R/saveRawVms.R

Defines functions saveRawVms

Documented in saveRawVms

#' Raw VMS editing function
#'
#' \code{saveRawVms} implements the routines that converts raw values
#'  to standard data.
#'
#' @param rawfile    The raw VMS dataset.
#' @param widget    The widget list that contains the editing infos.
#'
#' @return The function returns the standardized VMS data.
#'
#' @usage saveRawVms(rawfile, widget)
#'
#' @seealso \code{\link{gui_vms_editraw}}

saveRawVms <- function(rawfile, widget) {
  widget <- gsub("\"", "", as.character(widget))
  vessIdSel <- widget[1]
  latModeSel <- widget[2]
  latDeg <- widget[3]
  latMin <- widget[4]
  latSec <- widget[5]
  latDir <- widget[6]
  latDec <- widget[7]
  lonModeSel <- widget[8]
  lonDeg <- widget[9]
  lonMin <- widget[10]
  lonSec <- widget[11]
  lonDir <- widget[12]
  lonDec <- widget[13]
  timeMode <- widget[14]
  timeUtc <- widget[15]

  timeDate2a <- widget[16]
  timeDate2b <- widget[17]

  timeDate <- widget[18]
  timeHour <- widget[19]
  timeMinute <- widget[20]
  timeSecond <- widget[21]
  speedModeSel <- widget[22]
  speedCol <- widget[23]
  headModeSel <- widget[24]
  headCol <- widget[25]

  if (widget[26] == "DD/MM/YYYY") {
    data_frm <- c(dates = "d/m/y", times = "h:m:s")
  } else {
    data_frm <- c(dates = "m/d/y", times = "h:m:s")
  }

  numlines <- length(rawfile$data[, 1])
  cat("\n\n   ---   Raw Pings Editing Started!   ---\n",
    "\nProcessing ", numlines, " raw pings...\n",
    sep = ""
  )
  # to_rep <- paste(to_rep, "\nProcessed ", numlines, " raw pings.\n", sep = "")
  vmsdata <- data.frame(
    "I_NCEE" = numeric(numlines),
    "LAT" = numeric(numlines),
    "LON" = numeric(numlines),
    "DATE" = numeric(numlines),
    "SPE" = numeric(numlines),
    "HEA" = numeric(numlines)
  )

  vessid <- which(colnames(rawfile$data) == vessIdSel)
  vmsdata[, "I_NCEE"] <- rawfile$data[, vessid]

  if (latModeSel == "sex") {
    latdeg <- which(colnames(rawfile$data) == latDeg)
    latmin <- which(colnames(rawfile$data) == latMin)
    latsec <- which(colnames(rawfile$data) == latSec)
    latdir <- which(colnames(rawfile$data) == latDir)
    tole_ladeg <- which(is.na(rawfile$data[, latdeg]))
    cat("\n   -   ", length(tole_ladeg), " NAs found in latitude degrees...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_ladeg), " NAs found in latitude degrees...\n", sep = "")
    if (length(tole_ladeg) > 0) {
      rawfile$data <- rawfile$data[-tole_ladeg, ]
      vmsdata <- vmsdata[-tole_ladeg, ]
    }
    tole_lamin <- which(is.na(rawfile$data[, latmin]))
    cat("\n   -   ", length(tole_lamin), " NAs found in latitude minutes...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lamin), " NAs found in latitude minutes...\n", sep = "")
    if (length(tole_lamin) > 0) {
      rawfile$data <- rawfile$data[-tole_lamin, ]
      vmsdata <- vmsdata[-tole_lamin, ]
    }
    tole_lasec <- which(is.na(rawfile$data[, latsec]))
    cat("\n   -   ", length(tole_lasec), " NAs found in latitude seconds...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lasec), " NAs found in latitude seconds...\n", sep = "")
    if (length(tole_lasec) > 0) {
      rawfile$data <- rawfile$data[-tole_lasec, ]
      vmsdata <- vmsdata[-tole_lasec, ]
    }
    tole_ladir <- which(is.na(rawfile$data[, latdir]))
    cat("\n   -   ", length(tole_ladir), " NAs found in latitude direction...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_ladir), " NAs found in latitude direction...\n", sep = "")
    if (length(tole_ladir) > 0) {
      rawfile$data <- rawfile$data[-tole_ladir, ]
      vmsdata <- vmsdata[-tole_ladir, ]
    }
    pre_lat <- latsex2dec(rawfile$data[, latdeg], rawfile$data[, latmin], rawfile$data[, latsec], rawfile$data[, latdir])

