functions/f_Coord_Bioclim (1).R

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

Test=F
Coord_Bioclim=function(points,names_coord)
{
  
  library(data.table)
  library(sp)
  library(raster)
  FOccSL=points
  OccSL=fread(paste0(FOccSL,".csv"))
  CoordH=names_coord
  
  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]]))
  
  
  #Bioclimdir="C:/Users/Yves Bas/Documents/SIG/Bioclim_5m/" #where bioclim TIFF files are
  
  #coordinates(OccSL) <- c("decimalLongitude", "decimalLatitude")
  coordinates(OccSL) <- CoordH
  proj4string(OccSL) <- CRS("+init=epsg:4326") # WGS 84
  
  r1=getData('worldclim',var='bio',res=0.5,lon=0,lat=45)
  r2=getData('worldclim',var='bio',res=0.5,lon=-10,lat=45)
  
  
  #ListTifiles=list.files(args[2],full.names=T)
  
  SpBioc1=extract(r1,OccSL)
  SpBioc2=extract(r2,OccSL)
  SpBioc12=mapply(FUN=function(x,y) ifelse(is.na(x),y,x),SpBioc1,SpBioc2)
  SpBioc12=as.data.frame(matrix(SpBioc12,ncol=ncol(SpBioc1),nrow=nrow(SpBioc1)))
  subset(c(1:nrow(SpBioc12)),is.na(SpBioc12$V1))
  OccSL=subset(OccSL,!is.na(SpBioc12$V1))
  SpBioc12=subset(SpBioc12,!is.na(SpBioc12$V1))
  
  
  names(SpBioc12)=paste0("SpBioC",c(1:ncol(SpBioc12)))
  
  #AFAIRE = récupérer les données côtières qui donnent des NA dans worldclim
  Bioclim=cbind(coordinates(OccSL),SpBioc12)  
  fwrite(Bioclim,paste0(FOccSL,"_Bioclim.csv"))
  
  coordinates(Bioclim) <- CoordH
  
  SelCol=sample(names(SpBioc12),1)
  spplot(Bioclim,zcol=SelCol,main=SelCol)
  
}

if(Test)
{
#for test
Coord_Bioclim(
  points="./vigiechiro/GIS/PA_Thymus nitens" #table giving coordinates in WGS84
  ,names_coord=c("decimalLongitude","decimalLatitude") #vector of two values giving 
)
}