Nothing
# TEST INIZIALIZING --------------------------------------------------------
# TEST END --------------------------------------------------------
RoME <- function(TA, TB, TC, TE = NA, TL = NA, wd, suffix = NA, create_RSufi_files = FALSE, create_global_RSufi_files = FALSE, Year_start = NA, Year_end = NA, verbose = TRUE, Stratification = RoME::stratification_scheme, Ref_list = RoME::TM_list, DataTargetSpecies = RoME::DataTargetSpecies, Maturity = RoME::Maturity_parameters, ab_parameters = RoME::LW, stages_list = RoME::mat_stages, assTL = assTL) {
stringsAsFactors <- FALSE
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 (!file.exists(file.path(wd, "/files R-Sufi", sep = "/"))) {
dir.create(file.path(wd, "files R-Sufi"), showWarnings = FALSE)
}
if (is.na(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)
}
write(paste("\n ", date(), sep = ""), file = Errors, append = TRUE)
stop_ <- FALSE
check_without_errors <- TRUE
# START -------------------------------------------------------------------
write(paste("-------------------------------------------------------------\n
LIST OF ERRORS
\n-------------------------------------------------------------"), file = Errors, append = TRUE)
# check degli header ------------------------------------------------------
table <- "TA"
checkName <- "Check Headers"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- checkHeader(TA, "TA", wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
table <- "TB"
checkName <- "Check Headers"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- checkHeader(TB, "TB", wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
table <- "TC"
checkName <- "Check Headers"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- checkHeader(TC, "TC", wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
ResultDataTA_bkp <- TA
ResultDataTB_bkp <- TB
ResultDataTC_bkp <- TC
### TE ###
if (!(all(is.na(TE)) & length(TE) == 1)) {
table <- "TE"
checkName <- "Check Headers"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- checkHeader(TE, "TE", wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
ResultDataTE_bkp <- TE
}
### TL ###
if (!(all(is.na(TL)) & length(TL) == 1)) {
table <- "TL"
checkName <- "Check Headers"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- checkHeader(TL, "TL", wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
ResultDataTL_bkp <- TL
}
###########
### CHECK CLASS
table <- "TA"
checkName <- "Check CLASS"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- check_class(data = TA, tab = "TA", wd = wd, suffix = suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
table <- "TB"
checkName <- "Check CLASS"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- check_class(data = TB, tab = "TB", wd = wd, suffix = suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
table <- "TC"
checkName <- "Check CLASS"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- check_class(data = TC, tab = "TC", wd = wd, suffix = suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
if (!(all(is.na(TE)) & length(TE) == 1)) {
table <- "TE"
checkName <- "Check CLASS"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- check_class(data = TE, tab = "TE", wd = wd, suffix = suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
if (!(all(is.na(TL)) & length(TL) == 1)) {
table <- "TL"
checkName <- "Check CLASS"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName,table, "in progress..."))