    tole_prelat <- which(pre_lat < -90 | pre_lat > 90)
    if (length(tole_prelat) > 0) {
      pre_lat <- pre_lat[-tole_prelat]
      vmsdata <- vmsdata[-tole_prelat, ]
      rawfile$data <- rawfile$data[-tole_prelat, ]
    }
    cat("\n   -   ", length(tole_prelat), " Latitudes out of range ( -90 / 90 )", sep = "")

    vmsdata[, "LAT"] <- pre_lat
  }

  if (latModeSel == "dec") {
    latdec <- which(colnames(rawfile$data) == latDec)
    tole_lade <- which(is.na(rawfile$data[, latdec]))
    cat("\n   -   ", length(tole_lade), " NAs found in decimal latitude...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lade), " NAs found in decimal latitude...\n", sep = "")
    if (length(tole_lade) > 0) {
      rawfile$data <- rawfile$data[-tole_lade, ]
      vmsdata <- vmsdata[-tole_lade, ]
    }

    pre_lat <- rawfile$data[, latdec]

    tole_prelat <- which(pre_lat < -90 | pre_lat > 90)
    if (length(tole_prelat) > 0) {
      pre_lat <- pre_lat[-tole_prelat]
      vmsdata <- vmsdata[-tole_prelat, ]
      rawfile$data <- rawfile$data[-tole_prelat, ]
    }
    cat("\n   -   ", length(tole_prelat), " Latitudes out of range ( -90 / 90 )", sep = "")

    vmsdata[, "LAT"] <- pre_lat
  }


  if (lonModeSel == "sex") {
    londeg <- which(colnames(rawfile$data) == lonDeg)
    lonmin <- which(colnames(rawfile$data) == lonMin)
    lonsec <- which(colnames(rawfile$data) == lonSec)
    londir <- which(colnames(rawfile$data) == lonDir)
    tole_lodeg <- which(is.na(rawfile$data[, londeg]))
    cat("\n   -   ", length(tole_lodeg), " NAs found in longitude degrees...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lodeg), " NAs found in longitude degrees...\n", sep = "")
    if (length(tole_lodeg) > 0) {
      rawfile$data <- rawfile$data[-tole_lodeg, ]
      vmsdata <- vmsdata[-tole_lodeg, ]
    }
    tole_lomin <- which(is.na(rawfile$data[, lonmin]))
    cat("\n   -   ", length(tole_lomin), " NAs found in longitude minutes...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lomin), " NAs found in longitude minutes...\n", sep = "")
    if (length(tole_lomin) > 0) {
      rawfile$data <- rawfile$data[-tole_lomin, ]
      vmsdata <- vmsdata[-tole_lomin, ]
    }
    tole_losec <- which(is.na(rawfile$data[, lonsec]))
    cat("\n   -   ", length(tole_losec), " NAs found in longitude seconds...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_losec), " NAs found in longitude seconds...\n", sep = "")
    if (length(tole_losec) > 0) {
      rawfile$data <- rawfile$data[-tole_losec, ]
      vmsdata <- vmsdata[-tole_losec, ]
    }
    tole_lodir <- which(is.na(rawfile$data[, londir]))
    cat("\n   -   ", length(tole_lodir), " NAs found in longitude direction...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_lodir), " NAs found in longitude direction...\n", sep = "")
    if (length(tole_lodir) > 0) {
      rawfile$data <- rawfile$data[-tole_lodir, ]
      vmsdata <- vmsdata[-tole_lodir, ]
    }

    pre_lon <- lonsex2dec(rawfile$data[, londeg], rawfile$data[, lonmin], rawfile$data[, lonsec], rawfile$data[, londir])

