misc/Coord_Carthage.R

In cesco-lab/Vigie-Chiro_scripts: Predict Distribution Of Chiropter

Coord_Bioclim=function(points,names_coord,bs,bm,bl,carthagep,carthagec)
{
  
library(data.table)
library(sp)
library(raster)
library(maptools)
library(rgeos)
  FOccSL=points
  OccSL=fread(paste0(FOccSL,".csv"))
  CoordH=names_coord
  BufferLarge=bl
  
#library(Rnightlights)
BufferSmall=bs
BufferMedium=bm
BufferLarge=bl 
#récupération des données Carthage (eau)
Sys.time()
CarthageP <- shapefile(carthagep)
CarthageC <- shapefile(carthagec)
Split=F
#Start=10001
#End=20000
Start=1
End=5000


if(Split)
{
  OccSL=OccSL[Start:(min(End,nrow(OccSL))),]
}


testH=match(CoordH,names(OccSL))
OccSL=subset(OccSL,!is.na(as.data.frame(OccSL)[,testH[1]]))
OccSL=subset(OccSL,!is.na(as.data.frame(OccSL)[,testH[2]]))
OccSL$id=c(1:nrow(OccSL))

#coordinates(OccSL) <- c("decimalLongitude", "decimalLatitude")
coordinates(OccSL) <- CoordH
proj4string(OccSL) <- CRS("+init=epsg:4326") # WGS 84

#CRS.new <- CRS(proj4string(CarthageP))
OccSL_L93=spTransform(OccSL,CRS(proj4string(CarthageC)))

#subset des points d'eau douce
CarthagePP=CarthageP[CarthageP$NATURE=="Eau douce permanente",]
#subset des cours d'eau permanent
CarthageCP=CarthageC[CarthageC$ETAT=="Permanent",]

#buffers of water surface 
#loop to avoid exceeding memory

BufferS=gBuffer(OccSL_L93,width=BufferSmall,byid=T)

SpPPlistS=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPPlistS[[k]]=intersect(BufferS[((k-1)*1000+1)
                                   :(min(k*1000,nrow(OccSL_L93))),],CarthagePP) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePP=do.call(rbind,SpPPlistS) # 0.05 sec / pol
#plot(SpCarthagePP)
if(length(SpCarthagePP)>0)
{
  AreaB=gArea(SpCarthagePP,byid=T)
  AreaAgg=aggregate(AreaB,by=list(SpCarthagePP$id)
                    ,FUN=function(x) sum(x)/BufferSmall^2/pi)
  names(AreaAgg)[ncol(AreaAgg)]="SpWS_S"
  Sys.time()
  OccSL_L93PP=merge(OccSL_L93,AreaAgg,by.x="id",by.y="Group.1",all.x=T)
  OccSL_L93PP$SpWS_S[is.na(OccSL_L93PP$SpWS_S)]=0
  spplot(OccSL_L93PP,zcol="SpWS_S",col="transparent")
  
}else{
  OccSL_L93PP=OccSL_L93
  OccSL_L93PP$SpWS_S=0
}

BufferM=gBuffer(OccSL_L93,width=BufferMedium,byid=T)

SpPPlistS=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPPlistS[[k]]=intersect(BufferM[((k-1)*1000+1)
                                   :(min(k*1000,nrow(OccSL_L93))),],CarthagePP) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePP=do.call(rbind,SpPPlistS) # 0.05 sec / pol
plot(SpCarthagePP)
AreaB=gArea(SpCarthagePP,byid=T)
AreaAgg=aggregate(AreaB,by=list(SpCarthagePP$id)
                  ,FUN=function(x) sum(x)/BufferMedium^2/pi)
names(AreaAgg)[ncol(AreaAgg)]="SpWS_M"
Sys.time()
OccSL_L93PP=merge(OccSL_L93PP,AreaAgg,by.x="id",by.y="Group.1",all.x=T)
OccSL_L93PP$SpWS_M[is.na(OccSL_L93PP$SpWS_M)]=0
spplot(OccSL_L93PP,zcol="SpWS_M",col="transparent")

BufferL=gBuffer(OccSL_L93,width=BufferLarge,byid=T)

SpPPlistS=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPPlistS[[k]]=intersect(BufferL[((k-1)*1000+1)
                                   :(min(k*1000,nrow(OccSL_L93))),],CarthagePP) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePP=do.call(rbind,SpPPlistS) # 0.05 sec / pol
plot(SpCarthagePP)
AreaB=gArea(SpCarthagePP,byid=T)
AreaAgg=aggregate(AreaB,by=list(SpCarthagePP$id)
                  ,FUN=function(x) sum(x)/BufferLarge^2/pi)
names(AreaAgg)[ncol(AreaAgg)]="SpWS_L"
OccSL_L93PP=merge(OccSL_L93PP,AreaAgg,by.x="id",by.y="Group.1",all.x=T)
OccSL_L93PP$SpWS_L[is.na(OccSL_L93PP$SpWS_L)]=0
spplot(OccSL_L93PP,zcol="SpWS_L",col="transparent")