}
check_without_errors <- check_class(data = TL, tab = "TL", wd = wd, suffix = suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
### CHECK YEAR
years <- sort(unique(TA$YEAR))
checkName <- "Check YEAR"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_year(TA, TB, TC, TE, TL, years, wd, Errors)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
### CHECK TYPE_OF_FILE
checkName <- "Check TYPE_OF_FILE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_type(TA, TB, TC, TE, TL, years, wd, Errors)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
## CICLO PER ANNO ##
yea <- years[1]
for (yea in years) {
if (verbose) {
cat(paste0("\n########################"))
cat(paste0("\n### ",yea," ###"))
cat(paste0("\n########################"))
}
if (check_without_errors == TRUE & verbose == TRUE) {
message(paste("Checking year ", yea))
}
#------------------
ResultDataTA <- ResultDataTA_bkp[ResultDataTA_bkp$YEAR == yea, ]
ResultDataTB <- ResultDataTB_bkp[ResultDataTB_bkp$YEAR == yea, ]
ResultDataTC <- ResultDataTC_bkp[ResultDataTC_bkp$YEAR == yea, ]
if (!(all(is.na(TE)) & length(TE) == 1)) {
ResultDataTE <- ResultDataTE_bkp[ResultDataTE_bkp$YEAR == yea, ]
} else {
ResultDataTE <- NA
}
if (!(all(is.na(TL)) & length(TL) == 1)) {
ResultDataTL <- ResultDataTL_bkp[ResultDataTL_bkp$YEAR == yea, ]
} else {
ResultDataTL <- NA
}
# --------------------------------
# Check identical records
checkName <- "Check identical record TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_identical_records(Data = ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check identical record TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_identical_records(Data = ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check identical record TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_identical_records(Data = ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
if (!(all(is.na(TE)) & length(TE) == 1)) {
if (nrow(ResultDataTE) > 0) {
checkName <- "Check identical record TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_identical_records(Data = ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
if (!(all(is.na(TL)) & length(TL) == 1)) {
if (nrow(ResultDataTL) > 0) {
checkName <- "Check identical record TL"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_identical_records(Data = ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
# --------------------------------
# Check quasi-identical record
checkName <- "Check quasi-identical record in TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quasiidentical_records(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check quasi-identical record in TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quasiidentical_records(ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check quasi-identical record in TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quasiidentical_records(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
if (!(all(is.na(TE)) & length(TE) == 1)) {
if (nrow(ResultDataTE) > 0) {
checkName <- "Check quasi-identical record in TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quasiidentical_records(ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
if (!(all(is.na(TL)) & length(TL) == 1)) {
if (nrow(ResultDataTL) > 0) {
checkName <- "Check quasi-identical record in TL"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quasiidentical_records(ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
# --------------------------------
# Check consistency of area
checkName <- "Check consistency of area TA, TB, TC, TE, TL"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- suppressWarnings(check_area(ResultDataTA, ResultDataTB, ResultDataTC, ResultDataTE, ResultDataTL, year = yea, wd, suffix))
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
#--------------------------------------------------
# Dictionary checks
#--------------------------------------------------
minutes <- c("00","01","02","03","04","05","06","07","08","09", as.character(seq(10,59,1)))
h=0
for (h in 0:23) {
ht <- as.integer(paste(h, minutes,sep=""))
if (h==0){
time=minutes
} else {
time <- as.integer(c(time,ht))
}
}
# TA
checkName <- "Check dictionary for field:"
Field <- "COUNTRY"
Values <- as.character(unique(Stratification$COUNTRY))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
checkName <- "Check dictionary for field:"
Field <- "AREA"
Values <- as.character(unique(Stratification$GSA))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "GEAR"
Values <- c("GOC73")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "RIGGING"
Values <- c("GC73")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DOORS"
Values <- c("WHS8")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "MONTH"
Values <- seq(1, 12, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DAY"
Values <- seq(1, 31, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "HAUL_NUMBER"
Values = seq(1,999,1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "CODEND_CLOSING"
Values <- c("S", "C")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "PART_OF_THE_CODEND"
Values <- c("A", "M", "P", "S")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "SHOOTING_TIME"
Values = time # seq(0,2400,1)
if (check_without_errors == TRUE) {
if(verbose){
message(paste(checkName,Field,"in progress..."))
