misc/RP/DataRPPF_sorting_region.R

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

library(data.table)
library(raster)

DirRaw="C:/Users/yvesb/Documents/VigieChiro/Raw/forGLM2203/"
#SRt=45
#SpeciesList=fread("C:/Users/yvesb/Documents/Tadarida/Tadarida-C/tadaridaC_src/other_inputs/SpeciesList.csv")
#SpeciesList=c("Barbar","Pippip","Pipkuh","Pipnat","Pippyg","Nyclei","Eptser","Nycnoc","Hypsav","Minsch"
#             ,"Myospp","Plespp","Tadten","Nyclas","Rhihip","Rhifer")
Tmax=500
#ThresRP=20
#ThresPF=50
Region="ILE-DE-FRANCE"
Pregion=fread("Particip_region.csv")
FOut=paste0("C:/Users/yvesb/Documents/mnhn/Mathilde/forGLM2203_Custom_",Region,".csv")
CustomSorting=fread("SortingRPPFspecies.csv")
#FranceDep=shapefile()


SpeciesList=CustomSorting$Species

FRaw=list.files(DirRaw,full.names=T)

dir.create(dirname(FOut))

DataAll=list()
for (i in 1:length(FRaw))
{
  print(FRaw[i])
  datai=fread(FRaw[i])
  #print(nrow(datai))
  Sp=subset(datai$espece,datai$espece!="")[1]
  if(Sp %in% SpeciesList){
    testS=match(Sp,CustomSorting$Species)
    dataS=subset(datai,datai$x>CustomSorting$SRt[testS])
    testP=match(dataS$participation,Pregion$participation)
    dataS$region2=Pregion$region2[testP]
    table(dataS$region2,dataS$year)
    
    dataS=subset(dataS,dataS$region==Region)
    dataS$yearF2=round(dataS$year/2)*2+1
    table(dataS$yearF2)
    dataS$yearF4=round(dataS$year/4)*4
    table(dataS$yearF4)
    dataS=subset(dataS,dataS$temps_enr<Tmax)
    dataS=subset(dataS,!is.na(dataS$expansion_direct))
    dataS$score_max[is.na(dataS$score_max)]=1
    Sort=ifelse(dataS$protocole=="POINT_FIXE"
                ,dataS$score_max>CustomSorting$ThresPF[testS]/100
                ,dataS$score_max>CustomSorting$ThresRP[testS]/100)
    #table(Sort)
    dataS$nb_contacts=ifelse(Sort,dataS$nb_contacts,0)
    dataS$species=Sp
    dataS$ID=c(1:nrow(dataS))
    dataS$nb_contacts[is.na(dataS$nb_contacts)]=0
    if(sum(is.na(dataS$longitude))>0){
      dataS$latitude=NULL
      dataS$longitude=NULL
    }
    head(dataS$site)
    dataS$cjulian=cos(dataS$julian/365*2*3.1416)
    dataS$sjulian=sin(dataS$julian/365*2*3.1416)
    dataS$cjulian2=dataS$cjulian^2
    dataS$sjulian2=dataS$sjulian^2
    #dataS=subset(dataS,dataS$species %in% SpeciesList)
    DataAll[[i]]=dataS
  }
  #print(nrow(dataS))
  #fwrite(dataS,paste0(DirOut,"/",basename(FRaw[i])))
}
DataAllDF=rbindlist(DataAll)
fwrite(DataAllDF,FOut)