misc/DataSel_LocList.R

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

library(data.table)
library(rgbif)
library(readxl)
library(raster)
library(sp)
FDataSel="./VigieChiro/gbifData/DataSelDate/DataSelRare_Vocal_78.csv"
SpeciesAll=fread("SpeciesAll.csv",sep=";")
GroupList=read_excel("GroupeSp.xlsx")
#FZone="./VigieChiro/GIS/World_L93Radius_ 260000.shp"
FZone="./VigieChiro/GIS/France_dep_L93Radius_ 64000.shp"
SortAlready=T
Country=c("FR","IT")
Country=c("FR")


#Zone=shapefile("./VigieChiro/GIS/France_dep_L93.shp")
Zone=shapefile(FZone)
ZoneWGS84=spTransform(Zone,"+init=epsg:4326")
ZoneWGS84$id=c(1:nrow(ZoneWGS84))

match("Tettigetta argentata",SpeciesAll$Scientific.name)
DataSel=fread(FDataSel)

#SpOld=subset(DataSel,DataSel$ListSpValide %in% SpeciesAll$SpeciesGBIF)
if(!SortAlready)
{
SpNew=subset(DataSel,!(DataSel$ListSpValide %in% SpeciesAll$Scientific.name))
}else{
  SpNew=DataSel
}
#Presence
GroupNew=subset(GroupList,GroupList$Group %in% SpNew$Group)

DataNew=list()
h=0
for (i in 1:nrow(GroupNew))
{
  GroupTemp=GroupNew[i,]
  SpTemp=subset(SpNew,SpNew$Group==GroupTemp$Group)
  DataGroup=list()
  for (k in 1:length(Country))
  {
    if(file.exists(paste0("./VigieChiro/gbifData/DataGroup/done/DataGroup2_"
                          ,GroupTemp$Group,"_",Country[k],".csv")))
    {
      DataGroup[[k]]=fread(paste0("./VigieChiro/gbifData/DataGroup/done/DataGroup2_"
                                  ,GroupTemp$Group,"_",Country[k],".csv"))
      
    }
  }
  if(length(DataGroup)>0)
  {
    DataGroup=rbindlist(DataGroup,fill=T,use.names=T)
    
    
    DataGroup=subset(DataGroup,(DataGroup$name %in% SpNew$ListSpValide))
    DataGroup=subset(DataGroup,!is.na(DataGroup$decimalLatitude))
    DataGroup=subset(DataGroup,DataGroup$decimalLatitude!=0)
    if(nrow(DataGroup)>0)
    {
      table(DataGroup$name)
      DataGroup$Group=GroupTemp$Group
      #NumSel=GroupTemp$Importance*20
      
      
      coordinates(DataGroup)=c("decimalLongitude","decimalLatitude")
      crs(DataGroup)="+init=epsg:4326" # WGS 84
      DataTest=over(DataGroup,ZoneWGS84)
      DataLoc=subset(DataGroup,!is.na(DataTest$id))
      print(GroupTemp$Group)
      if(nrow(DataLoc)>0)
      {
        print(table(DataLoc$name))
        h=h+1
        DataNew[[h]]=as.data.frame(DataLoc)
      }
    }
  }
  
  
}
DataNewTot=rbindlist(DataNew,fill=T,use.names=T)
#fwrite(DataNewTot,paste0("./VigieChiro/GIS/PA/DataNew_"
#,gsub(".shp","",basename(FZone)),".csv"))


SpNbData=aggregate(DataNewTot$eventDate,by=c(list(DataNewTot$Group)
                                             ,list(DataNewTot$name)),length)

SpNbData=merge(SpNbData,GroupList,by.x="Group.1",by.y="Group")
SpNbData$Score=SpNbData$x*SpNbData$Importance
SpNbData=SpNbData[order(SpNbData$Score,decreasing=T),]
head(SpNbData,9)
head(SpNbData,12)


FLsp=list.files("C:/Users/Yves Bas/Documents/VigieChiro/gbifData/ListSp"
                ,full.names=T)
LLSp=list()
for (l in 1:length(FLsp))
{
  LLSp[[l]]=fread(FLsp[l])
}
ListSp=rbindlist(LLSp,fill=T,use.names = T)

ListSpSel=subset(ListSp,ListSp$country %in% Country)
NdataTot=aggregate(ListSp$Ntot,by=list(ListSp$species),FUN=sum)

SpNbDataNT=merge(SpNbData,NdataTot,by.x="Group.2",by.y="Group.1",all.x=T)
fwrite(SpNbDataNT,"SpNbDataNT.csv",sep=";")