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Feasibility_Maps.R
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## spatial climates
library(data.table)
library(sf)
library(RPostgreSQL)
library(dplyr)
library(foreach)
library(rmapshaper)
library(tictoc)
library(rasterVis)
library(raster)
library(ccissr)
library(RPostgreSQL)
library(sf)
library(pool)
library(RColorBrewer)
library(terra)
##some setup
con <- dbPool(
drv = RPostgres::Postgres(),
dbname = Sys.getenv("BCGOV_DB"),
host = Sys.getenv("BCGOV_HOST"),
port = 5432,
user = Sys.getenv("BCGOV_USR"),
password = Sys.getenv("BCGOV_PWD")
)
sppDb <- dbPool(
drv = RPostgres::Postgres(),
dbname = "spp_feas",
host = Sys.getenv("BCGOV_HOST"),
port = 5432,
user = Sys.getenv("BCGOV_USR"),
password = Sys.getenv("BCGOV_PWD")
)
#lookup tables
spps.lookup <- read.csv("../ccissr/data-raw/data_tables/Tree speciesand codes_2.0_25Aug2021.csv")
edatope.name <- c("Medium-Mesic", "Poor-Subxeric", "Rich-Hygric")
BGCcolors <- read.csv("../ccissr/data-raw/data_tables/WNAv11_Zone_Colours.csv")
# base raster
X <- raster("BC_Raster.tif")
X <- raster::setValues(X,NA)
#Feasibility tables
outline <- st_read(con,query = "select * from bc_outline")
S1 <- setDT(dbGetQuery(sppDb,"select bgc,ss_nospace,spp,newfeas from feasorig"))
setnames(S1,c("BGC","SS_NoSpace","Spp","Feasible"))
library(Rcpp)
cppFunction('NumericVector ModelDir(NumericMatrix x, NumericVector Curr, std::string dir){
int n = x.nrow();
NumericVector res(n);
NumericVector temp(5);
NumericVector temp2;
double curr_suit;
if(dir == "Improve"){
for(int i = 0; i < n; i++){
temp = x(i,_);
temp.push_front(0);
curr_suit = Curr[i];
if(curr_suit == 4){
curr_suit = 3;
}
res[i] = sum(temp[Range(0,curr_suit)]);
}
}else{
for(int i = 0; i < n; i++){
temp = x(i,_);
temp.push_back(0);
curr_suit = Curr[i];
if(curr_suit == 4){
curr_suit = 3;
}
res[i] = sum(temp[Range(curr_suit,4)]);
}
}
return(res);
}
')
##adapted feasibility function
ccissMap <- function(SSPred,suit,spp_select){
### generate raw feasibility ratios
suit <- suit[Spp == spp_select,.(BGC,SS_NoSpace,Spp,Feasible)]
suit <- unique(suit)
suit <- na.omit(suit)
SSPred <- SSPred[,.(SiteRef,FuturePeriod,BGC,SS_NoSpace,SS.pred,SSprob)]
Site_BGC <- unique(SSPred[,.(SiteRef,BGC)])
SSPred <- na.omit(SSPred)
setkey(SSPred,SS.pred)
setkey(suit,SS_NoSpace)
suitMerge <- suit[SSPred, allow.cartesian = T]
suitMerge <- na.omit(suitMerge)
setnames(suitMerge, old = c("SS_NoSpace", "i.SS_NoSpace"), new = c("SS.pred", "SS_NoSpace"))
suitVotes <- data.table::dcast(suitMerge, SiteRef + Spp + FuturePeriod + SS_NoSpace ~ Feasible,
value.var = "SSprob", fun.aggregate = sum)
# Fill with 0 if columns does not exist, encountered the error at SiteRef 3104856
colNms <- c("1","2","3","X")
set(suitVotes, j = as.character(1:5)[!as.character(1:5) %in% names(suitVotes)], value = 0)
suitVotes[,VoteSum := `1`+`2`+`3`+`4`+`5`]
suitVotes[,X := 1 - VoteSum]
suitVotes[,VoteSum := NULL]
suitVotes[,X := X + `5` + `4`]
suitVotes[,`:=`(`5` = NULL, `4` = NULL)]
setkey(suitVotes, SS_NoSpace, Spp)
setkey(suit, SS_NoSpace, Spp)
suitVotes[suit, Curr := i.Feasible]
suitVotes[is.na(Curr), Curr := 5]
setorder(suitVotes,SiteRef,SS_NoSpace,Spp,FuturePeriod)
suitVotes[Curr > 3.5, Curr := 4]
suitVotes[,Improve := ModelDir(as.matrix(.SD), Curr = Curr, dir = "Improve"),.SDcols = colNms]
suitVotes[,Decline := ModelDir(as.matrix(.SD), Curr = Curr, dir = "Decline"),.SDcols = colNms]
datRot <- suitVotes[,lapply(.SD, mean),.SDcols = c("Improve","Decline"), by = list(SiteRef,SS_NoSpace,Spp,Curr)]
datRot[,`:=`(Improve = round(Improve*100),Decline = round(Decline*100))]
datRot[,Curr := NULL]
suitVotes <- suitVotes[,lapply(.SD, sum),.SDcols = colNms,
by = .(SiteRef,FuturePeriod, SS_NoSpace,Spp,Curr)]
suitVotes[,NewSuit := `1`+(`2`*2)+(`3`*3)+(X*5)]
suitVotes <- merge(suitVotes, datRot, by = c('SiteRef','SS_NoSpace','Spp'),all = T)
suitRes <- suitVotes[,.(Curr = mean(Curr),NewSuit = mean(NewSuit), Improve = mean(Improve), Decline = mean(Decline)), by = .(SiteRef)]
return(suitRes)
}
##add/retreat (figure 3b)
add_retreat <- function(SSPred,suit,spp_select){
suit <- suit[Spp == spp_select,.(BGC,SS_NoSpace,Spp,Feasible)]
