R/check_date_haul.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 if in TB, TC or TE the date by haul is the same of the one reported in TA

check_date_haul <- function (DataTA, Data, 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 = RoME::TA
    DataTA[107,]
    DataTA[107,"DAY"] <- 24

    Data = RoME::TB
    year=2009
    # Data = read.csv("~/GitHub/RoME/data/TC_GSA18_1994-2018.csv", sep=";")
    # Data = read.csv("~/GitHub/RoME/data/TE_2012-2018 _GSA18.csv", sep=";")
    # Data = read.csv("~/GitHub/RoME/data/TL_GSA18 2012-2018.csv", sep=";")
    # check_date_haul(DataTA=DataTA, Data=Data, year, wd, suffix)
  }

  #### CHECK TL FIELDS ####
  {
    if ("LITTER_SUB.CATEGORY" %in% colnames(Data)){
      colnames(Data)[which(colnames(Data)=="LITTER_SUB.CATEGORY")] <- "LITTER_SUB-CATEGORY"
    }
    if ("TOTAL_WEIGHT_IN_THE_SUB.CATEGORY_HAUL" %in% colnames(Data)){
      colnames(Data)[which(colnames(Data)=="TOTAL_WEIGHT_IN_THE_SUB.CATEGORY_HAUL")] <- "TOTAL_WEIGHT_IN_THE_SUB-CATEGORY_HAUL"
    }
    if ("TOTAL_NUMBER_IN_THE_SUB.CATEGORY_HAUL" %in% colnames(Data)){
      colnames(Data)[which(colnames(Data)=="TOTAL_NUMBER_IN_THE_SUB.CATEGORY_HAUL")] <- "TOTAL_NUMBER_IN_THE_SUB-CATEGORY_HAUL"
    }
  }
  #### CHECK TL FIELDS - END ####


  numberError = 0
  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="")
  }
  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$YEAR == year, ]
  Data <- Data[Data$YEAR == year, ]
  ########################################

  DataTA <- DataTA[!is.na(DataTA$AREA),]
  Data <- Data[!is.na(Data$AREA),]

  Dataset = Data

         if (as.character(Dataset$TYPE_OF_FILE[1]) == "TB") {
    write(paste("\n----------- check correctness of date by haul in TB - ", Dataset$YEAR[1]), file = Errors, append = TRUE)
  } else if (as.character(Dataset$TYPE_OF_FILE[1]) == "TC") {
    write(paste("\n----------- check correctness of date by haul in TC - ", Dataset$YEAR[1]), file = Errors, append = TRUE)
  } else if (as.character(Dataset$TYPE_OF_FILE[1]) == "TE") {
    write(paste("\n----------- check correctness of date by haul in TE - ", Dataset$YEAR[1]), file = Errors, append = TRUE)
  } else if (as.character(Dataset$TYPE_OF_FILE[1]) == "TL") {
    write(paste("\n----------- check correctness of date by haul in TL - ", Dataset$YEAR[1]), file = Errors, append = TRUE)
  }


Dataset$Date = paste (Dataset$AREA, "-",Dataset$COUNTRY, "-",Dataset$HAUL_NUMBER, "-",Dataset$DAY,"-",Dataset$MONTH,"-",Dataset$YEAR ,sep="")
TA_df =DataTA
TA_df$Date = paste (TA_df$AREA, "-",TA_df$COUNTRY, "-",TA_df$HAUL_NUMBER,"-",TA_df$DAY,"-",TA_df$MONTH,"-",TA_df$YEAR,sep="")
# TA_df$hauls_by_gsa <- paste(TA_df$COUNTRY,TA_df$AREA,TA_df$HAUL_NUMBER,sep="_")
i=1
for (i in 1:nrow(Dataset)){
  if ( !(Dataset$Date[i] %in% TA_df$Date)) {
  if (Dataset$TYPE_OF_FILE[1] != "TL"){
    write(paste("Haul",Dataset$HAUL_NUMBER[i],", code species", Dataset$GENUS[i] , Dataset$SPECIES[i] ,": the date is not consistent with the date reported in TA."), file = Errors, append = TRUE)
    numberError = numberError+1
  } else if (Dataset$TYPE_OF_FILE[1] == "TL"){
    write(paste("Haul",Dataset$HAUL_NUMBER[i],": the date is not consistent with the date reported in TA."), file = Errors, append = TRUE)
    numberError = numberError+1
  }
}
}

# pivot_TA <- aggregate(TA_df$Date, by=list(TA_df$hauls_by_gsa), FUN="length")


 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) }

}