#for water courses
SpPClistS=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPClistS[[k]]=intersect(CarthageCP,BufferS[((k-1)*1000+1)
                                   :(min(k*1000,nrow(OccSL_L93))),]) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePC=do.call(rbind,SpPClistS) # 0.05 sec / pol
Sys.time()
#buftemp=intersect(CarthageCP,BufferS) # 0.05 sec / buffer
Sys.time()
LengthB=gLength(SpCarthagePC,byid=T)
Sys.time()
PC_50=aggregate(LengthB,by=list(SpCarthagePC$id),FUN=sum)
names(PC_50)[ncol(PC_50)]="SpWC_S"
OccSL_L93PP=merge(OccSL_L93PP,PC_50,by.x="id",by.y="Group.1",all.x=T)
OccSL_L93PP$SpWC_S[is.na(OccSL_L93PP$SpWC_S)]=0
spplot(OccSL_L93PP,zcol="SpWC_S",col="transparent")

SpPClistM=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPClistM[[k]]=intersect(CarthageCP,BufferM[((k-1)*1000+1)
                                              :(min(k*1000,nrow(OccSL_L93))),]) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePC=do.call(rbind,SpPClistM) # 0.05 sec / pol
Sys.time()
#buftemp=intersect(CarthageCP,BufferM) # 0.05 sec / buffer
Sys.time()
LengthB=gLength(SpCarthagePC,byid=T)
Sys.time()
PC_50=aggregate(LengthB,by=list(SpCarthagePC$id),FUN=sum)
names(PC_50)[ncol(PC_50)]="SpWC_M"
OccSL_L93PP=merge(OccSL_L93PP,PC_50,by.x="id",by.y="Group.1",all.x=T)
OccSL_L93PP$SpWC_M[is.na(OccSL_L93PP$SpWC_M)]=0
spplot(OccSL_L93PP,zcol="SpWC_M",col="transparent")

SpPClistL=list()
Sys.time()
for (k in 1:ceiling(nrow(OccSL_L93)/1000))
{
  SpPClistL[[k]]=intersect(CarthageCP,BufferL[((k-1)*1000+1)
                                              :(min(k*1000,nrow(OccSL_L93))),]) # 0.05 sec / pol
  print(paste(k,Sys.time()))
}
SpCarthagePC=do.call(rbind,SpPClistL) # 0.05 sec / pol
Sys.time()
#buftemp=intersect(CarthageCP,BufferL) # 0.05 sec / buffer
Sys.time()
LengthB=gLength(SpCarthagePC,byid=T)
Sys.time()
PC_50=aggregate(LengthB,by=list(SpCarthagePC$id),FUN=sum)
names(PC_50)[ncol(PC_50)]="SpWC_L"
OccSL_L93PP=merge(OccSL_L93PP,PC_50,by.x="id",by.y="Group.1",all.x=T)
OccSL_L93PP$SpWC_L[is.na(OccSL_L93PP$SpWC_L)]=0
spplot(OccSL_L93PP,zcol="SpWC_L",col="transparent")

OccSL_ARajouter=subset(OccSL_L93PP,select=grepl("Sp",names(OccSL_L93PP)))
  
Carthage=data.frame(cbind(coordinates(OccSL),as.data.frame(OccSL_ARajouter)))

if(Split)
{
  NewName=paste0(FOccSL,"_Carthage_",Start,"_",End,".csv")
}else{
  NewName=paste0(FOccSL,"_Carthage.csv")
}

fwrite(Carthage,NewName)

coordinates(Carthage) <- CoordH

SelCol=sample(names(OccSL_ARajouter),1)
spplot(Carthage,zcol=SelCol,main=SelCol)

}


#for testing
Coord_Carthage(
  points="./vigiechiro/GIS/PA_Gagea polidorii"
  ,names_coord=c("decimalLongitude", "decimalLatitude")
  ,bs=50
  ,bm=500
  ,bl=5000
  ,carthagep="C:/wamp64/www/CARTHAGE_PLAN/HYDROGRAPHIE_SURFACIQUE.shp"
  ,carthagec="C:/wamp64/www/CARTHAGE_COURS/TRONCON_HYDROGRAPHIQUE.shp"
)