}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){
stop_ = printError(paste(checkName,Field),check_without_errors, stop_)
}
Field <- "SHOOTING_QUADRANT"
Values <- c("1", "3", "5", "7")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "SHOOTING_LATITUDE"
Values = c(3400,4600)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "SHOOTING_LONGITUDE"
Values = c(0,3500)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "SHOOTING_DEPTH"
Values <- c(0, 10:800)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "HAULING_QUADRANT"
Values <- c("1", "3", "5", "7")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAULING_LATITUDE"
Values = c(3400,4600)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "HAULING_LONGITUDE"
Values = c(0,3500)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "HAULING_TIME"
Values <- time # seq(0, 2400, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "HAULING_DEPTH"
Values <- c(0, 10:800)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAUL_DURATION"
Values = c(5:90)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "VALIDITY"
Values <- c("V", "I")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "COURSE"
Values <- c("R", "N")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "DISTANCE"
Values = c(1000:9999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "VERTICAL_OPENING"
Values = c(10:100)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "WING_OPENING"
Values = c(50:250)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "GEOMETRICAL_PRECISION"
Values <- c("M", "E")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "MEASURING_SYSTEM"
Values <- c("VA", "SO", "XA", "SA", "SI", "CT", "SB",NA)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "RECORDED_SPECIES"
Values <- seq(0, 4, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "WARP_LENGTH"
Values <- seq(100, 2200, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "WARP_DIAMETER"
Values <- seq(10, 30, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "OBSERVATIONS"
Values <- seq(0, 9, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTA, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "BOTTOM_TEMPERATURE_BEGINNING"
Values = c(0,30)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "BOTTOM_TEMPERATURE_END"
Values = c(0,30)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "BOTTOM_SALINITY_BEGINNING"
Values = c(0,50)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "BOTTOM_SALINITY_END"
Values = c(0,50)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
# TB
Field <- "COUNTRY"
Values <- as.character(unique(Stratification$COUNTRY))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTB, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "AREA"
Values = as.character(unique(Stratification$GSA))
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTA, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "MONTH"
Values <- seq(1, 12, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTB, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DAY"
Values <- seq(1, 31, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTB, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAUL_NUMBER"
Values = seq(1,999,1)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "CODEND_CLOSING"
Values <- c("S", "C")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTB, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "PART_OF_THE_CODEND"
Values <- c("A", "M", "P", "S")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTB, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "TOTAL_WEIGHT_IN_THE_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "TOTAL_NUMBER_IN_THE_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NB_OF_FEMALES"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NB_OF_MALES"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NB_OF_UNDETERMINED"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTB, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
# TC
Field <- "COUNTRY"
Values <- as.character(unique(Stratification$COUNTRY))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "AREA"
Values = as.character(unique(Stratification$GSA))
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "MONTH"
Values <- seq(1, 12, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DAY"
Values <- seq(1, 31, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAUL_NUMBER"
Values = seq(1,999,1)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "CODEND_CLOSING"
Values <- c("S", "C")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "PART_OF_THE_CODEND"
Values <- c("A", "M", "P", "S")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "LENGTH_CLASSES_CODE"
Values = c("m", "0", "1")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
checkName = "Check numeric range"
Field = "WEIGHT_OF_THE_FRACTION"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "WEIGHT_OF_THE_SAMPLE_MEASURED"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NO_OF_INDIVIDUAL_OF_THE_ABOVE_SEX_MEASURED"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "SEX"
Values <- c("M", "F", "I", "N")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTC, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "LENGTH_CLASS"
Values = c(1:9999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "MATURITY"
Values = c(0:4,"ND")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTC, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
# TE
if (!(all(is.na(TE)) & length(TE) == 1)) {
if (nrow(ResultDataTE) > 0) {
Field <- "COUNTRY"
Values <- as.character(unique(Stratification$COUNTRY))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTE, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "AREA"
Values = as.character(unique(Stratification$GSA))
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "MONTH"
Values <- seq(1, 12, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTE, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DAY"
Values <- seq(1, 31, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTE, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAUL_NUMBER"
