R/check_bridles_length.r

In RoME: Multiple Checks on MEDITS Trawl Survey Data

############################################################################################################################
#   RoME: R code to perform multiple checks on MEDITS Survey data (TA, TB, TC and TE files)                                #
#   Authors: I. Bitetto, W. Zupa, M.T. Spedicato                                                                           #
#   Coispa Tecnologia & Ricerca - Stazione sperimentale per lo Studio delle Risorse del Mare                               #
#   If you have any comments or suggestions please contact the following e-mail address: bitetto@coispa.it, zupa@coispa.it #
#   January 2022                                                                                                           #
############################################################################################################################

# Check if the value of bridles length is consistent according to the mean depth (see INSTRUCTION MANUAL VERSION 5 MEDITS 2007)

check_bridles_length<-function(DataTA, year, wd, suffix){


  if (FALSE){
    library(RoME)
    wd <- tempdir()
    suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
    DataTA = ta # RoME::TA
    DataTA[1,"BRIDLES_LENGTH"] <- NA
    check_bridles_length(DataTA,year=2012, wd, suffix)
  }

  if (!file.exists(file.path(wd, "Logfiles"))){
    dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
  }

  numberError = 0
  if (!exists("suffix")){
    suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
  }
  Errors <- file.path(wd,"Logfiles",paste("Logfile_", suffix ,".dat",sep=""))
  if (!file.exists(Errors)){
    file.create(Errors)
  }

  ### FILTERING DATA FOR THE SELECTED YEAR
  arg <- "year"
  if (!exists(arg)) {
    stop(paste0("'",arg,"' argument should be provided"))
  } else if (length(year)!= 1) {
    stop(paste0("only one value should be provided for '",arg,"' argument"))
  } else if (is.na(year)){
    stop(paste0(arg," argument should be a numeric value"))
  }
    DataTA <- DataTA[DataTA$YEAR == year, ]
  ########################################

  ResultData = DataTA
  write(paste("\n----------- check consistency of bridles length TA - ",ResultData$YEAR[1]), file = Errors, append = TRUE)

  ResultData=ResultData[ResultData$VALIDITY=="V",]
  ResultData$mean_depth=(ResultData$SHOOTING_DEPTH +ResultData$HAULING_DEPTH)/2
  ResultData <- ResultData[!is.na(ResultData$BRIDLES_LENGTH),]
  # if (ResultData$YEAR[1]<1995){
  #   for (i in 1:nrow(ResultData)){
  #     if ( ( (ResultData$mean_depth[i]>=0) & (ResultData$mean_depth[i]<200)& (ResultData$BRIDLES_LENGTH[i]!=100) ) | ( (ResultData$mean_depth[i]>=200) & (ResultData$BRIDLES_LENGTH[i]!=150) ) )
  #     {
  #       write(paste("Haul",ResultData$HAUL_NUMBER[i],": BRIDLES_LENGTH not correct"), file = Errors, append = TRUE)
  #       numberError = numberError +1
  #     }
  #   }
  # } else {
    for (i in 1:nrow(ResultData)){
    if ( ( (ResultData$mean_depth[i]>=0) & (ResultData$mean_depth[i]<200) & (ResultData$BRIDLES_LENGTH[i]!=100) ) | ( (ResultData$mean_depth[i]>=200) & ((ResultData$BRIDLES_LENGTH[i]!=150)&(ResultData$BRIDLES_LENGTH[i]!=200)) )   )
    {
      write(paste("Warning: Haul",ResultData$HAUL_NUMBER[i],": BRIDLES_LENGTH not correct"), file = Errors, append = TRUE)
      numberError = numberError +1
    }
    if  ( (ResultData$mean_depth[i]>=500) & (ResultData$BRIDLES_LENGTH[i]!=200) ){
      write(paste("Warning: Haul",ResultData$HAUL_NUMBER[i],": MEDITS handbook recommends to increase the bridle length to 200 m in depths deeper than 500 m"), file = Errors, append = TRUE)
    }
  }
  # }


  if (numberError ==0) {
    write(paste("No error occurred"), file = Errors, append = TRUE)
  }	else {
    write(paste("ATTENTION: BRIDLES_LENGTH=100 between 0 and 200 m, BRIDLES_LENGTH=150 over 200 m"), file = Errors, append = TRUE)
  }
#   if (file.exists(file.path(tempdir(), "Logfiles"))){
#   unlink(file.path(tempdir(),"Logfiles"),recursive=T)
#   }
#   if (file.exists(file.path(tempdir(), "Graphs"))){
#   unlink(file.path(tempdir(),"Graphs"),recursive=T)
#     }
# 	if (file.exists(file.path(tempdir(), "Graphs"))){
#   unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)
#     }
   return(TRUE)
}