R/check_length_OLD.r

In RoME: Multiple Checks on MEDITS Trawl Survey Data

# check_length <- function(DataTC, DataSpecies = NA, year, wd, suffix, DataTargetSpecies = DataTargetSpecies) {
#
#   if (FALSE){
#     #library(MEDITS)
#     wd <- "D:\\OneDrive - Coispa Tecnologia & Ricerca S.C.A.R.L\\RDB3\\test"
#     DataSpecies=NA
#     suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
#     DataTC = read.table("D:/OneDrive - Coispa Tecnologia & Ricerca S.C.A.R.L/______ MEDITS DATA __OFFICIAL___/MEDBSsurvey/Demersal/TC_MEDITS_FORMAT_2025.csv",sep=";",header=TRUE)
#     DataTC <- DataTC[DataTC$AREA==25, ]
#
#
#     wd=tempdir()
#     DataTC <- RoME::TC # [1:20,]
#     DataSpecies=NA
#     suffix= "2020-03-05_time_h17m44s55"
#     check_length(DataTC,DataSpecies=NA,year=2015,wd,suffix)
#
#     # check_length(DataTC,DataSpecies=NA,year=2007,wd,suffix)
#   }
#
#   if (!file.exists(file.path(wd, "Logfiles"))) {
#     dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
#   }
#
#   if (!exists("suffix")) {
#     suffix <- paste(as.character(Sys.Date()), format(Sys.time(), "_time_h%Hm%Ms%OS0"), sep = "")
#   }
#
#   # Define paths for log files
#   Errors <- file.path(wd,"Logfiles",paste("Logfile_", suffix ,".dat",sep=""))
#   if (!file.exists(Errors)){
#     file.create(Errors)
#   }
#
#   AREA <- unique(DataTC$AREA)[1]
#   ErrorsCSV <- file.path(
#     wd,
#     "Logfiles",
#     paste("Check_Length_Classes_Logfile_GSA", AREA, "_Year", year, "_", suffix, ".csv", sep = "")
#   )
#
#   # Prepare list to collect warnings to write into CSV
#   warnings_list <- list()
#
#   # Create CSV header
#   csv_header <- data.frame(
#     GSA = integer(),
#     Year = integer(),
#     Species = character(),
#     Sex = character(),
#     Haul = integer(),
#     Length_Class = numeric(),
#     LMIN01 = numeric(),
#     LMAX99 = numeric(),
#     TYPE_OF_FILE = character(),
#     Type_of_Warning = character(),
#     stringsAsFactors = FALSE
#   )
#
#   # Write CSV header
#   write.table(
#     csv_header,
#     file = ErrorsCSV,
#     sep = ";",
#     row.names = FALSE,
#     col.names = TRUE
#   )
#
#   # Filter for 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"))
#   }
#
#   DataTC <- DataTC[DataTC$YEAR == year, ]
#
#   DataTC <- DataTC[!is.na(DataTC$LENGTH_CLASS), ]
#
#   if (nrow(DataTC) == 0) {
#     write("Empty TC data frame for the selected year.", file = Errors, append = TRUE)
#   } else {
#
#     Result <- DataTC
#     write(
#       paste("\n----------- check consistency of length classes TC - ", Result$YEAR[1]),
#       file = Errors,
#       append = TRUE
#     )
#
#     if (all(is.na(DataSpecies))) {
#       Target <- RoME::DataTargetSpecies
#     } else {
#       Target <- DataSpecies
#     }
#
#     Target <- Target[which(!is.na(Target$obs_in_TC) & Target$obs_in_TC > 50), ]
#
#     ResultData <- Result[, c("TYPE_OF_FILE", "HAUL_NUMBER", "GENUS", "SPECIES", "SEX", "LENGTH_CLASS")]
#     ResultData$species <- paste(ResultData$GENUS, ResultData$SPECIES, sep = "")
#
#     for (i in 1:nrow(ResultData)) {
#
#       # Check for NA or empty LENGTH_CLASS
#       if (is.na(ResultData$LENGTH_CLASS[i]) || ResultData$LENGTH_CLASS[i] == "") {