Values = seq(1,999,1)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "LENGTH_CLASSES_CODE"
Values <- c("0", "m")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTE, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
# ResultDataTE[is.na(ResultDataTE$LENGTH_CLASSES_CODE),]
Field <- "SEX"
Values <- c("M", "F", "I", "N")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTE, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "NO_PER_SEX_MEASURED_IN_SUB_SAMPLE_FOR_OTOLITH"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NO_PER_SEX_MEASURED_IN_SUB_SAMPLE_FOR_WEIGHT"
Values = c(1,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "NO_PER_SEX_MEASURED_IN_SUB_SAMPLE_FOR_AGEING"
Values = c(0,999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "RECORD_NUMBER"
Values = c(0,100000)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "LENGTH_CLASS"
Values = c(1:9999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "MATURITY"
Values = c(0:4)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "MATSUB"
Values = c("A","B","C","D","E","O")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "OTOLITH_SAMPLED"
Values = c("Y","N","NR")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "OTOLITH_READ"
Values = c("Y","N","NR")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field = "AGE"
Values = c(seq(-1,99,0.1),"UR","NR")
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTE, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
}
}
# TL
if (!(all(is.na(TL)) & length(TL) == 1)) {
if (nrow(ResultDataTL) > 0) {
Field <- "COUNTRY"
Values <- as.character(unique(Stratification$COUNTRY))
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTL, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "AREA"
Values = as.character(unique(Stratification$GSA))
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
Field <- "MONTH"
Values <- seq(1, 12, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTL, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field <- "DAY"
Values <- seq(1, 31, 1)
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, Field, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTL, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(paste(checkName, Field), check_without_errors, stop_)
}
Field = "HAUL_NUMBER"
Values = seq(1,999,1)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_dictionary(ResultData = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
checkName = "Check numeric range"
Field = "TOTAL_WEIGHT_IN_THE_CATEGORY_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
checkName = "Check numeric range"
Field = "TOTAL_NUMBER_IN_THE_CATEGORY_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
checkName = "Check numeric range"
Field = "TOTAL_WEIGHT_IN_THE_SUB-CATEGORY_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
checkName = "Check numeric range"
Field = "TOTAL_NUMBER_IN_THE_SUB-CATEGORY_HAUL"
Values = c(0,9999999)
if (check_without_errors == TRUE) {
if(verbose){message(paste(checkName,Field,"in progress..."))}
check_without_errors = check_numeric_range(Data = ResultDataTL, Field, Values, year=yea, wd, suffix)
}
if(verbose){stop_ = printError(paste(checkName,Field),check_without_errors, stop_)}
}
}
# End dictionary checks
#-------------------------------------
#-------------------------------------
# Check no empty fields
checkName <- "Check no empty fields TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_no_empty_fields(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check no empty fields TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_no_empty_fields(ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check no empty fields TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_no_empty_fields(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
if (!(all(is.na(TE)) & length(TE) == 1)) {
if (nrow(ResultDataTE) > 0) {
checkName <- "Check no empty fields TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_no_empty_fields(ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
if (!(all(is.na(TL)) & length(TL) == 1)) {
if (nrow(ResultDataTL) > 0) {
checkName <- "Check no empty fields TL"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_no_empty_fields(ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
#-------------------------------------
# checks on TA
checkName <- "Check 0 fields TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_0_fieldsTA(ResultDataTA, wd, suffix, year = yea)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check dm TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_dm(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency between duration and time TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_consistencyTA_duration(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency between distance and duration of the haul TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_consistencyTA_distance(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of the hauls coordinates with the distance (difference not greater than 30%)"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_distance(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of bridles length TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_bridles_length(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check difference between start depth and end depth (not greater than 20%) in TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_depth(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check start depth and end depth in the same stratum TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_stratum(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of stratum code in TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_stratum_code(ResultDataTA, year = yea, Strata = Stratification, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName = "Check swept area"
if (check_without_errors == TRUE) {
if(verbose){
message(paste(checkName,Field,"in progress..."))