suit <- unique(suit)
suit <- na.omit(suit)
SSPred <- SSPred[,.(SiteRef,FuturePeriod,BGC,SS_NoSpace,SS.pred,SSprob)]
Site_BGC <- unique(SSPred[,.(SiteRef,BGC)])
SSPred <- na.omit(SSPred)
setkey(SSPred,SS.pred)
setkey(suit,SS_NoSpace)
suitMerge <- suit[SSPred, allow.cartesian = T]
#suitMerge <- na.omit(suitMerge)
setnames(suitMerge, old = c("SS_NoSpace", "i.SS_NoSpace"), new = c("SS.pred", "SS_NoSpace"))
suit2 <- suit[,.(SS_NoSpace,Feasible)]
setnames(suit2, old = "Feasible",new = "OrigFeas")
suitMerge <- suit2[suitMerge, on = "SS_NoSpace",allow.cartesian =T]
suitMerge[OrigFeas > 3.5, OrigFeas := NA]
suitMerge[Feasible > 3.5, Feasible := NA]
suitMerge[,HasValue := if(any(!is.na(OrigFeas))|any(!is.na(Feasible))) T else F, by = .(SiteRef)]
suitMerge <- suitMerge[(HasValue),]
suitMerge <- suitMerge[,.(SiteRef,FuturePeriod,SS_NoSpace,OrigFeas,SS.pred,Feasible,SSprob)]
setnames(suitMerge, old = "Feasible", new = "PredFeas")
suitMerge[,Flag := NA_character_]
suitMerge[is.na(OrigFeas) & !is.na(PredFeas),Flag := "Expand"]
suitMerge[!is.na(OrigFeas) & is.na(PredFeas),Flag := "Retreat"]
suitMerge[!is.na(OrigFeas) & !is.na(PredFeas),Flag := "Same"]
suitMerge[is.na(OrigFeas) & is.na(PredFeas),Flag := "Same"]
suitMerge[,PropMod := sum(SSprob), by = .(SiteRef,FuturePeriod, Flag)]
suitMerge[,PropAll := sum(SSprob), by = .(SiteRef,FuturePeriod)]
suitMerge[,PropMod := PropMod/PropAll]
suitRes <- unique(suitMerge[,.(SiteRef,Flag,PropMod)])
suitRes[,SiteRef := as.integer(SiteRef)]
setkey(suitRes,SiteRef)
suitRes[Flag == "Retreat",PropMod := PropMod * -1]
}
# ##gcm and rcp weight
# gcm_weight <- data.table(gcm = c("ACCESS-ESM1-5", "BCC-CSM2-MR", "CanESM5", "CNRM-ESM2-1", "EC-Earth3",
# "GFDL-ESM4", "GISS-E2-1-G", "INM-CM5-0", "IPSL-CM6A-LR", "MIROC6",
# "MPI-ESM1-2-HR", "MRI-ESM2-0", "UKESM1-0-LL"),
# weight = c(0,0,0,1,1,0,0,0,0,0,0,1,0))
# #weight = c(1,1,0,0,1,1,1,0,1,1,1,1,0))
# rcp_weight <- data.table(rcp = c("ssp126","ssp245","ssp370","ssp585"),
# weight = c(0,1,1,0))
#
# all_weight <- as.data.table(expand.grid(gcm = gcm_weight$gcm,rcp = rcp_weight$rcp))
# all_weight[gcm_weight,wgcm := i.weight, on = "gcm"]
# all_weight[rcp_weight,wrcp := i.weight, on = "rcp"]
# all_weight[,weight := wgcm*wrcp]
# modWeights <- all_weight
# choices to iterate through
spps <- c("Ac", "At", "Ba", "Bg", "Bl", "Cw", "Dr", "Ep", "Fd", "Hm", "Hw", "Lw", "Mb", "Pl", "Pw", "Py", "Sb", "Ss", "Sx", "Yc")
edas <- c("C4", "B2", "D6")
timeperiods <- c(2001, 2021, 2041, 2061, 2081)
timeperiod.names <- c("2001-2020", "2021-2040", "2041-2060", "2061-2080", "2081-2100")
### PLOT LOOP
timeperiod <- "2041"
for(timeperiod in timeperiods[-1]){
###load up bgc predictions data
bgc <- setDT(dbGetQuery(con,paste0("select * from mapdata_2km where futureperiod = '",timeperiod,"'"))) ##takes about 15 seconds
setnames(bgc, c("SiteRef","FuturePeriod","BGC","BGC.pred","BGC.prop"))
# str(bgc)
#BGC zones
bgc.ref <- unique(bgc[,c(1,3)])
bgc.ref$SiteRef <- as.numeric(bgc.ref$SiteRef)
zones <- c("CDF", "CWH", "MH", "ESSF", "MS", "IDF", "PP", "BG", "ICH", "SBPS", "SBS", "BWBS", "SWB", "CMA", "IMA", "BAFA")
zone <- rep(NA, dim(bgc.ref)[1])
for(i in zones){ zone[grep(i,bgc.ref$BGC)] <- i }
table(zone)
zone <- factor(zone, levels=zones)
# loop through edatope and species
eda <- "C4"
for(eda in edas){
spp <- "Bl"
for(spp in spps){ ##ignore warnings,"Fd","Sx","Pl", "Yc", "Yc", "Oa", "Yp"
cat("Plotting ",spp, eda,"\n")
edaTemp <- data.table::copy(E1)
edaTemp <- edaTemp[is.na(SpecialCode),]
edaTemp[,HasPos := if(any(Edatopic == eda)) T else F, by = .(SS_NoSpace)]
edaZonal <- edaTemp[(HasPos),]
edaZonal[,HasPos := NULL]
##edatopic overlap
SSPreds <- edatopicOverlap(bgc,edaZonal,E1_Phase,onlyRegular = TRUE) ##takes about 30 seconds
