misc/Data_pourobservateurs (1).r

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

library(data.table)
#args="C:/wamp64/www/export.txt"
args="DataRP_SpTronSeuil90.csv"
args[2]="pourGuillaumeDuthion" #suffixe export
Loc=T
SelRP=T
SelPF=F
SelSite=T
ListSite=350004
SelLongLat=F
LatMin=48.47
LatMax=48.86
LongMin=1.57
LongMax=2.1
OutNoise=T
SelValid=F
FiltrValid="SUR" 
SelU=F
ListUM=fread("C:/wamp64/www/liste_utilisateurs_mail.txt",h=F)
SelYear=F
ListYear="2018"
SelSp=F
FiltSp="Nyclei"


Data=fread(args[1])
if(ncol(Data)>8)
{
  if(names(Data)[9]=="temps_debut")
  {
    names(Data)[10]="temps_fin"
  }
}
SpeciesList=fread("SpeciesList.csv")
SpecShort=subset(SpeciesList,select=c("Esp","Scientific name","NomFR","GroupFR"))


SiteLoc=fread("C:/wamp64/www/sites_localites.txt")
Particip=fread("C:/wamp64/www/p_export.csv",encoding="UTF-8")
Utilisateurs=fread("C:/wamp64/www/utilisateurs.txt")


if(SelU)
{
  U=subset(Utilisateurs,Utilisateurs$email %in% ListUM$V1)
  PU=subset(Particip,Particip$idobservateur %in% U$identifiant)
  Data=subset(Data,Data$participation %in% PU$participation)
}

if(SelYear)
{
  PYear=subset(Particip,substr(Particip$date_debut,7,10) %in% ListYear)
  Data=subset(Data,Data$participation %in% PYear$participation)
}


if(Loc){
  
  
  ListPar=levels(as.factor(Data$participation))
  SelPar=subset(Particip,Particip$participation %in% ListPar)
  
  if(SelSite)
  {
    SLSel=subset(SiteLoc,grepl(as.character(ListSite),SiteLoc$site))
  }else{
      if(SelLongLat)
  {
    SLSel=subset(SiteLoc,(SiteLoc$latitude>LatMin)
                 &(SiteLoc$latitude<LatMax)
                 &(SiteLoc$longitude>LongMin)
                 &(SiteLoc$longitude<LongMax))
  }else{
    SLSel=SiteLoc
  }
    
  }
  
  if(SelRP){
    if(sum(grepl("donnee",names(Data)))>0)
    {
      
      SLSelR=subset(SLSel,SLSel$protocole=="ROUTIER")
      #trondetail=tstrsplit(SLSelRP$nom," ")
      SelParSLR=merge(SLSelR,SelPar,by="site",allow.cartesian=TRUE)
      DataRP=subset(Data,substr(Data$donnee,1,3)=="Cir")
      RPdetail=tstrsplit(DataRP$donnee,"-")
      DataRP$Tron=substr(RPdetail[[4]],5,nchar(RPdetail[[4]]))
      RPtempsdetail=tstrsplit(RPdetail[[5]],"_")
      DataRP$section=pmin(floor(as.numeric(RPtempsdetail[[3]])/70)+1,5)
      DataRP$TronR=paste("T",DataRP$Tron,DataRP$section,sep=" ")
      
      DataSLR=merge(DataRP,SelParSLR,by.x=c("participation","TronR"),by.y=c("participation","nom"))
      
      
      
      SLSelP=subset(SLSel,SLSel$protocole=="CARRE")
      #trondetail=tstrsplit(SLSelRP$nom," ")
      SelParSLP=merge(SLSelP,SelPar,by="site",allow.cartesian=TRUE)
      
      
      #test=subset(SelPar,SelPar$participation=="5a076e96fe80cc000db43afb")
      #test=subset(SLSelP,SLSelP$id_site=="564c90b7eea470000e1d19a3")
      
      DataSLP=merge(DataRP,SelParSLP,by.x=c("participation","Tron"),by.y=c("participation","nom"))
    }else{
      SelParSLR=merge(SLSel,SelPar,by="site",allow.cartesian=TRUE)
      trondetail=tstrsplit(SelParSLR$nom," ")
      if(length(trondetail)>1)
      {
      SelParSLR$Tron=as.numeric(trondetail[[2]])
      }else{
        SelParSLR$Tron=as.numeric(trondetail[[1]])
        
      }
      DataSLR=merge(Data,SelParSLR,by=c("participation","Tron"))
      
    }
    
  }else{
    DataSLR=data.frame()
  }
  
  if(SelPF){
    SLSelPF=subset(SLSel,SLSel$protocole=="POINT_FIXE")
    
    SelParSLPF=merge(SLSelPF,SelPar,by.x=c("site","nom"),by.y=c("site","point"))
    
    DataSLPF=merge(Data,SelParSLPF,by="participation")
    
    DataSLPFP=rbind(DataSLPF,DataSLP,fill=T,use.names=T)
    DataSL=rbind(DataSLPFP,DataSLR,fill=T,use.names=T)
  }else{
    DataSL=DataSLR
  }
  
  
  
}else{
  DataSL=Data
  
}

if(SelValid){
  if(sum(grepl("valid.espece",names(DataSL)))==1)
  {
    DataSp1=merge(DataSL,SpecShort,by.x="valid.espece",by.y="Esp")
    DatasansV=subset(DataSL,DataSL$valid.espece=="")
    DataSp2=merge(DatasansV,SpecShort,by.x="obs.espece",by.y="Esp")
    DataSp=rbind(DataSp1,DataSp2)
  }else{
    DataSp=merge(DataSL,SpecShort,by.x="espece",by.y="Esp")
  }
  DataSp=subset(DataSp,DataSp$valid.proba %in% FiltrValid)
  
}else{
  DataSp=merge(DataSL,SpecShort,by.x="espece",by.y="Esp")
}

if(OutNoise)
{
  is.upper <- "[A-Z]"
  result <- grepl(pattern = is.upper, x = substr(DataSp$NomFR,1,1))
  DataSp=subset(DataSp,result)
}

if(SelSp)
{
  DataSp=subset(DataSp,grepl(FiltSp,DataSp$espece))
}

NomExport=paste0("./VigieChiro/Exports/",substr(basename(args[1]),1,nchar(basename(args[1]))-4),"_",args[2],"_SL.csv")
fwrite(DataSp,NomExport,row.names=F,sep=";")