}
check_without_errors = check_swept_area(ResultDataTA, year=yea, wd, suffix)
}
if(verbose){
stop_ = printError_cc(checkName,check_without_errors, stop_)
}
checkName <- "Check start quadrant and end quadrant TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_quadrant(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check uniqueness of valid hauls TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_unique_valid_haul(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Visual check of the haul positions"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_position(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Relation between shooting depth and warp length, and between warp length and wing opening"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
graphs_TA(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check if the coordinates are in the Mediterranean Sea"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_position_in_Med(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check on temperature by haul"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_temperature(ResultDataTA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# checks on TB
checkName <- "Check correctness of species codes TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_rubincode(ResultData=ResultDataTB, year = yea, TMlist = Ref_list, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of NB_TOTAL and number per sex TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_nbtotTB(ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check presence of NB_TOTAL and number per sex TB for species G1"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_nm_TB(ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency between not null weight and not null total number"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_weight_tot_nb(ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of weight and number TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_weight(ResultDataTB, year = yea, DataTargetSpecies = RoME::DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# checks on TC
graphics.off()
checkName <- "Check correctness of species codes TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_rubincode(ResultDataTC, year = yea, TMlist = Ref_list, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of LENGTH_CLASSES_CODE TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_length_class_codeTC(ResultDataTC, Specieslist = Ref_list, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of length classes TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_length(ResultDataTC, DataSpecies = NA, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of number per sex in TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_nb_per_sexTC(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of maturity stages TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_mat_stages(ResultDataTC, year = yea, wd, suffix, stages = stages_list)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check sub-sampling"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_subsampling(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of maturity stages TC by the comparison with the length of smallest mature individuals reported in bibliography"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_smallest_mature(ResultDataTC, year = yea, MaturityParameters = Maturity, TargetSpecies = DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of sex TC by means of spawning period"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_spawning_period(ResultDataTA, ResultDataTC, year = yea, Maturity_parameters = Maturity, DataTargetSpecies = DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# checkName = "Check consistency of sex data TC by means of sex-inversion size"
# if (check_without_errors == TRUE) {
# if(verbose){message(paste(checkName,"in progress..."))}
# check_without_errors = check_sex_inversion(ResultDataTC,Maturity,wd,suffix)
# }
# if(verbose){stop_ = printError(checkName,check_without_errors, stop_)}
checkName <- "Check consistency of length distribution TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_step_length_distr(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check total weight in the haul in TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_individual_weightTC(ResultDataTC, LW = ab_parameters, year = yea, wd, suffix, verbose = FALSE)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of species codes TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_rubincode(ResultDataTC, year = yea, TMlist = Ref_list, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check presence of lengths for G1 and G2 Medits species in TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_G1_G2(ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# cross checks
checkName <- "Check presence in TB of TA hauls"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_hauls_TATB(ResultDataTA, ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check presence in TA of TB hauls"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_hauls_TBTA(ResultDataTA, ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check presence in TC of TB target species"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_species_TBTC(ResultDataTB, ResultDataTC, year = yea, DataSpecies = DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check presence in TB of TC species"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_haul_species_TCTB(ResultDataTB, ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of the number per sex in TB in case of sub-sampling in TC "