# ## ------------------------------------
# ## 3 panel map with add/retreat and mean feasibility change
#
# #initialise plot
# png(file=paste("./FeasibilityMaps/Three_Panel",spp,eda,timeperiod,"png",sep = "."), type="cairo", units="in", width=6.5, height=2.9, pointsize=9, res=300)
#
# par(plt=c(0,1,0,1), bg="white")
# plot(0, col="white", xaxt="n", yaxt="n", xlab="", ylab="")
# Common <- as.character(spps.lookup$EnglishName[which(spps.lookup$TreeCode==spp)])
# Latin <- as.character(spps.lookup$ScientificName[which(spps.lookup$TreeCode==spp)])
# # panel <- paste("(", LETTERS[which(spps==spp)],")", sep="")
# mtext(if(spp%in%spps.lookup$TreeCode) bquote(bold(.(spp))~"-"~.(Common)) else bquote(bold(.(spp))),
# side=3, line=-1.25, adj=0.01, cex=0.8, font=2)
# # mtext(if(spp%in%spps.lookup$TreeCode) bquote(.(panel)~bold(.(spp))~"-"~.(Common)~"("*italic(.(Latin)*")")) else bquote(.(panel)~bold(.(spp))),
# # side=3, line=-1.75, adj=0.01, cex=0.8, font=2)
# mtext(paste("Site type: ", eda, " (", edatope.name[which(eda==edas)], ")", sep=""), side=3, line=-2., adj=0.01, cex=0.7, font=1)
#
# ##=================================
# ###historic suitability
# newFeas <- ccissMap(SSPreds,S1,spp)##~ 15 seconds
# newFeas[NewSuit > 4, NewSuit := 4]
# newFeas[,FeasChange := Curr - NewSuit]
# newFeas <- unique(newFeas, by = "SiteRef")
# newFeas[,SiteRef := as.integer(SiteRef)]
# ##newFeas <- newFeas[Curr %in% c(1,2,3),] ##uncomment this line to only show where currently feasible
# newFeas <- newFeas[!(Curr == 4 & FeasChange == 0),]
#
# X <- raster::setValues(X,NA)
# X[newFeas$SiteRef] <- newFeas$Curr
# breakseq <- c(0.5,1.5,2.5,3.5,5)
# ColScheme <- c("darkgreen", "dodgerblue1", "gold2", "white")
#
# par(plt = c(0, 0.3, 0, 0.6),new = TRUE, xpd = TRUE)
#
# image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n",
# col=ColScheme, breaks=breakseq, maxpixels= ncell(X),asp = 1)
# plot(outline, add=T, border="black",col = NA, lwd=0.4)
# legend("topleft", legend=c("1 (primary)", "2 (secondary)", "3 (tertiary)"),
# fill=ColScheme, bty="n", cex=0.8, title="Historical feasibility", inset=c(0,-0.3))
# mtext(paste("(", letters[1],")", sep=""), side=3, line=-2.75, adj=0.05, cex=0.8, font=2)
#
# ##=================================
# ##add/retreat
# breakpoints <- seq(-1,1,0.2); length(breakpoints)
# labels <- c("Retreat", "Expand")
# ColScheme <- c(brewer.pal(11,"RdBu")[c(1:4)], "grey90", brewer.pal(11,"RdBu")[c(7:11)]); length(ColScheme)
# addret <- add_retreat(SSPreds,S1,spp) ##~ 15 seconds
# addret[Flag == "Same",PropMod := 0]
# addret <- addret[addret[, .I[which.max(abs(PropMod))], by= .(SiteRef)]$V1]
# X <- raster::setValues(X,NA)
# X[addret$SiteRef] <- addret$PropMod
#
# par(plt = c(0.25,0.75,0,1),xpd = TRUE, new = TRUE)
# image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n",
# col=ColScheme, breaks=breakpoints, maxpixels= ncell(X),asp = 1,
# main = paste0(T1[TreeCode == spp,EnglishName]," (",spp,")\nSite Type: ",eda, "\nTime Period: ",timeperiod.names[which(timeperiods==timeperiod)]))
# plot(outline, add=T, border="black",col = NA, lwd=0.4)
#
# xl <- 325000; yb <- 900000; xr <- 400000; yt <- 1525000 #xl <- 1600000; yb <- 1000000; xr <- 1700000; yt <- 1700000
# rect(xl, head(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), xr, tail(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), col=ColScheme)
# text(rep(xr+10000,length(labels)),seq(yb,yt,(yt-yb)/(15-1))[c(3,9)],labels,pos=4,cex=0.9,font=0.8, srt=90)
# text(rep(xr-20000,length(labels)),seq(yb,yt,(yt-yb)/(15-1))[c(1,8,15)],c("100%", "0%", "100%"),pos=4,cex=0.8,font=1)
# text(xl-30000, mean(c(yb,yt))-30000, paste("Change to feasible/unfeasible\n(", timeperiod.names[which(timeperiods==timeperiod)], "); % of GCMs", sep=""), srt=90, pos=3, cex=0.85, font=2)
# mtext(paste("(", letters[2],")", sep=""), side=3, line=-2.75, adj=0.095, cex=0.8, font=2)
#
# ##=================================
# ##mean feasibility change
# feasVals <- newFeas[,.(SiteRef,FeasChange)]
# X <- raster::setValues(X,NA)
# X[feasVals$SiteRef] <- feasVals$FeasChange
#
# breakpoints <- seq(-3,3,0.5); length(breakpoints)
# labels <- c("-3","-2", "-1", "no change", "+1","+2","+3")
# ColScheme <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", brewer.pal(11,"RdBu")[c(7,8,8,9,10,11)]);
#
# par(plt = c(0.6, 0.95, 0.25, 1), xpd = TRUE, new = TRUE)
# image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme,
# breaks=breakpoints, maxpixels= ncell(X), asp = 1)
# plot(outline, add=T, border="black",col = NA, lwd=0.4)
#
# xl <- 1600000; yb <- 1000000; xr <- 1700000; yt <- 1700000
