# Converts a file of Tuscon format tree ring data to long-format

# This reads original Tucson ring width files from each site, per species, and EW/LW/RWL 
#and combines into one site RW file with species and measurement type (EWR/LWR/RWL) as columns

# FOlder setup: 
  # "LTER Long Form" 
    #"Site" folder should contain one folder per site, with a folder called "Tucson RWL" within it
      # In the Tucson RWL folder should only be rwl, ewr, and lwr files to read into the script
    #"Long form RWL" will be the output folder 

# Open packages
library(dplR)
library(reshape)
library(reshape2)
library(dplyr)
library(stringr)
library(tools)

# Set working directory to site folder
setwd("/Users/tem583/OneDrive - Harvard University/LTER long form/Sites")

# List of site folders
folder_list = list.files()

for(j in 1:length(folder_list)){
  
  setwd(file.path("/Users/tem583/OneDrive - Harvard University/LTER long form/Sites", folder_list[j], "/Tucson RWL"))

  # Compile a list of file names in that folder
  file_list = list.files()
  
  long_site <- data.frame()
  
  # Convert .rwl to .csv with ring width value for each individual and year
  for(i in 1:length(file_list)){
    
    #read the chronology
    setwd(file.path("/Users/tem583/OneDrive - Harvard University/LTER long form/Sites", folder_list[j], "/Tucson RWL"))
    a <- read.rwl(file_list[i])
    a <- tibble::rownames_to_column(a, "Year")
    #drop extension from filename
    b <- tools::file_path_sans_ext(basename(file_list[i]))
    #read file extension (EW/LW/RWL)
    ext <- file_ext(file_list[i])
    site <- word(b,1,sep = "_")
  
    # Set working directory to folder with converted csv
    setwd("/Users/tem583/OneDrive - Harvard University/LTER long form/Long Form RWL")

    # Convert from Tucson to long format using "melt" function

    long <- melt(a, na.rm = TRUE, id.vars = 1)
    colnames(long) <- c("year","core","rw")
    long$species <- word(b, 2, sep = "_")
    long$site <- word(b,1,sep = "_")
    long$type <- ext
    long <- long[c("site","species","core","type","year","rw")]
    long_site <- rbind(long_site,long)
  }
  write.csv(long_site, file=paste(site,".csv",sep=""), row.names = FALSE, quote=FALSE)
}