    tole_prelon <- which(pre_lon < -180 | pre_lon > 180)
    if (length(tole_prelon) > 0) {
      pre_lon <- pre_lon[-tole_prelon]
      vmsdata <- vmsdata[-tole_prelon, ]
      rawfile$data <- rawfile$data[-tole_prelon, ]
    }
    cat("\n   -   ", length(tole_prelon), " Longitudes out of range ( -180 / 180 )", sep = "")

    vmsdata[, "LON"] <- pre_lon
  }

  if (lonModeSel == "dec") {
    londec <- which(colnames(rawfile$data) == lonDec)
    tole_lode <- which(is.na(rawfile$data[, londec]))
    cat("\n   -   ", length(tole_lode), " NAs found in decimal longitude...", sep = "")
    if (length(tole_lode) > 0) {
      rawfile$data <- rawfile$data[-tole_lode, ]
      vmsdata <- vmsdata[-tole_lode, ]
    }

    pre_lon <- rawfile$data[, londec]

    tole_prelon <- which(pre_lon < -180 | pre_lon > 180)
    if (length(tole_prelon) > 0) {
      pre_lon <- pre_lon[-tole_prelon]
      vmsdata <- vmsdata[-tole_prelon, ]
      rawfile$data <- rawfile$data[-tole_prelon, ]
    }
    cat("\n   -   ", length(tole_prelon), " Longitudes out of range ( -180 / 180 )", sep = "")

    vmsdata[, "LON"] <- pre_lon
  }


  if (timeMode == "UTC") {
    timeutc <- which(colnames(rawfile$data) == timeUtc)
    tole_ti <- which(is.na(rawfile$data[, timeutc]))
    cat("\n   -   ", length(tole_ti), " NAs found in UTC times...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_ti), " NAs found in UTC times...\n", sep = "")
    if (length(tole_ti) > 0) {
      rawfile$data <- rawfile$data[-tole_ti, ]
      vmsdata <- vmsdata[-tole_ti, ]
    }
    vmsdata[, "DATE"] <- rawfile$data[, timeutc]
  }

  if (timeMode == "Date + Time") {
    date <- which(colnames(rawfile$data) == timeDate2a)
    time <- which(colnames(rawfile$data) == timeDate2b)
    tole_tida <- which(is.na(rawfile$data[, time]))
    cat("\n   -   ", length(tole_tida), " NAs found in times...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_tida), " NAs found in times...\n", sep = "")
    if (length(tole_tida) > 0) {
      rawfile$data <- rawfile$data[-tole_tida, ]
      vmsdata <- vmsdata[-tole_tida, ]
    }
    tole_dati <- which(is.na(rawfile$data[, date]))
    cat("\n   -   ", length(tole_dati), " NAs found in dates...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_dati), " NAs found in dates...\n", sep = "")
    if (length(tole_dati) > 0) {
      rawfile$data <- rawfile$data[-tole_dati, ]
      vmsdata <- vmsdata[-tole_dati, ]
    }
    vmsdata[, "DATE"] <- as.numeric(chron(
      as.character(rawfile$data[, date]),
      as.character(rawfile$data[, time]),
      data_frm
    ))
  }

  if (timeMode == "Date + H M S") {
    date <- which(colnames(rawfile$data) == timeDate)
    hour <- which(colnames(rawfile$data) == timeHour)
    minute <- which(colnames(rawfile$data) == timeMinute)
    second <- which(colnames(rawfile$data) == timeSecond)
    tole_dat <- which(is.na(rawfile$data[, date]))
    cat("\n   -   ", length(tole_dat), " NAs found in dates...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_dat), " NAs found in dates...\n", sep = "")
    if (length(tole_dat) > 0) {
      rawfile$data <- rawfile$data[-tole_dat, ]
      vmsdata <- vmsdata[-tole_dat, ]
    }
    tole_hou <- which(is.na(rawfile$data[, hour]))
    cat("\n   -   ", length(tole_hou), " NAs found in hours...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_hou), " NAs found in hours...\n", sep = "")
    if (length(tole_hou) > 0) {
      rawfile$data <- rawfile$data[-tole_hou, ]
      vmsdata <- vmsdata[-tole_hou, ]
    }
    tole_min <- which(is.na(rawfile$data[, minute]))
    cat("\n   -   ", length(tole_min), " NAs found in minutes...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_min), " NAs found in minutes...\n", sep = "")
    if (length(tole_min) > 0) {
      rawfile$data <- rawfile$data[-tole_min, ]
      vmsdata <- vmsdata[-tole_min, ]
    }
    tole_sec <- which(is.na(rawfile$data[, second]))
    cat("\n   -   ", length(tole_sec), " NAs found in seconds...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_sec), " NAs found in seconds...\n", sep = "")
    if (length(tole_sec) > 0) {
      rawfile$data <- rawfile$data[-tole_sec, ]
      vmsdata <- vmsdata[-tole_sec, ]
    }
    time <- paste(rawfile$data[, hour], rawfile$data[, minute], rawfile$data[, second], sep = ":")
    vmsdata[, "DATE"] <- as.numeric(chron(
      as.character(rawfile$data[, date]),
      as.character(time),
      data_frm
    ))
  }

