functions/extractGI/f_Coord_ALAN.R

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

Test=F

if(exists("Pipeline")){Test=F}

Coord_ALAN=function(points,names_coord,bl,layer)
{
  
  library(data.table)
  library(sp)
  library(raster)
  library(maptools)
  FOccSL=points
  OccSL=fread(paste0(FOccSL,".csv"))
  CoordH=names_coord
  BufferLarge=bl
  ALAN=raster(layer)

  
  #library(Rnightlights)
  #OccSL=fread("./vigiechiro/Traits/GBIF/OccSL_bush-cricket.csv")

  
  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]]))
  
  #ALAN=getCtryNlData("FRA","FRA_adm0",nlTypes="OLS.Y",nlPeriods=2012,nlStats="mean")
  
  coordinates(OccSL) <- CoordH
  proj4string(OccSL) <- CRS("+init=epsg:4326") # WGS 84
  
  Sys.time()
  SpALAN_M=extract(ALAN,OccSL)
  Sys.time()
  OccSL=spCbind(OccSL,SpALAN_M)
  #OccSL$test=log(OccSL$SpALAN_M)
  spplot(OccSL,zcol="SpALAN_M",main="SpALAN_M",col="transparent")
  #spplot(OccSL,zcol="test",main="SpALAN_M",col="transparent")
  
  Sys.time()
  SpALAN_L=extract(ALAN,OccSL,buffer=BufferLarge,fun=mean) # 0.1 sec / données
  Sys.time()
  OccSL=spCbind(OccSL,SpALAN_L)
  
  spplot(OccSL,zcol="SpALAN_L",main="SpALAN_L",col="transparent")
  
  ALAN=data.frame(cbind(coordinates(OccSL),SpALAN_M,SpALAN_L))
  
  fwrite(ALAN,paste0(FOccSL,"_ALAN.csv"))
  
  coordinates(ALAN) <- CoordH
  
  SelCol=sample(c("SpALAN_M","SpALAN_L"),1)
  spplot(ALAN,zcol=SelCol,main=SelCol)
  
}

if(Test){
#for test
Coord_ALAN(
  points="./vigiechiro/GIS/PA_Thymus nitens" #table giving coordinates in WGS84
  ,names_coord=c("decimalLongitude","decimalLatitude") #vector of two values giving 
  ,bl=5000
  ,layer="C:/Users/Yves Bas/Downloads/SVDNB_npp_20161201-20161231_75N060W_vcmslcfg_v10_c201701271138.avg_rade9.tif"
)
}