build/scs 2020/scsset.2020.R

In TobieSurette/gulf.manage: Southern Gulf Data Management Functions

library(gulf.data)
library(gulf.spatial)

year <- 2020

# Load raw data export:
x <- read.table(paste0("data/raw/scs.set.", year, ".csv"), header = TRUE, sep =",", stringsAsFactors = FALSE, fileEncoding = "Windows-1252")
names(x) <- gsub("_", ".", tolower(names(x)))

# Rename fields:
x$tow.id <- toupper(x$gpnumber)

# Reformat data:
x$bottom.temperature <- gsub(",", ".", x$bottom.temperature)
x$bottom.temperature <- gsub("O", "0", x$bottom.temperature)
x$bottom.temperature[x$bottom.temperature == ""] <- NA
x$bottom.temperature <- as.numeric(x$bottom.temperature)

# Parse comment fields:
x$comment <- gsub("[ ]*$", "", x$comment)
index <- x$comment == ""
x$comment[index] <- x$speed.comment[index]
x$speed.comment <- gsub("[ ]*$", "", x$speed.comment)
x$comment[!index] <- paste0(x$comment[!index], " - ", x$speed.comment[!index])
x$comment <- paste0(substr(x$comment, 1, 1), substr(tolower(x$comment), 2, nchar(x$comment)))

# Parse date fields:
x$day   <- as.numeric(unlist(lapply(strsplit(x$date, ".", fixed = TRUE), function(x) x[1])))
x$month <- as.numeric(unlist(lapply(strsplit(x$date, ".", fixed = TRUE), function(x) x[2])))
x$year  <- as.numeric(unlist(lapply(strsplit(x$date, ".", fixed = TRUE), function(x) x[3])))

# Zone and tow ID fields:
x$zone <- gsub("ZONE", "", toupper(x$zone))

# Fix time fields:
x$gpa.time.start <- gsub("?", "", x$gpa.time.start, fixed = TRUE)
x$gpa.time.start[x$gpa.time.start == ""] <- "        "
x$gpa.time.mid <- gsub("?", "", x$gpa.time.mid, fixed = TRUE)
x$gpa.time.mid[x$gpa.time.mid == ""] <- "        "
x$gpa.time.end <- gsub("?", "", x$gpa.time.end, fixed = TRUE)
x$gpa.time.end[x$gpa.time.end == ""] <- "        "

# Observed time fields:
x$start.time.logbook <- x$gpa.time.start
x$mid.time.logbook   <- x$gpa.time.mid
x$stop.time.logbook   <- x$gpa.time.end
x$start.time.logbook[nchar(x$start.time.logbook) > 8] <- "        "
x$mid.time.logbook[nchar(x$mid.time.logbook) > 8]     <- "        "
x$stop.time.logbook[nchar(x$stop.time.logbook) > 8]     <- "        "
x$haul.time <- x$net.end

x$longitude.start.logbook <- -abs(x$gpa.lon.start)
x$longitude.stop.logbook  <- -abs(x$gpa.lon.end)
x$latitude.start.logbook  <- x$gpa.lat.start
x$latitude.stop.logbook   <- x$gpa.lat.end

# Tow validity:
x$valid <- as.numeric(tolower(x$tow.quality) == "good")

# Add variables to be filled-in later:
x$start.time        <- "        "
x$stop.time          <- "        "
x$swept.area        <- as.numeric(NA)
x$swept.area.method <- as.numeric(NA)
x$groundfish.sample	<- 0
x$water.sample      <- as.numeric(NA)
x$longitude         <- as.numeric(NA)
x$latitude          <- as.numeric(NA)
x$longitude.start   <- as.numeric(NA)
x$longitude.stop    <- as.numeric(NA)
x$latitude.start    <- as.numeric(NA)
x$latitude.stop     <- as.numeric(NA)

x$tow.number <- x$trawl.number
x$warp <- x$cables

x <- x[setdiff(names(x), "date")]
x$date <- as.character(date(year = x$year, month = x$month, day = x$day))

# Remove irrelevant variables:
vars <- c("date", "zone", "tow.number", "tow.id", "valid",
          "start.time.logbook", "stop.time.logbook", "start.time", "stop.time", "haul.time",
          "longitude", "latitude", "longitude.start", "longitude.stop", "latitude.start", "latitude.stop",
          "longitude.start.logbook", "longitude.stop.logbook", "latitude.start.logbook", "latitude.stop.logbook",
          "depth", "bottom.temperature", "warp", "swept.area", "swept.area.method", "groundfish.sample", "water.sample", "comment")
x <- x[vars]

