R/haul_at_sea.R

In RoME: Multiple Checks on MEDITS Trawl Survey Data

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#   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                                                                                                           #
############################################################################################################################
# MedSea <- shapefile("D:\\GIS\\vettori\\GSA\\GFCM - GSA - shp\\GSAs\\gsas (11_unita)2.shp")
# save(MedSea, file="data/MedSea.rda", compress="xz")

haul_at_sea <- function(DataTA, year, seas=RoME::MedSea, verbose=TRUE) {


  ### 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 <- MEDITS.to.dd(DataTA)

  start_coord <- data[ , colnames(data) %in% c("HAUL_NUMBER","AREA","YEAR","MONTH","DAY","SHOOTING_LONGITUDE","SHOOTING_LATITUDE","SHOOTING_QUADRANT")]
  end_coord <- data[ , colnames(data) %in% c("HAUL_NUMBER","AREA","YEAR","MONTH","DAY","HAULING_LONGITUDE","HAULING_LATITUDE","HAULING_QUADRANT")]
  suppressWarnings(sp::coordinates(start_coord) <- ~ SHOOTING_LONGITUDE + SHOOTING_LATITUDE)
  suppressWarnings(sp::coordinates(end_coord) <- ~ HAULING_LONGITUDE + HAULING_LATITUDE)
  # proj4string(MedSea) <- CRS("+proj=longlat")
  suppressWarnings(sp::proj4string(start_coord) <- sp::proj4string(seas))
  suppressWarnings(sp::proj4string(end_coord) <- sp::proj4string(seas))

  suppressWarnings(res_start <- sp::over(start_coord,seas))
  start_coord$over <- res_start$sel
  start_coord <- as.data.frame(start_coord)
  start_coord <- start_coord[is.na(start_coord$over),]



  suppressWarnings(res_end <- sp::over(end_coord, seas))
  end_coord$over <- res_end$sel
  end_coord <- as.data.frame(end_coord)
  end_coord <- end_coord[is.na(end_coord$over),]


  l_start <- length(start_coord[,1])
  l_end <- length(end_coord[,1])

  if (verbose){
    if(l_start > 0) {
      message("Check the shooting coordinates in the following hauls:\n")
    }
    if(l_end > 0) {
      message("Check the hauling coordinates in the following hauls:\n")
    }
  } # verbose
  if (l_start > 0 & l_end > 0 ){
    results <- list(start_coord, end_coord)
  } else {
    if(l_start > 0){ results <- start_coord} else {
      if(l_end > 0){ results <- end_coord}
    }
  }
  if (l_start == 0 & l_end == 0 ){
    results <- NA
    if (verbose){
      message("\nNone of the coordinates is on the land\n")
    }
  }
  return(results)
}