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Multiple Checks on MEDITS Trawl Survey Data

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R/check_dictionary_OLD.r

R/check_dictionary_OLD.r
In RoME: Multiple Checks on MEDITS Trawl Survey Data 

# check_dictionary <-function(ResultData,Field,Values,year, wd, suffix){
#
#   if (FALSE){
#     wd <- tempdir() #"C:\\Users\\walte\\Documents\\GitHub\\RoME\\data TEST Neglia"
#     suffix=NA  # non modificare
#     Field = "MEASURING_SYSTEM"
#     Values = c("VA","SO","XA","SA","SI","CD","CT","SB",NA)
#     ResultData=ta
#     year=2021
#     # Field = "LITTER_CATEGORY"
#     # Values = c("L0","L1","L2","L3","L4","L5","L6","L7","L8")
#
#     # ResultData = read.csv("~/GitHub/RoME/data/TA_GSA18_1994-2018.csv", sep=";")
#     # ResultData = read.csv("~/GitHub/RoME/data/TB_GSA18_1994-2018.csv", sep=";")
#     # ResultData = read.csv("~/GitHub/RoME/data/TC_GSA18_1994-2018.csv", sep=";")
#     ResultData = RoME::TL # read.table(file=paste(wd, "\\2019 GSA18 TL.csv",sep=""), sep=";", header=T)
#     year=2012
#     ResultData$CODEND_CLOSING[1] <- NA
#
#
#     # check_dictionary(ResultData,Field,Values, year, wd, suffix)
#   }
#
#   if (!file.exists(file.path(wd, "Logfiles"))){
#     dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
#   }
#   numberError = 0
#   if (!exists("suffix")){
#     suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
#   }
#   Errors <- file.path(wd,"Logfiles",paste("Logfile_", suffix ,".dat",sep=""))
#   if (!file.exists(Errors)){
#     file.create(Errors)
#   }
#
#   ### FILTERING DATA FOR THE SELECTED YEAR
#   arg <- "year"
#   if (!exists(arg)) {
#     stop(paste0("'",arg,"' argument should be provided"))
#   } else if (length(year)!= 1) {
#     stop(paste0("only one value should be provided for '",arg,"' argument"))
#   } else if (is.na(year)){
#     stop(paste0(arg," argument should be a numeric value"))
#   }
#
#   ResultData <- ResultData[ResultData$YEAR == year, ]
#   ########################################
#
#   Result = ResultData
#     write(paste("\n----------- check dictionary for field:", Field, "-", Result$YEAR[1]), file = Errors, append = TRUE)
#
#   Valuesf <- factor(Values)
#
#
#     if (any(is.na(Result[, which(colnames(Result)==Field)]))){
#           na.results <- Result[ is.na(Result[, which(colnames(Result)==Field)]) , ]
#           l.na <- nrow(na.results)
#           if (!any(is.na(Valuesf))){
#         for (x.na in 1:l.na){
#               write(paste("Haul",na.results$HAUL_NUMBER[x.na], ": value not allowed for", Field, "in",  na.results$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#               numberError = numberError +1
#         }
#             }
#     }
#
#   indexcol= which(names(Result)==Field)
#
#   if ( (nrow(Result)!=0)){
#     k=1
#     for (k in 1:nrow(Result)){
#       if (is.na(as.character(Result[k,indexcol])) & !any(is.na(Valuesf))){
#         if (Result$TYPE_OF_FILE[1] == "TA") {
#
#                                           write(paste("Haul",as.character(Result$HAUL_NUMBER[k]), ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#                                           numberError = numberError +1
#
#           } else if (Result$TYPE_OF_FILE[1] == "TB") {
#                 write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#                 numberError = numberError +1
#                 } else if (Result$TYPE_OF_FILE[1] == "TC") {
#                   write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#                   numberError = numberError +1
#                 } else if (Result$TYPE_OF_FILE[1] == "TE") {
#                   write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#                   numberError = numberError +1
#                 } else if (Result$TYPE_OF_FILE[1] == "TL") {
#                   write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#                   numberError = numberError +1
#                 }
#       } else if (!is.na(as.character(Result[k,indexcol])) & as.character(Result[k,indexcol])==""){
#         if (Result$TYPE_OF_FILE[1] == "TA") {
#
#           write(paste("Haul",as.character(Result$HAUL_NUMBER[k]), ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#           numberError = numberError +1
#
#         } else if (Result$TYPE_OF_FILE[1] == "TB") {
#           write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#           numberError = numberError +1
#         } else if (Result$TYPE_OF_FILE[1] == "TC") {
#           write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#           numberError = numberError +1
#         } else if (Result$TYPE_OF_FILE[1] == "TE") {
#           write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#           numberError = numberError +1
#         } else if (Result$TYPE_OF_FILE[1] == "TL") {
#           write(paste("Haul",Result$HAUL_NUMBER[k], Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k], ": the field", Field, "is empty in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#           numberError = numberError +1
#         }
#       } else {  #  if ((is.na(as.character(Result[k,indexcol]))==TRUE )
#
#         if (any(as.character(Result[k,indexcol])==Valuesf) == FALSE & !is.na(as.character(Result[k,indexcol]))) {
#           if (Result$TYPE_OF_FILE[1] == "TA") {
#
#             write(paste("Haul",Result$HAUL_NUMBER[k], ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#             numberError = numberError +1
#
#           } else if (Result$TYPE_OF_FILE[1] == "TB") {
#
#             write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#             numberError = numberError +1
#
#           } else if (Result$TYPE_OF_FILE[1] == "TC") {
#           if ((Field!="SEX")) {
#             write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k],  ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1] ), file = Errors, append = TRUE)
#             numberError = numberError +1
#           } else {
#              if ((as.character(Result[k,indexcol])!="FALSE")) {
#                  write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k],  ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1] ), file = Errors, append = TRUE)
#                  numberError = numberError +1
#              }
#           }
#
#           } else if (Result$TYPE_OF_FILE[1] == "TE") {
#             if ((Field!="SEX")) {
#               write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k],  ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1] ), file = Errors, append = TRUE)
#               numberError = numberError +1
#             } else {
#               if ((as.character(Result[k,indexcol])!="FALSE")) {
#                 write(paste("Haul",Result$HAUL_NUMBER[k],Result$GENUS[k], Result$SPECIES[k], Result$SEX[k], Result$LENGTH_CLASS[k],  ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1] ), file = Errors, append = TRUE)
#                 numberError = numberError +1
#               }
#             }
#           } else if (Result$TYPE_OF_FILE[1] == "TL") {
#
#               if ((as.character(Result[k,indexcol])!="FALSE")) {
#                 write(paste("Haul",Result$HAUL_NUMBER[k], ": value not allowed for", Field, "in",  Result$TYPE_OF_FILE[1], " (",as.character(Result[k,indexcol]),")" ), file = Errors, append = TRUE)
#                 numberError = numberError +1
#
#             }
#           }
#         }
#       }
#       }  #  for (k in 1:nrow(Result))
#   }  # nrow(Result)!=0
#
#   if (numberError ==0) {
#     write(paste("No error occurred for field", Field, "in",  Result$TYPE_OF_FILE[1]), file = Errors, append = TRUE)
#   }
#
# if (numberError ==0) {
#     return(TRUE)
#   } else { return(FALSE) }
#
# }

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RoME documentation built on April 24, 2026, 1:07 a.m.

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