=600)
par(oma=c(0,0,0,0))
par(mar=c(4,0,0,0))
par(xpd=NA)
par(cex=1)
plot.norm = refineries.norm
features.to.plot = which(plot.norm[[1]] > 0)
plot(bound,lwd=0.5)
cols = col2rgb(brewer.pal(length(plot.norm[[2]]),"PuRd"))
#Make the colours darker
cols = round(cols*0.8)
cols = apply(cols,2,function(x) paste(as.hexmode(x),collapse =""))
cols = paste("#",cols,sep="")
palette(cols)
plot(comb[features.to.plot,],col = plot.norm[[1]][features.to.plot], border = NA, add=T)
plot(world, add=T,lwd=0.5)
#mtext("a",at=bbox(bound)[1,1],line=-2,cex=1.2,font=2)
t=legend(bbox(bound)[1,1]*0.5,bbox(bound)[2,1]*1.0,rep(" ",length(plot.norm[[2]])),
title=expression(paste("Refineries (250 km"^{-2},")",sep="")),