#         warnings_list[[length(warnings_list) + 1]] <- data.frame(
#           GSA = AREA,
#           Year = year,
#           Species = ResultData$species[i],
#           Sex = ResultData$SEX[i],
#           Haul = ResultData$HAUL_NUMBER[i],
#           Length_Class = NA,
#           LMIN01 = NA,
#           LMAX99 = NA,
#           TYPE_OF_FILE = ResultData$TYPE_OF_FILE[i],
#           Type_of_Warning = "Missing LENGTH_CLASS",
#           stringsAsFactors = FALSE
#         )
#       }
#
#       # Check for negative LENGTH_CLASS
#       if (!is.na(ResultData$LENGTH_CLASS[i]) && ResultData$LENGTH_CLASS[i] < 0) {
#         warnings_list[[length(warnings_list) + 1]] <- data.frame(
#           GSA = AREA,
#           Year = year,
#           Species = ResultData$species[i],
#           Sex = ResultData$SEX[i],
#           Haul = ResultData$HAUL_NUMBER[i],
#           Length_Class = ResultData$LENGTH_CLASS[i],
#           LMIN01 = NA,
#           LMAX99 = NA,
#           TYPE_OF_FILE = ResultData$TYPE_OF_FILE[i],
#           Type_of_Warning = "Negative LENGTH_CLASS",
#           stringsAsFactors = FALSE
#         )
#       }
#
#       # Check if length is out of range
#       FoundInTable <- Target[as.character(Target$SPECIES) == as.character(ResultData$species[i]), ]
#       FoundInTable <- FoundInTable[!is.na(FoundInTable$LMIN01[1]), ]
#
#       if (nrow(FoundInTable) != 0) {
#         if (!is.na(ResultData$LENGTH_CLASS[i])) {
#           if (ResultData$LENGTH_CLASS[i] < FoundInTable$LMIN01[1] ||
#               ResultData$LENGTH_CLASS[i] > FoundInTable$LMAX99[1]) {
#
#             warnings_list[[length(warnings_list) + 1]] <- data.frame(
#               GSA = AREA,
#               Year = year,
#               Species = ResultData$species[i],
#               Sex = ResultData$SEX[i],
#               Haul = ResultData$HAUL_NUMBER[i],
#               Length_Class = ResultData$LENGTH_CLASS[i],
#               LMIN01 = FoundInTable$LMIN01[1],
#               LMAX99 = FoundInTable$LMAX99[1],
#               TYPE_OF_FILE = ResultData$TYPE_OF_FILE[i],
#               Type_of_Warning = "LENGTH_CLASS out of reference range",
#               stringsAsFactors = FALSE
#             )
#           }
#         }
#       }
#     }
#   }
#
#   # Write all warnings to CSV
#   if (length(warnings_list) > 0) {
#     warnings_df <- do.call(rbind, warnings_list)
#     warnings_df <- warnings_df[order(warnings_df$Species, warnings_df$Haul, warnings_df$Sex), ]
#     write.table(
#       warnings_df,
#       file = ErrorsCSV,
#       sep = ";",
#       row.names = FALSE,
#       col.names = FALSE,
#       append = TRUE
#     )
#
#     # Write summary to log
#     write(
#       paste(
#         nrow(warnings_df), "rows written to CSV file",
#         basename(ErrorsCSV),
#         "- possible inconsistencies detected in LENGTH_CLASS values."
#       ),
#       file = Errors,
#       append = TRUE
#     )
#   } else {
#     write("No inconsistencies detected. All length classes within expected ranges.", file = Errors, append = TRUE)
#   }
#
#   # Function always returns TRUE
#   return(TRUE)
# }