R/check_consistencyTA_distance.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 between duration of the haul and distance (tolerance of 15%)

check_consistencyTA_distance<-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,"DISTANCE"] <- NA
    check_consistencyTA_distance(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, ]
  ########################################

  Matrix = DataTA[!is.na(DataTA$DISTANCE), ]
  write(paste("\n----------- check consistency between duration and distance TA - ",Matrix$YEAR[1]), file = Errors, append = TRUE)

  Matrix$mean_distance=1852*Matrix$HAUL_DURATION/20
  Matrix$low_distance=Matrix$mean_distance-Matrix$mean_distance*0.15
  Matrix$up_distance=Matrix$mean_distance+Matrix$mean_distance*0.15
  distance=which(Matrix$DISTANCE<Matrix$low_distance | Matrix$DISTANCE>Matrix$up_distance)
  if (length(distance)!=0){
    for (j in 1:length(distance)){
      write(paste("Warning: in haul",Matrix$HAUL_NUMBER[distance[j]],"distance measure",Matrix$DISTANCE[distance[j]],"inconsistent with the duration of the haul (",Matrix$HAUL_DURATION[distance[j]],"min )"), file = Errors, append = TRUE)
    }
  }


    #unlink(file.path(tempdir(),"Graphs"),recursive=T)
  #unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)

  if (numberError ==0) {
    write("No error occurred",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(), "files R-Sufi"))){
#   unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)
#     }
return(TRUE)
  } else { return(FALSE) }

}