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_raising(ResultDataTB, ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check on date by haul TB"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_date_haul(ResultDataTA, ResultDataTB, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check on date by haul TC"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_date_haul(ResultDataTA, ResultDataTC, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# Check on TE
if (!(all(is.na(TE)) & length(TE) == 1)) {
if (nrow(ResultDataTE) > 0) {
checkName <- "Check on date by haul TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_date_haul(ResultDataTA, ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of maturity stages TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_mat_stages(ResultDataTE, year = yea, wd, suffix, stages = stages_list)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Cross check on number between TC and TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_TE_TC(ResultDataTC, ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of maturity stages TE by the comparison with the length of smallest mature individuals reported in bibliography"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_smallest_mature(ResultDataTE, year = yea, MaturityParameters = Maturity, TargetSpecies = DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency of maturity stages in TE by means of spawning period"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_spawning_period(ResultDataTA, ResultDataTE, year = yea, Maturity_parameters = Maturity, DataTargetSpecies = DataTargetSpecies, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check individual weight in TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_individual_weightTE(ResultDataTE, LW = ab_parameters, year = yea, wd, suffix, verbose = FALSE)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of species codes TE"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_rubincode(ResultDataTE, year = yea, TMlist = Ref_list, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check consistency TE check-fields"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_nb_TE(ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Summary individual data sampling"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- scheme_individual_data(DataTC = ResultDataTC, DataTE = ResultDataTE, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
# Checks on TL
if (!(all(is.na(TL)) & length(TL) == 1)) {
if (nrow(ResultDataTL) > 0) {
checkName <- "Check allowed values for category on Litter data"
Field <- "LITTER_CATEGORY"
Values <- c("L0", "L1", "L2", "L3", "L4", "L5", "L6", "L7", "L8", "L9")
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTL, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check allowed values for sub-category on Litter data"
Field <- "LITTER_SUB-CATEGORY"
Values <- c("0", "A", "B", "C", "D", "E", "F", "G", "H", "I", "J","a","b","c","d","e","f","g","h","i","j")
colnames(ResultDataTL)[10] <- "LITTER_SUB-CATEGORY"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_dictionary(ResultData = ResultDataTL, Field, Values, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check correctness of associations between category and sub-category on Litter data"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_associations_category_TL(ResultDataTL, assTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
# checkName = "Check if the number is always filled in on Litter data"
# if (check_without_errors == TRUE) {
# if(verbose){message(paste(checkName,"in progress..."))}
# check_without_errors = check_no_empty_fields(ResultDataTL,year=yea,wd,suffix)
# }
# if(verbose){stop_ = printError(checkName,check_without_errors, stop_)}
checkName <- "Check if the hauls in TL are present in TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_hauls_TLTA(ResultDataTA, ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check if the hauls in TA are present in TL"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_hauls_TATL(ResultDataTA, ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
checkName <- "Check if the date in TL is consistent with TA"
if (check_without_errors == TRUE) {
if (verbose) {
message(paste(checkName, "in progress..."))
}
check_without_errors <- check_date_haul(ResultDataTA, ResultDataTL, year = yea, wd, suffix)
}
if (verbose) {
stop_ <- printError(checkName, check_without_errors, stop_)
}
}
}
if (!stop_) {
message("All the checks have been performed!")
}
# Create files for R_Sufi
if ((!stop_) & (create_RSufi_files == TRUE)) {
AREA <- ResultDataTA[1, "AREA"]
create_strata(Stratification = Stratification, AREA, wd, save = TRUE)
create_haul(ResultDataTA, year = yea, wd, save = TRUE)
create_catch(ResultDataTB, year = yea, wd, save = TRUE)
# if (!(all(is.na(TE)) & length(TE)==1)) {
# if (nrow(ResultDataTE)>0){
# create_length(ResultDataTE,DataSpecies=Ref_list,wd)
# }
# }
if (nrow(ResultDataTC) > 0) {
create_length(ResultDataTC, year = yea, DataSpecies = Ref_list, wd, save = TRUE)
}
message(paste("R-Sufi files have been created for the ", yea, "and the GSA selected! They have been stored in files R-Sufi directory."))
}
} # ciclo years
# END ---------------------------------------------------------------------
# -------------------------------------------------------
# -------------------------------------------------------
# -------------------------------------------------------
# -------------------------------------------------------
if ((!stop_) & (create_global_RSufi_files == TRUE)) {
if (is.na(Year_start) | is.na(Year_end)) {
warning("One or both variables Year_start and Year_end not declared")
} else {
RSufi_files(Year_start, Year_end, AREA, wd)
message("R-Sufi files have been created for the Years and the GSA selected! They have been stored in files R-Sufi directory.")
}
}
# -------------------------------------------------------
# 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)
# }
} # funzione RoME
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