setwd("J:/Documents/Arbete/Fortlöpande miljöanalys/Fenologi/Skoglig fenologi vid SLU")
library(dplyr)

xpre<-91:320
ypre<-rep(0,230)
minxpre<-min(xpre)
maxxpre<-max(xpre)
xtspre<-seq(0,2000,by=5)
ytspre<-rep(0,401)

PEP.table<-data.frame(koder=0,doy=0,year=0,station=0,species=0)[FALSE, ]
Interpol.table<-data.frame(doy=0,Flowers=0,Unripe=0,Ripe=0,Total=0,FlowersProc=0,UnripeProc=0,RipeProc=0,TotProc=0,FLowersTotProc=0,UnripeTotProc=0,RipeTotProc=0,Year=0,Station=0,Species=0)[FALSE, ]
Interpol.tsum<-data.frame(Station=0,Species=0,Year=0,Tempsum=0,Flowers=0,Unripe=0,Ripe=0,Total=0,FlowersProc=0,UnripeProc=0,RipeProc=0,TotProc=0,FLowersTotProc=0,UnripeTotProc=0,RipeTotProc=0)[FALSE, ]

berrydata0<- read.csv("berry_data.csv", header=TRUE, sep=",", dec=".")
tempsum<- read.csv("Tempsum.csv", header=TRUE, sep=",", dec = ".")

berrydata<-arrange(berrydata0,Species,Station,Year,doy)

specieslist<-unique(berrydata$Species)

plot.new()
par(mfrow = c(2,1))

for (l in 1:length(specieslist)) {
  testspecies<-subset(berrydata,berrydata$Species==specieslist[l])
  stationlist<-unique(testspecies$Station)

  for (k in 1:length(stationlist)) {
    teststation<-subset(testspecies,testspecies$Station==stationlist[k])
    yearlist<-unique(teststation$Year)
    
    plot(xpre,ypre, xlab="", ylab = paste("Station ", stationlist[k], ", species " ,specieslist[l]), xlim= c(80,300), ylim = c(0,100), col="white")

    for (j in 1:length(yearlist)) {
      testyear<-subset(teststation,teststation$Year==yearlist[j])

        flower<-as.data.frame(approx(testyear$doy,testyear$Flowers,xout=xpre,yleft = 0, yright = 0), col.names = c("doy","Flowers"))
        unripe<-as.data.frame(approx(testyear$doy,testyear$Unripe,xout=xpre,yleft = 0, yright = 0), col.names = c("doy","Unripe"))
        ripe<-as.data.frame(approx(testyear$doy,testyear$Ripe,xout=xpre,yleft = 0, yright = 0), col.names = c("doy","Ripe"))
  
        Interpol.tmp<-merge(flower,unripe,by="doy")
        Interpol.tmp<-merge(Interpol.tmp,ripe,by="doy")
        Interpol.tmp$Total<-Interpol.tmp$Flowers+Interpol.tmp$Unripe+Interpol.tmp$Ripe
        
        maxflower<-max(Interpol.tmp$Flowers)
        Interpol.tmp$FlowersProc<-Interpol.tmp$Flowers/maxflower*100
        maxunripe<-max(Interpol.tmp$Unripe)
        Interpol.tmp$UnripeProc<-Interpol.tmp$Unripe/maxunripe*100
        maxripe<-max(Interpol.tmp$Ripe)
        Interpol.tmp$RipeProc<-Interpol.tmp$Ripe/maxripe*100
        maxtot<-max(Interpol.tmp$Total)
        Interpol.tmp$TotProc<-Interpol.tmp$Total/maxtot*100
        Interpol.tmp$FlowersTotProc<-Interpol.tmp$Flowers/maxtot*100
        Interpol.tmp$UnripeTotProc<-Interpol.tmp$Unripe/maxtot*100
        Interpol.tmp$RipeTotProc<-Interpol.tmp$Ripe/maxtot*100
        
        lines(Interpol.tmp$doy,Interpol.tmp$FlowersTotProc, col = 6)
        lines(Interpol.tmp$doy,Interpol.tmp$UnripeTotProc, col = 3)
        lines(Interpol.tmp$doy,Interpol.tmp$RipeTotProc, col = 4)
        
        Interpol.tmp$Year <-yearlist[j]
        Interpol.tmp$Station<-stationlist[k]
        Interpol.tmp$Species<-specieslist[l]
        
        Interpol.table<-rbind(Interpol.table,Interpol.tmp)
        
        koder<-c(61,65,67,81,89)
        doy<-c(0,0,0,0,0)
        
        for (i in 1:length(xpre)) {
          if (Interpol.tmp$FlowersProc[i]>=10 & doy[1]==0) doy[1]=Interpol.tmp$doy[i] else doy[1]
          if (Interpol.tmp$FlowersProc[i]==100 & doy[2]==0) doy[2]=doy[2]=Interpol.tmp$doy[i] else doy[2]
          if (Interpol.tmp$FlowersProc[i]<=10 & doy[2]>0 & doy[3]==0) doy[3]=Interpol.tmp$doy[i] else doy[3]
          if (Interpol.tmp$RipeProc[i]>=10 & doy[4]==0) doy[4]=Interpol.tmp$doy[i] else doy[4]
          if (Interpol.tmp$RipeProc[i]==100 & doy[5]==0) doy[5]=Interpol.tmp$doy[i] else doy[5]
        }
        
