R/check_year.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_year <- function(TA, TB, TC,TE,TL, years, wd, Errors){

  if (FALSE) {
    TA <- ta[ta$AREA ==22, ]
    TB <- tb[tb$AREA ==22, ]
    TC <- tc[tc$AREA ==22, ]
    TE <- NA
    TL <- NA
    years = unique (TA$YEAR)
  }

  Format="from_2012"

  if (!file.exists(file.path(wd, "Logfiles"))){
    dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
  }
  if (!file.exists(file.path(wd,"Graphs"))){
    dir.create(file.path(wd, "Graphs"), showWarnings = FALSE)
  }
  # if (!exists("suffix")){
  #   suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
  # }

  if (!file.exists(Errors)){
    file.create(Errors)
  }

  numberError = 0

write(paste("\n----------- check on YEAR field "), file = Errors, append = TRUE)

# TA
if (any(!(TA$YEAR %in% seq(1900,2100,1)))) {
  write(paste("YEAR value not expected in TA"), file = Errors, append = TRUE)
  numberError=numberError+1
}

# TB
if (any(!(TB$YEAR %in% seq(1900,2100,1)))) {
  write(paste("YEAR value not expected in TB"), file = Errors, append = TRUE)
  numberError=numberError+1
}
if (any(!(unique(TB$YEAR) %in% years))){
  write("YEAR value in TB not included in TA table", file = Errors, append = TRUE)
  numberError=numberError+1
} else {
  int <- intersect(unique(TB$YEAR),  years)
  if (length(int) != length(years)) {
    write(paste("missing YEAR/s in TB"), file = Errors, append = TRUE)
    numberError=numberError+1
  }
}

# TC
if (any(!(TC$YEAR %in% seq(1900,2100,1)))) {
  write("YEAR value not expected in TC", file = Errors, append = TRUE)
  numberError=numberError+1
}
if (any(!(unique(TC$YEAR) %in% years))){
  write("YEAR value in TC not included in TA table", file = Errors, append = TRUE)
  numberError=numberError+1
}  else {
  int <- intersect(unique(TC$YEAR),  years)
  if (length(int) != length(years)) {
    write(paste("missing YEAR/s in TC"), file = Errors, append = TRUE)
    numberError=numberError+1
  }
}



# TE

if (!(all(is.na(TE)) & length(TE)==1)){
if (any(!(TE$YEAR %in% seq(1900,2100,1)))) {
  write("YEAR value not expected in TE", file = Errors, append = TRUE)
  numberError=numberError+1
}
if (any(!(unique(TE$YEAR) %in% years))){
  write("YEAR value in TE not included in TA table", file = Errors, append = TRUE)
  numberError=numberError+1
}  else {
  int <- intersect(unique(TE$YEAR),  years)
  if (length(int) != length(years)) {
    write(paste("missing YEAR/s in TE"), file = Errors, append = TRUE)
    numberError=numberError+1
  }
}
}


# TL

if (!(all(is.na(TL)) & length(TL)==1)){
  if (any(!(TL$YEAR %in% seq(1900,2100,1)))) {
    write("YEAR value not expected in TL", file = Errors, append = TRUE)
    numberError=numberError+1
  }
  if (any(!(unique(TL$YEAR) %in% years))){
    write("YEAR value in TL not included in TA table", file = Errors, append = TRUE)
    numberError=numberError+1
  }  else {
    int <- intersect(unique(TL$YEAR),  years)
    if (length(int) != length(years)) {
      write(paste("missing YEAR/s in TL"), file = Errors, append = TRUE)
      numberError=numberError+1
    }
  }
}



if (numberError ==0) {
  write(paste("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)
#     }
if (numberError ==0) {
          return(TRUE)
        } else {
          return(FALSE)
        }

}