  tole_vda <- which(is.na(vmsdata[, "DATE"]))
  cat("\n   -   ", length(tole_vda), " dates found with bad format...", sep = "")
  # to_rep <- paste(to_rep, "\n   -   ", length(tole_vda), " dates found with bad format...\n", sep = "")
  if (length(tole_vda) > 0) {
    rawfile$data <- rawfile$data[-tole_vda, ]
    vmsdata <- vmsdata[-tole_vda, ]
  }

  if (speedModeSel == "Knots") {
    knots <- which(colnames(rawfile$data) == speedCol)
    tole_kn <- which(is.na(rawfile$data[, knots]))
    cat("\n   -   ", length(tole_kn), " NAs found in knots speed...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_kn), " NAs found in knots speed...\n", sep = "")
    if (length(tole_kn) > 0) {
      rawfile$data <- rawfile$data[-tole_kn, ]
      vmsdata <- vmsdata[-tole_kn, ]
    }
    vmsdata[, "SPE"] <- kno2kmh(rawfile$data[, knots])
  }

  if (speedModeSel == "Km/h") {
    kmh <- which(colnames(rawfile$data) == speedCol)
    tole_km <- which(is.na(rawfile$data[, kmh]))
    cat("\n   -   ", length(tole_km), " NAs found in km/h speed...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_km), " NAs found in km/h speed...\n", sep = "")
    if (length(tole_km) > 0) {
      rawfile$data <- rawfile$data[-tole_km, ]
      vmsdata <- vmsdata[-tole_km, ]
    }
    vmsdata[, "SPE"] <- rawfile$data[, kmh]
  }


  if (headModeSel == "Rad") {
    rad <- which(colnames(rawfile$data) == headCol)
    tole_ra <- which(is.na(rawfile$data[, rad]))
    cat("\n   -   ", length(tole_ra), " NAs found in radiants heading...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_ra), " NAs found in radiants heading...\n", sep = "")
    if (length(tole_ra) > 0) {
      rawfile$data <- rawfile$data[-tole_ra, ]
      vmsdata <- vmsdata[-tole_ra, ]
    }
    vmsdata[, "HEA"] <- rad2deg(rawfile$data[, rad])
  }

  if (headModeSel == "Deg") {
    deg <- which(colnames(rawfile$data) == headCol)
    tole_de <- which(is.na(rawfile$data[, deg]))
    cat("\n   -   ", length(tole_de), " NAs found in degrees heading...", sep = "")
    # to_rep <- paste(to_rep, "\n   -   ", length(tole_de), " NAs found in degrees heading...\n", sep = "")
    if (length(tole_de) > 0) {
      rawfile$data <- rawfile$data[-tole_de, ]
      vmsdata <- vmsdata[-tole_de, ]
    }
    vmsdata[, "HEA"] <- rawfile$data[, deg]
  }
  cat("\nRemoved ", round((100 / numlines) * (numlines - nrow(vmsdata)), 2), "% of data, that is ", numlines - nrow(vmsdata), " pings\n",
    "\n\n   ---   Raw Pings Editing Complete!   ---\n\n",
    sep = ""
  )

  return(vmsdata)
}

Try the vmsbase package in your browser

Any scripts or data that you put into this service are public.

vmsbase documentation built on Dec. 3, 2018, 5:03 p.m.