        'points(doy[1],Interpol.tmp$FlowersTotProc[doy[1]-90], col = 6, pch = 1, cex = 0.7)'
        'points(doy[2],Interpol.tmp$FlowersTotProc[doy[2]-90], col = 6, pch = 0, cex = 0.5)'
        'points(doy[3],Interpol.tmp$FlowersTotProc[doy[3]-90], col = 6, pch = 5, cex = 0.8)'
        'points(doy[4],Interpol.tmp$RipeTotProc[doy[4]-90], col = 4, pch = 1, cex = 0.7)'
        'points(doy[5],Interpol.tmp$RipeTotProc[doy[5]-90], col = 4, pch = 0, cex = 0.5)'
        
        koddoy<-as.data.frame(koder)
        koddoy<-merge(koddoy,as.data.frame(doy),0)
        koddoy$Row.names=NULL
        
        koddoy$Year <-yearlist[j]
        koddoy$Station<-stationlist[k]
        koddoy$Species<-specieslist[l]
        
        PEP.table<-rbind(PEP.table,koddoy)
        

        tempsumyear<-subset(tempsum,tempsum$Station==stationlist[k] & tempsum$Year==yearlist[j] & tempsum$doy>=minxpre & tempsum$doy<=maxxpre)
      
      Interpol.tmp1<-merge(Interpol.tmp, tempsumyear, by = "doy")
      
      flower1<-as.data.frame(approx(Interpol.tmp1$Tempsum,Interpol.tmp1$Flowers,xout=xtspre, yleft = 0, yright = 0, ties = mean), col.names = c("Tempsum","Flowers"))
      unripe1<-as.data.frame(approx(Interpol.tmp1$Tempsum,Interpol.tmp1$Unripe,xout=xtspre, yleft = 0, yright = 0, ties = mean), col.names = c("Tempsum","Unripe"))
      ripe1<-as.data.frame(approx(Interpol.tmp1$Tempsum,Interpol.tmp1$Ripe,xout=xtspre, yleft = 0, yright = 0, ties = mean), col.names = c("Tempsum","Ripe"))
      
      Interpol.tmp2<-merge(flower1,unripe1,by="Tempsum")
      Interpol.tmp2<-merge(Interpol.tmp2,ripe1,by="Tempsum")
      Interpol.tmp2$Total<-Interpol.tmp2$Flowers+Interpol.tmp2$Unripe+Interpol.tmp2$Ripe
      
      maxflower<-max(Interpol.tmp2$Flowers)
      Interpol.tmp2$FlowersProc<-Interpol.tmp2$Flowers/maxflower*100
      maxunripe<-max(Interpol.tmp2$Unripe)
      Interpol.tmp2$UnripeProc<-Interpol.tmp2$Unripe/maxunripe*100
      maxripe<-max(Interpol.tmp$Ripe)
      Interpol.tmp2$RipeProc<-Interpol.tmp2$Ripe/maxripe*100
      maxtot<-max(Interpol.tmp2$Total)
      Interpol.tmp2$TotProc<-Interpol.tmp2$Total/maxtot*100
      Interpol.tmp2$FlowersTotProc<-Interpol.tmp2$Flowers/maxtot*100
      Interpol.tmp2$UnripeTotProc<-Interpol.tmp2$Unripe/maxtot*100
      Interpol.tmp2$RipeTotProc<-Interpol.tmp2$Ripe/maxtot*100


      
      Interpol.tmp2$Year <-yearlist[j]
      Interpol.tmp2$Station<-stationlist[k]
      Interpol.tmp2$Species<-specieslist[l]
      Interpol.tmp2<-Interpol.tmp2 %>% relocate(Station,Species,Year)
      
      Interpol.tsum<-rbind(Interpol.tsum,Interpol.tmp2)
      
      Interpol.table<-rbind(Interpol.table,Interpol.tmp)
      
    }
    
  }
}

Intpoltab<-Interpol.table %>% relocate(Species,Station,Year)
colnames(Intpoltab)[4]<-"doy"
PEPtab<-PEP.table %>% relocate(Station,Species,koder,Year)
colnames(PEPtab)[3]<-"phase_id"

Intpoltab<-arrange(Intpoltab,Species,Station,Year,doy)
PEPtab<-arrange(PEPtab,Species,Station,Year,phase_id)

write.csv(Intpoltab, "InterpolBerryData.csv", row.names = FALSE)
#write.csv(PEPtab, "PEP-BerryData.csv", row.names = FALSE)
write.csv(Interpol.tsum, "InterpolTsumBerryData.csv", row.names = FALSE)