misc/Presence_Absence.R

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

library(data.table)

Occurences=fread("./VigieChiro/Traits/GBIF/OccSL_Gagea polidorii.csv")
SpTarget="Gagea polidorii"
#SpTarget="Scorus"
Sample=1000


OccPtot=subset(Occurences,Occurences$Esp==SpTarget)
if(nrow(OccPtot)>1000)
{
  OccP=subset(OccPtot,OccPtot$coordinateUncertaintyInMeters<100)
  if(nrow(OccP)<1000)
  {
    OccPsup=subset(OccPtot,is.na(OccPtot$coordinateUncertaintyInMeters))
    if(nrow(OccPsup)>Sample-nrow(OccP))
  {
    OccPsup=OccPsup[sample.int(nrow(OccPsup),Sample-nrow(OccP)),]
    }
    OccP=rbind(OccP,OccPsup)
    if(nrow(OccP)<1000)
    {
      OccPsup=subset(OccPtot,(OccPtot$coordinateUncertaintyInMeters<1000)
                     &(OccPtot$coordinateUncertaintyInMeters>=100))
      if(nrow(OccPsup)>Sample-nrow(OccP))
      {
        OccPsup=OccPsup[sample.int(nrow(OccPsup),Sample-nrow(OccP)),]
      }
      OccP=rbind(OccP,OccPsup)
      if(nrow(OccP)<1000)
      {
        OccPsup=subset(OccPtot,(OccPtot$coordinateUncertaintyInMeters>=1000))
        if(nrow(OccPsup)>Sample-nrow(OccP))
        {
          OccPsup=OccPsup[sample.int(nrow(OccPsup),Sample-nrow(OccP)),]
        }
        OccP=rbind(OccP,OccPsup)
      }
    }
  }else{
    OccP=OccP[sample.int(nrow(OccP),Sample),]
  }
}else{
  OccP=OccPtot
}

OccAtot=subset(Occurences,Occurences$Esp!=SpTarget)
if(nrow(OccAtot)>1000)
{
  OccA=subset(OccAtot,OccAtot$coordinateUncertaintyInMeters<100)
  if(nrow(OccA)<1000)
  {
    OccAsup=subset(OccAtot,is.na(OccAtot$coordinateUncertaintyInMeters))
    if(nrow(OccAsup)>Sample-nrow(OccA))
    {
      OccAsup=OccAsup[sample.int(nrow(OccAsup),Sample-nrow(OccA)),]
    }
    OccA=rbind(OccA,OccAsup)
    if(nrow(OccA)<1000)
    {
      OccAsup=subset(OccAtot,(OccAtot$coordinateUncertaintyInMeters<1000)
                     &(OccAtot$coordinateUncertaintyInMeters>=100))
      if(nrow(OccAsup)>Sample-nrow(OccA))
      {
        OccAsup=OccAsup[sample.int(nrow(OccAsup),Sample-nrow(OccA)),]
      }
      OccA=rbind(OccA,OccAsup)
      if(nrow(OccA)<1000)
      {
        OccAsup=subset(OccAtot,(OccAtot$coordinateUncertaintyInMeters>=1000))
        if(nrow(OccAsup)>Sample-nrow(OccA))
        {
          OccAsup=OccAsup[sample.int(nrow(OccAsup),Sample-nrow(OccA)),]
        }
        OccA=rbind(OccA,OccAsup)
      }
    }
  }else{
    OccA=OccA[sample.int(nrow(OccA),Sample),]
  }
}else{
  OccA=OccAtot
}


OccP$presence=1
OccA$presence=0
plot(OccA$decimalLongitude,OccA$decimalLatitude)
points(OccP$decimalLongitude,OccP$decimalLatitude,col=2,pch=2)
table(OccA$Esp)
Occ=rbind(OccP,OccA)

fwrite(Occ,paste0("./VigieChiro/GIS/PA_",SpTarget,".csv"))