# Corrections:
x <- x[x$date != "2020-07-10", ]
x$stop.time.logbook[x$tow.id == "GP263F"] <- "10:30:55"
x$stop.time.logbook[x$tow.id == "GP159F"] <- "12:55:47"

# Load touchdown times:
if (file.exists(paste0("data/raw/scs.touchdown.time.", year, ".csv"))){
   tmp <- read.csv(paste0("data/raw/scs.touchdown.time.", year, ".csv"), header = TRUE, stringsAsFactors = FALSE)
   x$touchdown.time <- tmp$touchdown[match(x$tow.id, tmp$tow.id)]
   x$touchdown.time[is.na(x$touchdown.time)] <- "        "
   index <- nchar(x$touchdown.time) == 7
   x$touchdown.time[index] <- paste0("0", x$touchdown.time[index])
}

# Load liftoff times:
if (file.exists(paste0("data/raw/scs.liftoff.time.", year, ".csv"))){
   tmp <- read.csv(paste0("data/raw/scs.liftoff.time.", year, ".csv"), header = TRUE, stringsAsFactors = FALSE)
   x$liftoff.time <- tmp$liftoff[match(x$tow.id, tmp$tow.id)]
   x$liftoff.time[is.na(x$liftoff.time)] <- "        "
   index <- nchar(x$liftoff.time) == 7
   x$liftoff.time[index] <- paste0("0", x$liftoff.time[index])
}

# Load trawl swept area and swept area method:
if (file.exists(paste0("data/raw/scs.swept.area.", year, ".csv"))){
   tmp <- read.csv(paste0("data/raw/scs.swept.area.", year, ".csv"), header = TRUE, stringsAsFactors = FALSE)
   x$swept.area <- tmp$swept.area[match(x$tow.id, tmp$tow.id)]
   x$swept.area.method <- tmp$swept.area.method[match(x$tow.id, tmp$tow.id)]
   x$swept.area.method[is.na(x$swept.area.method)] <- ""
}

x <- scsset(x)

# Update touchdown and stop time coordinates using eSonar files:
tows <- setdiff(x$tow.id[x$valid == 1], "GP276F")
for (j in 1:length(tows)){
   i <- which(x$tow.id == tows[j])
   print(i)
   e <- read.esonar(x[i,])
   d <- abs(time(e) - time(x[i, ], "touchdown"))
   if (min(d) <= 5){
      x$longitude.start[i] <- gulf.spatial::deg2dmm(e$longitude[which.min(d)])
      x$latitude.start[i] <- gulf.spatial::deg2dmm(e$latitude[which.min(d)])
   }
   d <- abs(time(e) - time(x[i, ], "stop"))
   if (min(d) <= 5){
      x$longitude.stop[i] <- gulf.spatial::deg2dmm(e$longitude[which.min(d)])
      x$latitude.stop[i] <- gulf.spatial::deg2dmm(e$latitude[which.min(d)])
   }
}

# Update bottom temperatures using headline Star Oddi files:
for (j in 1:length(tows)){
   i <- which(x$tow.id == tows[j])
   s <- read.star.oddi(x[i,], probe = "headline")
   if (!is.null(s)){
      t <- time2min(time(s), time(x[i, ], "touchdown"))
      liftoff <- time2min(time(x[i, ], "liftoff"), time(x[i, ], "touchdown"))
      index <- which((t >= 3) & (t <= liftoff))
      tmp <- round(mean(s$temperature[index], na.rm = TRUE), 2)
      if (!is.na(tmp)) x$bottom.temperature[i] <- tmp
      print(c(i, tmp))
   }
}

# Re-order variables:
tvars <- names(x)[grep("time", names(x))]
vars <- c("date", "zone", "tow.number", "tow.id", "valid", tvars, setdiff(vars, c("date", "zone", "tow.number", "tow.id", "valid", tvars)))
x <- x[vars]

# Write to stock assessment repository:
write.csv(x, file = paste0("data/scs.set.", year, ".csv"), row.names = FALSE)

# Write to gulf.data repository:
if (file.exists("/Users/crustacean/Desktop/gulf.data")){
   file <- paste0("/Users/crustacean/Desktop/gulf.data/inst/extdata/scs.set.", year, ".csv")
   write.csv(x, file = file, row.names = FALSE)
}