# rect(xl, head(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), xr, tail(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), col=ColScheme)
# text(rep(xr-10000,length(labels)),seq(yb,yt,(yt-yb)/(length(labels)-1)),labels,pos=4,cex=0.8,font=1)
# text(xl-30000, mean(c(yb,yt))-30000, paste("Mean change\nin feasibility (", timeperiod.names[which(timeperiods==timeperiod)], ")", sep=""), srt=90, pos=3, cex=0.85, font=2)
# par(xpd=F)
# mtext(paste("(", letters[3],")", sep=""), side=3, line=-3.25, adj=0.1, cex=0.8, font=2)
#
# ##=================================
# ## Summary by zone
#
# # par(mar=c(0,0,0,0), plt = c(0.77, 0.995, 0.001, 0.31), new = TRUE, mgp=c(1.25,0.15,0))
# # plot(0, xlim=c(0,1), ylim=c(0,1), col="white", xlab="", ylab="", xaxt="n", yaxt="n", bty="n")
# FeasChange <- values(X)[bgc.ref$SiteRef]
# FeasChange[is.na(FeasChange)] <- 0
# par(mar=c(4.5,2,0.1,0.1), plt = c(0.79, 0.995, 0.1, 0.275), new = TRUE, mgp=c(1.25,0.15,0))
# ylim=c(-3,3)
# xlim=c(1, length(levels(droplevels(zone))))
# z <- boxplot(FeasChange~zone, ylab="", vertical = TRUE, plot=F)
# for(i in 1:length(levels(zone))){
# temp <- FeasChange[which(zone==levels(zone)[i])]
# z$stats[c(1,5), i] <- quantile(temp[!is.na(temp)],c(0.05, 0.95))
# }
# bxp(z, xlim=xlim, ylim=ylim, xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
# lines(c(-99,99), c(0,0), lwd=2, col="darkgrey")
# bxp(z, add=T, boxfill = as.character(BGCcolors$colour[match(levels(zone), BGCcolors$classification)]), xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
# axis(1, at=1:length(levels(zone)), levels(zone), tick=F, las=2, cex.axis=0.65)
# axis(2,at=seq(ylim[1], ylim[2], 3), seq(ylim[1], ylim[2], 3), las=2, tck=0)
# mtext("Mean change in feasibility", side=3, line=0.1, adj=.975, cex=0.65, font=2)
# mtext(paste("(", letters[4],")", sep=""), side=3, line=1, adj=0.975, cex=0.8, font=2)
#
# dev.off()
## ------------------------------------------------------------
## 2 panel map
# initialise plot
png(file=paste("./FeasibilityMaps/Two_Panel",spp,eda,timeperiod,"png",sep = "."), type="cairo", units="in", width=6.5, height=5, pointsize=12, res=300)
par(plt=c(0,1,0,1), bg="white")
plot(0, col="white", xaxt="n", yaxt="n", xlab="", ylab="")
Common <- as.character(spps.lookup$EnglishName[which(spps.lookup$TreeCode==spp)])
Latin <- as.character(spps.lookup$ScientificName[which(spps.lookup$TreeCode==spp)])
# panel <- paste("(", LETTERS[which(spps==spp)],")", sep="")
mtext(if(spp%in%spps.lookup$TreeCode) bquote(bold(.(spp))~"-"~.(Common)) else bquote(bold(.(spp))),
side=3, line=-2.5, adj=0.01, cex=0.9, font=2)
# mtext(if(spp%in%spps.lookup$TreeCode) bquote(.(panel)~bold(.(spp))~"-"~.(Common)~"("*italic(.(Latin)*")")) else bquote(.(panel)~bold(.(spp))),
# side=3, line=-1.75, adj=0.01, cex=0.8, font=2)
mtext(paste("Site type: ", eda, " (", edatope.name[which(eda==edas)], ")", sep=""), side=3, line=-3.5, adj=0.01, cex=0.8, font=1)
mtext(paste("Time period: ", timeperiod.names[which(timeperiods==timeperiod)], sep=""), side=3, line=-4.5, adj=0.01, cex=0.8, font=1)
##=================================
###historic suitability
newFeas <- ccissMap(SSPreds,S1,spp)##~ 15 seconds
newFeas[NewSuit > 4, NewSuit := 4]
newFeas[,FeasChange := Curr - NewSuit]
newFeas <- unique(newFeas, by = "SiteRef")
newFeas[,SiteRef := as.integer(SiteRef)]
##newFeas <- newFeas[Curr %in% c(1,2,3),] ##uncomment this line to only show where currently feasible
newFeas <- newFeas[!(Curr == 4 & FeasChange == 0),]
X <- raster::setValues(X,NA)
X[newFeas$SiteRef] <- newFeas$Curr
breakseq <- c(0.5,1.5,2.5,3.5,5)
ColScheme <- c("darkgreen", "dodgerblue1", "gold2", "white")
par(plt = c(0, 0.5, 0.05, 0.6),new = TRUE, xpd = TRUE)
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n",
col=ColScheme, breaks=breakseq, maxpixels= ncell(X),asp = 1)
plot(outline, add=T, border="black",col = NA, lwd=0.4)
legend("topleft", legend=c("1 (primary)", "2 (secondary)", "3 (tertiary)"),
fill=ColScheme, bty="n", cex=0.8, title="Historical feasibility", inset=c(0,-0.3))
# mtext(paste("(", letters[1],")", sep=""), side=3, line=-2.75, adj=0.05, cex=0.8, font=2)
##=================================
##mean feasibility change
feasVals <- newFeas[,.(SiteRef,FeasChange)]
