Solution

[Ana Carolina Bonfim]

Hi, here is the solution to the problem which I was facing.

I was trying to extract  month data from the output.wql file. In this file, the data are daily, even if I select in SWAT to run monthly.

The script attached was made by Dr. Tam to extract the variable in column 16 for the reach 22.

[osama Hassan]

Dear Ana Carolina Bonfim, 

Thank you very much for the provided solution. However, I still got NA monthly values when i ran the calibration monthly using 'userReadSwatOutput'.
I'm trying to extract the monthly outflow from subbasin 11 (output.rch), and the simulated discharge is located in column 7. 
Please take a look at my file below! I would appreciate your help!
Thank you!

#########################################################################################################################

#' User-defined function for reading SWAT/SWAT+
#'
#' @description
#' This is a user-defined function for reading SWAT/SWAt+ outputs, do not use
#' as it is now, please modify the source code of this function if you use
#' according to your need and then install RSWAT app again from your local
#' folder to update this function.DO NOT CHANGE the name of this function
#' (mus be updateUserReadSwatOutput). ONLY CHANGE the code at the place where indicates
#' "START TO CHANGE FROM HERE" and STOP at "END OF CHANGE". This functions
#' must NOT receive any input. By default, you are NOW INSIDE the TxtInOut folder
#' and you can read any output files there by just using the file name.
#' RSWAT will use this function to get SWAT outputs (from the respective core)
#' after each model run and save it in combination with other outputs.
#'
#' Please TEST your function before running R-SWAT
#'
#' @return a list of vector (of simulated data)
#' @importFrom stats aggregate
#'
#'
#' @export
#'

updateUserReadSwatOutput <- function(){

  output <- list()
  # -------------------------------------------------------------------------#
  #       Delete the existing code below and add your code below this line   #
  #                 START TO CHANGE FROM HERE                                #
  # -------------------------------------------------------------------------#
  # Example: This function extracts data in the 7th column of the file  output.rch
  #          and aggregate to monthly

  # --------------------------------------------------------------------------
  date <- seq(from = as.Date("1998-01-01", "%Y-%m-%d"),
              to = as.Date("2012-12-31", "%Y-%m-%d"),
              by = 1)
  year <- as.numeric(format(date, "%Y"))
  month <- as.numeric(format(date, "%m"))

  # Reach number to extract
  reach <- 11
  column <- 7

  # --------------------------------------------------------------------------

  # Read all data from output.rch
  output_rch<- read.table("output.rch", header = FALSE, sep = "", skip = 9)

  # Subset only selected colum and reach
  output_rch <- output_rch[output_rch[,2]  == reach ,column]

  # Aggregate to monthly
  dataFrame <- data.frame(month = month,
                          year = year,
                          data = output_rch)

  # Aggreate by sum or mean
  dataFrameMonthly <- aggregate(.~ month + year, dataFrame, FUN = sum)

  # Only get the values of aggregated data
  output[[1]] <- dataFrameMonthly$data


  # ----------------------------------------------------------------------------
  # END OF CHANGE: Don't modify anything after this line
  # ----------------------------------------------------------------------------
  print(output)
  return(output)

}

# Overwrite the userReadSwatOutput with our updateUserReadSwatOutput
environment(updateUserReadSwatOutput) <- asNamespace('RSWAT')
assignInNamespace("userReadSwatOutput", updateUserReadSwatOutput, ns = "RSWAT")