library(data.table)

if (Sys.info()[["user"]] == "seb") {
  data_dir <- path.expand("~/Data/Yaws/") # Seb
} else {
  data_dir <- path.expand("~/Documents/Modelling Data/") # Michael
}

for (months in c(6, 12))
{
  data_dir_months <- paste0(data_dir, "/", months, "MonthFreq")
  
  ## get list of files in data directory
  files <- list.files(data_dir_months, pattern = ".*\\.rds", full.names = TRUE)
  
  pb <- txtProgressBar(min = 0, max = length(files), style = 3)
  
  system.time(for (file_idx in seq_along(files))
  {
    l <- readRDS(paste(path, files[file_idx], sep = "/"))
    runs <- data.table(t(sapply(l, function(x) { x[["params"]] } )))
    runs[, extinct := sapply(l, function(x) {
      last.state <- tail(x[["trajectory"]], 1)
      return(ifelse(last.state[, I1 + I2 + L] == 0, 1, 0))
    })]
    
    integer <- sapply(files[file_idx], function(x) as.integer(substr(x, 10, 11)))
    nb_events1 <- integer %/% 6 + 1 ## divide index by 6, keep integer part, add 1
    nb_events2 <- integer %% 6 ## divide index by 6, keep modulus
    
    mdatimes <- data.table(cbind(nb_events1, nb_events2))
    setnames(mdatimes, c("Rounds of TCT","Rounds of TTT"))
    runs <- cbind(runs, mdatimes)
    
    if (is.null(dt))
    {
      dt <- copy(runs)
    } else
    {
      dt <- rbind(dt, runs)
    }
    setTxtProgressBar(pb, file_idx)
  })
  
  close(pb)
  
  saveRDS(dt, paste0("yaws_res_", months, ".rds"))
}