R/check_G1_G2.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 about the presence of lengths for G1 and G2 species

check_G1_G2 <- function (DataTC, year, wd, suffix){
  if (FALSE){
    library(RoME)
    wd <- tempdir() # "D:\\Documents and Settings\\Utente\\Documenti\\GitHub\\RoME\\temp"
    suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
    DataTC = tc # RoME::TC # read.csv("~/GitHub/RoME/data/TC_GSA18_1994-2018.csv", sep=";")
    DataTC[83,"LENGTH_CLASS"] <- NA
    year = 2015
    check_G1_G2(DataTC,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"))
  }
  DataTC <- DataTC[DataTC$YEAR == year, ]
  ########################################

  ResultDataTC = DataTC[!is.na(DataTC$LENGTH_CLASS),]
  write(paste("\n----------- check presence of lengths for G1 and G2 species in TC - ",ResultDataTC$YEAR[1]), file = Errors, append = TRUE)

ResultDataTC$Species = paste  (ResultDataTC$GENUS,ResultDataTC$SPECIES)

list_g1_g2 <- RoME::list_g1_g2

G1 =  data.frame(as.character(list_g1_g2[!is.na(list_g1_g2$MEDITS_G1),"CODE"]))
G2 =  data.frame(as.character(list_g1_g2[!is.na(list_g1_g2$MEDITS_G2),"CODE"]) )

colnames(G1)="Species"
colnames(G2)="Species"

G1_G2 = rbind(G1,G2)
spe=2
for (spe in 1:length(G1_G2)){
ResultDataTC_temp = ResultDataTC[ResultDataTC$Species == G1_G2[spe,],]
       # haul= unique(ResultDataTC_temp$HAUL_NUMBER)[1] # counter
       for (haul in unique(ResultDataTC_temp$HAUL_NUMBER))  {
       Lengths=ResultDataTC_temp$LENGTH_CLASS[ResultDataTC_temp$HAUL_NUMBER == haul]
       if (length(Lengths)==0){
       write(paste("Warning: Haul",haul,": for MEDITS species G1 and G2 the collection of the length is mandatory. No length data for", G1_G2[spe,]), 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)
#     }
    return(TRUE)

}