misc/ListSp_DataGroup.R

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

library(rgbif)
library(data.table)

ListAll=T
FListSp="ListSp_CISTACEAE_FR_ES_IT_CH.csv"
Rank="FAMILY"
Pattern="DE_AT_BE_NL_LU"

if(ListAll)
{
  LListSp=list.files("./VigieChiro/gbifData/ListSp"
                     ,full.names=T,pattern=Pattern)
  
}else{
  LListSp=FListSp
}

for (g in 34:length(LListSp))
{
  ListSp=fread(LListSp[g])
  
  
  if(nrow(ListSp)>0)
  {
    
    InfoLS=tstrsplit(basename(LListSp[g]),"_")
    
    InfoLS=gsub(".csv","",InfoLS)
    
    #Group=name_lookup(InfoLS[[2]],rank=Rank,return="data",limit=99999)
    Group=name_backbone(name=InfoLS[[2]])
    #Group$key
    
    YearToday=as.numeric(substr(Sys.time(),1,4))
    Period=paste(YearToday-50,YearToday-1,sep=",")
    
    CountryFilter=vector()
    for (i in 3:length(InfoLS))
    {
      CountryFilter=c(CountryFilter,InfoLS[[i]])
    }
    
    
    #name_lookup(rank="SPECIES",higherTaxonKey = 137356451,country=france_code)
    #test=name_lookup("Bos gruniens",rank="SPECIES")
    
    #NOcc=rep(0,length(Group))
    #NOcc=vector()
    #for (h in 1:length(CountryList))
    #{
    #for (i in 1:nrow(Group))
    #{
    #  #NOcc[i]=NOcc[i]+occ_count(taxonKey=Group$key[i], country=CountryFilter[1])
    #  NOcc=c(NOcc,occ_count(taxonKey=Group$usageKey[i], country=CountryFilter[1]))
    #  if(i%%100==1){print(paste(i,Sys.time()))}
    #}
    
    #}
    #plot(NOcc)
    #if(max(NOcc)>0)
    #{
    # NumSel=which.max(NOcc)
    
    Sys.time()
    Kids=name_lookup(higherTaxonKey = Group$usageKey,return='data',limit=99999
                     ,status='ACCEPTED')
    Sys.time()
    #Kids_short=subset(Kids,!grepl(" ",Kids$scientificName))
    Kids_sp=subset(Kids,Kids$rank=="SPECIES")
    Sys.time()
    
    
    
    for (h in 1:length(CountryFilter))
    {
      DGL=list()
      j=0
      
      ListSpCountry=subset(ListSp,ListSp$country==CountryFilter[h])
      KidsCountry=subset(Kids_sp,Kids_sp$canonicalName %in% ListSpCountry$species)
      print(paste(CountryFilter[h],nrow(KidsCountry)))
      if(nrow(KidsCountry)>0)
      {
        for (i in 1:nrow(KidsCountry))
        {
          
          Sys.time()
          DataGroup=occ_search(taxonKey=KidsCountry$key[i], return='data'
                               ,country=CountryFilter[h],limit=200000,eventDate=Period
                               #,familyKey=Group$key[NumSel]
                               ,fields=c('decimalLatitude','decimalLongitude'
                                         ,'individualCount'
                                         ,'coordinateUncertaintyInMeters'
                                         ,'year','month','day','eventDate'
                                         ,'publishingOrgKey')
          )
          Sys.time()
          
          #DataGroup2=rbindlist(DataGroup,fill=T,use.names=T)
          if(is.data.frame(DataGroup))
          {
            DataGroup$name=KidsCountry$canonicalName[i]
            j=j+1
            DGL[[j]]=DataGroup
            #if(j%%10==1){
            print(paste(Sys.time(),CountryFilter[h],i,nrow(KidsCountry),nrow(DataGroup),KidsCountry$scientificName[i]))
            #}
          }
        }
        
        if(length(DGL)>0)
        {
          DataGroup2=rbindlist(DGL,fill=T,use.names=T)
          torder=table(DataGroup2$name)[order(table(DataGroup2$name),decreasing=T)]
          barplot(torder[1:min(20,length(torder))],las=2,cex.names=0.7)
          
          if(sum(grepl("individualCount",names(DataGroup2))))
          {
            DataGroup2Pos=subset(DataGroup2,DataGroup2$individualCount!=0)
            DataGroup2NA=subset(DataGroup2,is.na(DataGroup2$individualCount))
            DataGroup2=rbind(DataGroup2NA,DataGroup2Pos)
          }
          DataGroup2$yday=(DataGroup2$month-1)*30+DataGroup2$day #dirty
          
          DataGroup2=subset(DataGroup2,(DataGroup2$yday>1)&(DataGroup2$yday<361))
          if(nrow(DataGroup2)>0)
          {
            if("day" %in% names(DataGroup2))
            {
              barplot(table(DataGroup2$day))
              barplot(table(DataGroup2$month))
            }
          }
          Data_D1=subset(DataGroup2,DataGroup2$day==1)
          if(nrow(Data_D1)>0)
          {
            Ratio=nrow(DataGroup2)/30/nrow(Data_D1)
            Data_D1_rs=Data_D1[sample(nrow(Data_D1)
                                      ,min(nrow(Data_D1),ceiling(nrow(Data_D1)*Ratio))),] #correct oversampling of day 1
            DataGroup2=subset(DataGroup2,DataGroup2$day!=1)
            DataGroup2=rbind(DataGroup2,Data_D1_rs)
          }
          fwrite(DataGroup2,paste0("F:/DataGroup/DataGroup2_",InfoLS[[2]],"_",CountryFilter[h],".csv"))
          
          
        }
        
      }
    }
    
  } 
  
  #AggSp=aggregate(DataGroup2$eventDate,by=list(DataGroup2$name),FUN=length)
  
}