X <- raster::setValues(X,NA)
X[feasVals$SiteRef] <- feasVals$FeasChange
X2 <- raster::setValues(X,NA)
X2[feasVals$SiteRef[newFeas$Curr==4]] <- newFeas$FeasChange[newFeas$Curr==4]
X3 <- raster::setValues(X,NA)
values(X3)[feasVals$SiteRef[newFeas$Curr<4 & newFeas$NewSuit>3.5]] <- 1
breakpoints <- seq(-3,3,0.5); length(breakpoints)
labels <- c("-3","-2", "-1", "no change", "+1","+2","+3")
ColScheme <- c("black", brewer.pal(11,"RdBu")[c(1,2,3,4)], "grey90", "grey90", brewer.pal(11,"RdBu")[c(7,8,9,10,11)]);
# ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", c("beige", "khaki1", "khaki2", "khaki3", "khaki4", "darkolivegreen"));
# ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("beige", "yellow", "black"))(6));
# ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("beige", "khaki1", "yellow"))(6));
# ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("grey95", "beige", "khaki1", "yellow2", "gold"))(6));
ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("white", "khaki1", "gold"))(6));
ColScheme3 <- 1
par(plt = c(0.25, 0.95, 0.175, 1), xpd = TRUE, new = TRUE)
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme, breaks=breakpoints, maxpixels= ncell(X), asp = 1)
image(X2, add=T, xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme2, breaks=breakpoints, maxpixels= ncell(X), asp = 1)
image(X3, add=T, xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme3, maxpixels= ncell(X), asp = 1)
plot(outline, add=T, border="black",col = NA, lwd=0.4)
xl <- 1600000; yb <- 1000000; xr <- 1700000; yt <- 1700000; xadj <- 10000
y.int <- (yt-yb)/length(ColScheme)
rect(xl+xadj, head(seq(yb,yt,y.int),-1), xr, tail(seq(yb,yt,y.int),-1), col=ColScheme)
rect(xl-diff(c(xl+xadj, xr)), head(seq(yb,yt,y.int),-1), xl-xadj, tail(seq(yb,yt,y.int),-1), col=ColScheme2)
rect(xl-diff(c(xl+xadj, xr)), yb, xl-xadj, (yb+yt)/2, col="white")
text(xl-diff(c(xl+xadj, xr))/2, yb+(yt-yb)/4, "Expansion", srt=90, cex=0.85, font=1)
text(rep(xr-10000,length(labels)),seq(yb,yt,(yt-yb)/(length(labels)-1)),labels,pos=4,cex=0.8,font=1)
text(xl-diff(c(xl+xadj, xr))-30000, mean(c(yb,yt))-30000, paste("Mean change in feasibility", sep=""), srt=90, pos=3, cex=0.85, font=2)
rect(xl+xadj, yb-y.int-20000, xr, yb-20000, col="black")
text(xr, yb-y.int/2-30000, "Loss", pos=4, cex=0.8, font=1)
par(xpd=F)
# mtext(paste("(", letters[3],")", sep=""), side=3, line=-3.25, adj=0.1, cex=0.8, font=2)
##=================================
## Summary by zone
# par(mar=c(0,0,0,0), plt = c(0.77, 0.995, 0.001, 0.31), new = TRUE, mgp=c(1.25,0.15,0))
# plot(0, xlim=c(0,1), ylim=c(0,1), col="white", xlab="", ylab="", xaxt="n", yaxt="n", bty="n")
FeasChange <- values(X)[bgc.ref$SiteRef]
FeasChange[is.na(FeasChange)] <- 0
par(mar=c(4.5,2,0.1,0.1), plt = c(0.7, 0.995, 0.08, 0.2), new = TRUE, mgp=c(1.25,0.15,0))
ylim=c(-3,3)
xlim=c(1, length(levels(droplevels(zone))))
z <- boxplot(FeasChange~zone, ylab="", vertical = TRUE, plot=F)
for(i in 1:length(levels(zone))){
temp <- FeasChange[which(zone==levels(zone)[i])]
z$stats[c(1,5), i] <- quantile(temp[!is.na(temp)],c(0.05, 0.95))
}
bxp(z, xlim=xlim, ylim=ylim, xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
lines(c(-99,99), c(0,0), lwd=2, col="darkgrey")
bxp(z, add=T, boxfill = as.character(BGCcolors$colour[match(levels(zone), BGCcolors$classification)]), xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
axis(1, at=1:length(levels(zone)), levels(zone), tick=F, las=2, cex.axis=0.65)
axis(2,at=seq(ylim[1], ylim[2], 3), seq(ylim[1], ylim[2], 3), las=2, tck=0)
mtext("Mean change in feasibility", side=3, line=0.1, adj=.975, cex=0.65, font=2)
# mtext(paste("(", letters[4],")", sep=""), side=3, line=1, adj=0.975, cex=0.8, font=2)
dev.off()
## ------------------------------------
## 3 panel map with mean feasibility change and model agreement
#initialise plot
png(file=paste("./FeasibilityMaps/Three_Panel",spp,eda,timeperiod,"png",sep = "."), type="cairo", units="in", width=6.5, height=2.9, pointsize=9, res=300)
par(plt=c(0,1,0,1), bg="white")
plot(0, col="white", xaxt="n", yaxt="n", xlab="", ylab="")
Common <- as.character(spps.lookup$EnglishName[which(spps.lookup$TreeCode==spp)])
