#
#
#currently set to only add tod and filter for date/min spm
#
#
rm(list=ls())

#packages
library(dplyr)
library(ggplot2)
library(sp)
library(maptools)

#file list
file_list <- list.files("data/find ladder/final SSF dataframes",full.names=T)

#track ratings
#basically just has track numbers and attributes
ratings <- read.csv("data/find ladder/attributes_of_all_tracks_with_entries_my_ratings.csv")

#filter track ratings to keep only good
#keep only tracks where max_nsd >40


#get list of Good track ids and fish

#need to do filtering in track_straightness as well to get Same Tracks

for(p in 1:length(file_list)){ 
  data <-  read.csv(file_list[[p]])
  
  id <- data$fish_id[1]
  
  data$t1_ <- as.POSIXct(data$t1_)
  data$t2_ <- as.POSIXct(data$t2_)
  
  #date constraint <3
  if(data$species[1]=="Barbel"){
    data <- filter(data,t2_<"2018-06-16"&t2_>"2018-05-01")
  }
  if(data$species[1]=="Grayling"){
    data <- filter(data,t2_<"2018-04-16"&t2_>"2018-03-15")
  }

  if(length(data$fish_id)>1){
    #add tod
    dat2 <- matrix(c(10.227961934279923,47.817415435039486),nrow=1) %>%  SpatialPoints(proj4string=CRS("+proj=longlat +datum=WGS84"))
    
    data$tod_start_NEW <- 0
    
    data$tod_end_NEW <- 0
    
    for(i in 1:length(data$approach)){
      tim1 <- as.POSIXct(data$t1_[i],tz="Europe/Berlin")
      tim2 <-as.POSIXct(data$t2_[i],tz="Europe/Berlin")
      
      dawn <- crepuscule(crds=dat2,dateTime=tim1,solarDep=12, direction=c("dawn"),POSIXct.out=T) 
      
      dusk <- crepuscule(crds=dat2,dateTime=tim1,solarDep=12, direction=c("dusk"),POSIXct.out=T) 
      sunrise <- sunriset(crds=dat2,dateTime=tim1,direction=c("sunrise"),POSIXct.out=T) 
      sunset <- sunriset(crds=dat2,dateTime=tim1,direction=c("sunset"),POSIXct.out=T) 
      
      #start
      
      if(tim1>dawn$time&sunrise$time>tim1){
        data$tod_start_NEW[i] <- "dawn"
      }
      
      if(tim1>sunset$time&dusk$time>tim1){
        data$tod_start_NEW[i] <- "dusk"
      }
      
      else{
        data$tod_start_NEW[i] <- data$tod_start_[i]
      }
      
      #end
      
      if(tim2>dawn$time&sunrise$time>tim2){
        data$tod_end_NEW[i] <- "dawn"
      }
      
      if(tim2>sunset$time&dusk$time>tim2){
        data$tod_end_NEW[i] <- "dusk"
      }
      
      else{
        data$tod_end_NEW[i] <- data$tod_end_[i]
      }
      
      
      
    }
    
    #renumber tracks
    approach_list <- data %>% group_by(fish_id) %>% summarise(approach=unique(approach))
    
    approach_list$track <- ave(approach_list$approach,approach_list$fish_id,
                               FUN = seq_along)
    
    data <- merge(data,approach_list,by=c('approach','fish_id'))
    
    #min step per min and remove <15min
    
    #get number steps and duration
    dat_dur <- data %>% filter(case_==TRUE) %>% group_by(fish_id,track) %>% summarise(duration=(max(t2_)-min(t1_)),steps=n())
    
    dat_dur$av_steps <- dat_dur$steps/as.numeric(dat_dur$duration)
    
    #set limit in time to 15min and ave steps >2
    data_dur <- dat_dur %>% filter(av_steps>2&duration>15)
    data <- data %>% filter(track %in%unique(data_dur$track))
    
    #renumber tracks again xx
    
    approach_list <- data  %>% group_by(fish_id) %>% summarise(approach=unique(approach))
    
    approach_list$track2 <- ave(approach_list$approach,approach_list$fish_id,
                                FUN = seq_along)
    
    data <- merge(data,approach_list,by=c('approach','fish_id'))
    
    data$track <- data$track2
    
    dat_filt_final <- data 
    write.csv(dat_filt_final,
              paste0("data/find ladder/SSF data with tod filtered for migration and min spm over 2/",id,".csv"),
              row.names = F)
  } else{
    print(paste0("fish id ",id," no data post date filtering"))
  }
  
}