misc/Data_SIG.r

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

library(data.table)
args="ETV_filtree"
args[2]="pourBenoit" #suffixe export

SelLongLat=F
LatMin=43.43
LatMax=43.73
LongMin=4.02
LongMax=4.50

OutNoise=T
#FiltrValid="SUR" 
FiltrValid=c("","POSSIBLE","PROBABLE","SUR") 


Data=fread(paste0(args[1],".csv"))
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")

ListPar=levels(as.factor(Data$participation))
SelPar=subset(Particip,Particip$participation %in% ListPar)

if(SelLongLat)
{
  SLSel=subset(SiteLoc,(SiteLoc$latitude>LatMin)
               &(SiteLoc$latitude<LatMax)
               &(SiteLoc$longitude>LongMin)
               &(SiteLoc$longitude<LongMax))
}else{
  SLSel=SiteLoc
}

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"))


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)


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")
}

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

DataSp=subset(DataSp,DataSp$valid.proba %in% FiltrValid)

NomExport=paste0("./VigieChiro/Exports/",args[1],"_",args[2],"_SL.csv")
write.csv2(DataSp,NomExport,row.names=F)