Latin <- as.character(spps.lookup$ScientificName[which(spps.lookup$TreeCode==spp)])
# panel <- paste("(", LETTERS[which(spps==spp)],")", sep="")
mtext(if(spp%in%spps.lookup$TreeCode) bquote(bold(.(spp))~"-"~.(Common)) else bquote(bold(.(spp))),
side=3, line=-1.25, adj=0.01, cex=0.8, font=2)
# mtext(if(spp%in%spps.lookup$TreeCode) bquote(.(panel)~bold(.(spp))~"-"~.(Common)~"("*italic(.(Latin)*")")) else bquote(.(panel)~bold(.(spp))),
# side=3, line=-1.75, adj=0.01, cex=0.8, font=2)
mtext(paste("Site type: ", eda, " (", edatope.name[which(eda==edas)], ")", sep=""), side=3, line=-2.0, adj=0.01, cex=0.7, font=1)
mtext(paste("Time period: ", timeperiod.names[which(timeperiods==timeperiod)], sep=""), side=3, line=-2.75, adj=0.01, cex=0.7, font=1)
##=================================
###historic suitability
newFeas <- ccissMap(SSPreds,S1,spp)##~ 15 seconds
newFeas[NewSuit > 4, NewSuit := 4]
newFeas[,FeasChange := Curr - NewSuit]
newFeas <- unique(newFeas, by = "SiteRef")
newFeas[,SiteRef := as.integer(SiteRef)]
##newFeas <- newFeas[Curr %in% c(1,2,3),] ##uncomment this line to only show where currently feasible
newFeas <- newFeas[!(Curr == 4 & FeasChange == 0),]
X <- raster::setValues(X,NA)
X[newFeas$SiteRef] <- newFeas$Curr
breakseq <- c(0.5,1.5,2.5,3.5,5)
ColScheme <- c("darkgreen", "dodgerblue1", "gold2", "white")
par(plt = c(0, 0.3, 0, 0.6),new = TRUE, xpd = TRUE)
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n",
col=ColScheme, breaks=breakseq, maxpixels= ncell(X),asp = 1)
plot(outline, add=T, border="black",col = NA, lwd=0.4)
legend("topleft", legend=c("1 (primary)", "2 (secondary)", "3 (tertiary)"),
fill=ColScheme, bty="n", cex=0.8, title="Historical feasibility", inset=c(0,-0.3))
mtext(paste("(", letters[1],")", sep=""), side=3, line=-2.75, adj=0.05, cex=0.8, font=2)
##=================================
##mean feasibility change
feasVals <- newFeas[,.(SiteRef,FeasChange)]
X <- raster::setValues(X,NA)
X[feasVals$SiteRef] <- feasVals$FeasChange
X2 <- raster::setValues(X,NA)
X2[feasVals$SiteRef[newFeas$Curr==4]] <- newFeas$FeasChange[newFeas$Curr==4]
X3 <- raster::setValues(X,NA)
values(X3)[feasVals$SiteRef[newFeas$Curr<4 & newFeas$NewSuit>3.5]] <- 1
breakpoints <- seq(-3,3,0.5); length(breakpoints)
labels <- c("-3","-2", "-1", "no change", "+1","+2","+3")
ColScheme <- c("black", brewer.pal(11,"RdBu")[c(1,2,3,4)], "grey90", "grey90", brewer.pal(11,"RdBu")[c(7,8,9,10,11)]);
ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("white", "khaki1", "gold"))(6));
ColScheme3 <- 1
par(plt = c(0.25,0.75,0,1),xpd = TRUE, new = TRUE)
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme, breaks=breakpoints, maxpixels= ncell(X), asp = 1)
image(X2, add=T, xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme2, breaks=breakpoints, maxpixels= ncell(X), asp = 1)
image(X3, add=T, xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme3, maxpixels= ncell(X), asp = 1)
plot(outline, add=T, border="black",col = NA, lwd=0.4)
xl <- 325000; yb <- 900000; xr <- 400000; yt <- 1525000; xadj <- 10000
rect(xl+xadj, head(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), xr, tail(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), col=ColScheme)
rect(xl-diff(c(xl+xadj, xr)), head(seq(yb,yt,(yt-yb)/length(ColScheme2)),-1), xl-xadj, tail(seq(yb,yt,(yt-yb)/length(ColScheme2)),-1), col=ColScheme2)
rect(xl-diff(c(xl+xadj, xr)), yb, xl-xadj, (yb+yt)/2, col="white")
text(xl-diff(c(xl+xadj, xr))/2, yb+(yt-yb)/4, "Expansion", srt=90, cex=0.85, font=1)
text(rep(xr-10000,length(labels)),seq(yb,yt,(yt-yb)/(length(labels)-1)),labels,pos=4,cex=0.8,font=1)
text(xl-diff(c(xl+xadj, xr))-30000, mean(c(yb,yt))-30000, paste("Mean change in feasibility", sep=""), srt=90, pos=3, cex=0.85, font=2)
rect(xl+xadj, yb-y.int-20000, xr, yb-20000, col="black")
text(xr, yb-y.int/2-30000, "Loss", pos=4, cex=0.8, font=1)
mtext(paste("(", letters[2],")", sep=""), side=3, line=-2.75, adj=0.095, cex=0.8, font=2)
##=================================
## Summary by zone
# par(mar=c(0,0,0,0), plt = c(0.77, 0.995, 0.001, 0.31), new = TRUE, mgp=c(1.25,0.15,0))
# plot(0, xlim=c(0,1), ylim=c(0,1), col="white", xlab="", ylab="", xaxt="n", yaxt="n", bty="n")
FeasChange <- values(X)[bgc.ref$SiteRef]
FeasChange[is.na(FeasChange)] <- 0
par(xpd=F, mar=c(4.5,2,0.1,0.1), plt = c(0.79, 0.995, 0.1, 0.275), new = TRUE, mgp=c(1.25,0.15,0))
ylim=c(-3,3)
xlim=c(1, length(levels(droplevels(zone))))
z <- boxplot(FeasChange~zone, ylab="", vertical = TRUE, plot=F)
for(i in 1:length(levels(zone))){
temp <- FeasChange[which(zone==levels(zone)[i])]
z$stats[c(1,5), i] <- quantile(temp[!is.na(temp)],c(0.05, 0.95))
}
bxp(z, xlim=xlim, ylim=ylim, xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
lines(c(-99,99), c(0,0), lwd=2, col="darkgrey")
bxp(z, add=T, boxfill = as.character(BGCcolors$colour[match(levels(zone), BGCcolors$classification)]), xaxt="n", yaxt="n", xaxs="i", ylab="", pch=0,outline=FALSE)
axis(1, at=1:length(levels(zone)), levels(zone), tick=F, las=2, cex.axis=0.65)
axis(2,at=seq(ylim[1], ylim[2], 3), seq(ylim[1], ylim[2], 3), las=2, tck=0)
mtext("Mean change in feasibility", side=3, line=0.1, adj=.975, cex=0.65, font=2)
mtext(paste("(", letters[4],")", sep=""), side=3, line=1, adj=0.975, cex=0.8, font=2)
##=================================
## Model Agreement
X <- raster::setValues(X,NA)
X[newFeas$SiteRef[newFeas$FeasChange>0]] <- newFeas$Improve[newFeas$FeasChange>0]
X[newFeas$SiteRef[newFeas$FeasChange<0]] <- 0-newFeas$Decline[newFeas$FeasChange<0]
values(X)[values(X2)<0.5] <- NA # remove cells where the feasibility expansion is less than 0.5 (X2 is from the mean feasibilty panel)
breakpoints <- c(seq(-100, -50,10), seq(60, 100,10));length(breakpoints)
labels <- c("Decline", "Improve")
ColScheme <- c(brewer.pal(11,"RdBu")[c(1:4)], "grey90", "grey90", brewer.pal(11,"RdBu")[c(8:11)]); length(ColScheme)
par(plt = c(0.6, 0.95, 0.25, 1), xpd = TRUE, new = TRUE)
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme, breaks=breakpoints, asp = 1)
plot(outline, add=T, border="black",col = NA, lwd=0.4)
xl <- 1600000; yb <- 1000000; xr <- 1700000; yt <- 1700000
rect(xl, head(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), xr, tail(seq(yb,yt,(yt-yb)/length(ColScheme)),-1), col=ColScheme)
text(rep(xr+10000,length(labels)),seq(yb,yt,(yt-yb)/(15-1))[c(3,9)],labels,pos=4,cex=0.7,font=0.7, srt=90)
text(rep(xr-20000,length(labels)),seq(yb,yt,(yt-yb)/(15-1))[c(1,8,15)],c("100%", "50%", "100%"),pos=4,cex=0.7,font=1)
text(xl-30000, mean(c(yb,yt))-30000, paste("Ensemble agreement\n(% of GCMs)", sep=""), srt=90, pos=3, cex=0.75, font=2)
par(xpd=F)
mtext(paste("(", letters[3],")", sep=""), side=3, line=-3.25, adj=0.1, cex=0.8, font=2)
dev.off()
print(spp)
}
print(eda)
}
print(timeperiod)
}
qry <- "WITH sspred as (
select * from map2km_sspred
where ss_nospace in (
select distinct ss_nospace from edatopic where edatopic = 'C4'
)
),
feas as (select ss_nospace, newfeas from feasibility where spp = 'Fd')
SELECT siteref, sspred.ss_nospace, feas.newfeas, SUM(ss_prob)
FROM sspred INNER JOIN feas ON (sspred.ss_pred = feas.ss_nospace)
GROUP BY (siteref, sspred.ss_nospace, newfeas)
"
dat <- dbGetQuery(con, qry)
suitMerge <- as.data.table(dat)
feas_spp <- S1[Spp == 'Fd',.(SS_NoSpace,Feasible)]
suitVotes <- data.table::dcast(suitMerge, siteref + ss_nospace ~ newfeas,
value.var = "sum")
colNms <- c("1","2","3","X")
set(suitVotes, j = as.character(1:5)[!as.character(1:5) %in% names(suitVotes)], value = 0)
suitVotes[is.na(suitVotes)] <- 0
suitVotes[,VoteSum := `1`+`2`+`3`+`4`+`5`]
suitVotes[,X := 1 - VoteSum]
suitVotes[,VoteSum := NULL]
suitVotes[,X := X + `5` + `4`]
suitVotes[,`:=`(`5` = NULL, `4` = NULL)]
setkey(suitVotes, ss_nospace)
setkey(feas_spp, SS_NoSpace)
suitVotes[feas_spp, Curr := i.Feasible]
suitVotes[is.na(Curr), Curr := 5]
#setorder(suitVotes,SiteRef,SS_NoSpace,Spp,FuturePeriod)
suitVotes[Curr > 3.5, Curr := 4]
suitVotes <- suitVotes[,lapply(.SD, sum),.SDcols = colNms,
by = .(siteref, ss_nospace,Curr)]
suitVotes[,NewSuit := `1`+(`2`*2)+(`3`*3)+(X*5)]
suitRes <- suitVotes[,.(Curr = mean(Curr),NewSuit = mean(NewSuit)), by = .(siteref)]
##send sspred to database
SSPreds[,BGC.prop := NULL]
SSPreds[,allOverlap := NULL]
SSPreds[,SSratio := NULL]
setnames(SSPreds,c("siteref","period","bgc","bgc_pred","ss_nospace","ss_pred","ss_prob"))
dbWriteTable(con, "map2km_sspred", SSPreds, row.names = F, append = T)
dbExecute(con,"create index on map2km_sspred(ss_nospace)")
eda <- fread("data-raw/data_tables/Edatopic_v12_15.csv")
setnames(eda, c("source","bgc","ss_nospace","edatopic"))
dbWriteTable(con,"edatopic",eda, row.names = F)
feas <- fread("data-raw/data_tables/Feasibility_v12_15.csv")
dbWriteTable(con, "feasibility", feas, row.names = F)
### -------------------------------------------------------
### -------------------------------------------------------
### export rasters of mean feasibility change
timeperiod <- "2041"
for(timeperiod in timeperiods){
bgc <- setDT(dbGetQuery(con,paste0("select * from mapdata_2km where futureperiod = '",timeperiod,"'"))) ##takes about 15 seconds
setnames(bgc, c("SiteRef","FuturePeriod","BGC","BGC.pred","BGC.prop"))
# str(bgc)
#BGC zones
bgc.ref <- unique(bgc[,c(1,3)])
bgc.ref$SiteRef <- as.numeric(bgc.ref$SiteRef)
# loop through edatope and species
eda <- "C4"
for(eda in edas){
spp <- "Bl"
for(spp in spps){ ##ignore warnings,"Fd","Sx","Pl", "Yc", "Yc", "Oa", "Yp"
edaTemp <- data.table::copy(E1)
edaTemp <- edaTemp[is.na(SpecialCode),]
edaTemp[,HasPos := if(any(Edatopic == eda)) T else F, by = .(SS_NoSpace)]
edaZonal <- edaTemp[(HasPos),]
edaZonal[,HasPos := NULL]
##edatopic overlap
SSPreds <- edatopicOverlap(bgc,edaZonal,E1_Phase,onlyRegular = TRUE) ##takes about 30 seconds
newFeas <- ccissMap(SSPreds,S1,spp)##~ 15 seconds
newFeas[NewSuit > 4, NewSuit := 4]
newFeas[,FeasChange := Curr - NewSuit]
newFeas <- unique(newFeas, by = "SiteRef")
newFeas[,SiteRef := as.integer(SiteRef)]
##newFeas <- newFeas[Curr %in% c(1,2,3),] ##uncomment this line to only show where currently feasible
newFeas <- newFeas[!(Curr == 4 & FeasChange == 0),]
# ##=================================
# ###historic suitability
# X <- raster::setValues(X,NA)
# X[newFeas$SiteRef] <- newFeas$Curr
# writeRaster(X, datatype="FLT4S", paste("./FeasibilityMaps/rasters/HistoricFeas",spp,eda,"tif",sep = "."), overwrite=T)
##=================================
##mean feasibility change
feasVals <- newFeas[,.(SiteRef,FeasChange)]
X <- raster::setValues(X,NA)
X[feasVals$SiteRef] <- feasVals$FeasChange
X[feasVals$SiteRef[newFeas$Curr==4]] <- newFeas$FeasChange[newFeas$Curr==4]+10
values(X)[feasVals$SiteRef[newFeas$Curr<4 & newFeas$NewSuit>3.5]] <- -10
X <- round(X, digits = 1)
writeRaster(X, datatype="FLT4S", paste("./FeasibilityMaps/rasters/FeasChange",spp,eda,timeperiod,"tif",sep = "."), overwrite=T)
print(spp)
}
print(eda)
}
print(timeperiod)
}
### ----------------------------------
### legend for mean feasibility change
png(file=paste("./FeasibilityMaps/Legend.FeasChange.png",sep = "."), type="cairo", units="in", width=6.5, height=5, pointsize=14, res=400)
par(mar=c(0,0,0,0), bg="white")
plot(0, col="white", xaxt="n", yaxt="n", xlab="", ylab="")
X <- raster::setValues(X,NA)
breakpoints <- seq(-3,3,0.5); length(breakpoints)
labels <- c("-3","-2", "-1", "no change", "+1","+2","+3")
ColScheme <- c("black", brewer.pal(11,"RdBu")[c(1,2,3,4)], "grey90", "grey90", brewer.pal(11,"RdBu")[c(7,8,9,10,11)]);
ColScheme2 <- c(brewer.pal(11,"RdBu")[c(1,2,3,4,4)], "grey90", colorRampPalette(c("white", "khaki1", "gold"))(6));
ColScheme3 <- 1
image(X,xlab = NA,ylab = NA,bty = "n", xaxt="n", yaxt="n", col=ColScheme, breaks=breakpoints, maxpixels= ncell(X), asp = 1)
xl <- 1600000; yb <- 1000000; xr <- 1700000; yt <- 1700000; xadj <- 10000
y.int <- (yt-yb)/length(ColScheme)
rect(xl+xadj, head(seq(yb,yt,y.int),-1), xr, tail(seq(yb,yt,y.int),-1), col=ColScheme)
rect(xl-diff(c(xl+xadj, xr)), head(seq(yb,yt,y.int),-1), xl-xadj, tail(seq(yb,yt,y.int),-1), col=ColScheme2)
rect(xl-diff(c(xl+xadj, xr)), yb, xl-xadj, (yb+yt)/2, col="white")
text(xl-diff(c(xl+xadj, xr))/2, yb+(yt-yb)/4, "Expansion", srt=90, cex=0.85, font=1)
text(rep(xr-10000,length(labels)),seq(yb,yt,(yt-yb)/(length(labels)-1)),labels,pos=4,cex=0.8,font=1)
text(xl-diff(c(xl+xadj, xr))-30000, mean(c(yb,yt))-30000, paste("Mean change in feasibility", sep=""), srt=90, pos=3, cex=0.85, font=2)
rect(xl+xadj, yb-y.int-20000, xr, yb-20000, col="black")
text(xr, yb-y.int/2-30000, "Loss", pos=4, cex=0.8, font=1)
dev.off()