library(gulf.data)
library(gulf.spatial)
# Define survey year:
year <- 2023
# Load raw data export:
path <- paste0("build/scs.", year, "/data/")
x <- read.table(paste0(path, "scs.set.", year, ".csv"), header = TRUE, sep =",", stringsAsFactors = FALSE)
names(x) <- gsub("_", ".", tolower(names(x)))
# Load file containing original survey station coordinates:
file <- paste0(gsub("gulf.manage", "gulf.data", getwd(), fixed = TRUE), "/inst/extdata/scs.stations.", year, ".csv")
y <- read.csv(file)
# 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$comment[is.na(x$comment)] <- ""
x$comment <- gsub("[ ]*$", "", x$comment)
ix <- x$comment == ""
x$comment[ix] <- x$speed.comment[ix]
x$speed.comment <- gsub("[ ]*$", "", x$speed.comment)
x$comment[!ix] <- paste0(x$comment[!ix], " - ", x$speed.comment[!ix])
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))
x$zone[x$zone == "E"] <- "12E"
x$zone[x$zone == "F"] <- "12F"
# 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
# Stop time fixes:
x$stop.time.logbook[x$tow.id == "GP158F"] <- "16:54:13"
x$stop.time.logbook[x$tow.id == "GP176F"] <- "15:34:34"
x$start.time.logbook[x$tow.id == "GP147F"] <- "05:33:18"
x$stop.time.logbook[x$tow.id == "GP147F"] <- "05:40:08"
x$start.time.logbook[x$tow.id == "GP159F"] <- "06:52:25"
x$stop.time.logbook[x$tow.id == "GP159F"] <- "06:58:33"
x$start.time.logbook[x$tow.id == "GP055F"] <- "05:40:28"
x$stop.time.logbook[x$tow.id == "GP055F"] <- "05:46:37"
x$start.time.logbook[x$tow.id == "GP269F"] <- "19:26:29"
x$stop.time.logbook[x$tow.id == "GP269F"] <- "19:40:59"
# Quick coordinate fixes:
x$gpa.lon.end <- as.numeric(x$gpa.lon.end)
x$gpa.lon.start <- as.numeric(x$gpa.lon.start)
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")
head(x[setdiff(names(x), vars)])
x <- x[vars]
# Remove empty data rows:
x <- x[x$tow.id != "GP000F", ]
# Standardize time formats:
x$start.time.logbook <- time(x$start.time.logbook)
x$stop.time.logbook <- time(x$stop.time.logbook)
x$haul.time <- time(x$haul.time)
# Assign fishing captain:
x$captain <- "Ghislain Bourgeois"
# Load touchdown times:
t <- read.csv(paste0(gsub("manage", "data", "C:/Users/SuretteTJ/Desktop/gulf.manage"), "/inst/extdata/scs.event.times.", year, ".csv"))
t <- t[t$location == "footrope" & t$position == "center" & t$event == "touchdown", ]
t$time <- time(t$time)
ix <- match(x$tow.id, t$tow.id)
x$start.time[!is.na(ix)] <- t$time[ix[!is.na(ix)]]
ix <- x$start.time == " " & x$valid == 1
x$start.time[ix] <- x$start.time.logbook[ix]
# Load liftoff times:
t <- read.csv(paste0(gsub("manage", "data", "C:/Users/SuretteTJ/Desktop/gulf.manage"), "/inst/extdata/scs.event.times.", year, ".csv"))
t <- t[t$location == "footrope" & t$position == "center" & t$event == "liftoff", ]
t$time <- time(t$time)
ix <- match(x$tow.id, t$tow.id)
x$liftoff.time[!is.na(ix)] <- t$time[ix[!is.na(ix)]]
ix <- is.na(x$liftoff.time) & x$valid == 1
x$liftoff.time[ix] <- x$stop.time.logbook[ix]
x$liftoff.time[is.na(x$liftoff.time)] <- " "
# Update bottom temperatures using headline Star Oddi files:
files <- locate.star.oddi(location = "headline", position = "center", year = year)
files <- files[grep("center", files)]
for (i in 1:nrow(x)){
if (x$valid[i] == 1){
file <- files[grep(x$tow.id[i], files)]
s <- read.star.oddi(file)
if (!is.null(s)){
start.time <- as.POSIXct(paste0(x$date[i], x$start.time[i]))
end.time <- as.POSIXct(paste0(x$date[i], x$liftoff.time[i]))
t <- time2min(time(s), start.time)
liftoff <- time2min(end.time, start.time)
ix <- which((t >= 3) & (t <= liftoff))
tmp <- round(mean(s$temperature[ix], na.rm = TRUE), 2)
if (!is.na(tmp)) x$bottom.temperature[i] <- tmp
print(c(i, tmp))
}
}
}
# Point fix:
#x$bottom.temperature[x$tow.id == "GP080F"] <- 0.57 # Original observation.
# Update touchdown and stop time coordinates using eSonar files:
files <- locate.esonar(year)
for (i in 1:nrow(x)){
if (x$valid[i] == 1){
print(i)
file <- files[grep(x$tow.id[i], files)]
if (length(file) > 0){
e <- read.esonar(files[grep(x$tow.id[i], files)])
start <- as.POSIXct(paste(x$date[i], x$start.time[i]))
stop <- as.POSIXct(paste(x$date[i], x$stop.time.logbook[i]))
# Start time coordinates:
d <- abs(time2sec(time(e), start))
if (min(d) <= 5){
x$longitude.start[i] <- gulf.spatial::deg2dmm(e$longitude[which.min(d)])
x$latitude.start[i] <- gulf.spatial::deg2dmm(e$latitude[which.min(d)])
}
# Stop time coordinates:
d <- abs(time2sec(time(e), stop))
if (min(d) <= 5){
x$longitude.stop[i] <- gulf.spatial::deg2dmm(e$longitude[which.min(d)])
x$latitude.stop[i] <- gulf.spatial::deg2dmm(e$latitude[which.min(d)])
}
}
}
}
# Determine which stations were fixed to 2013 positions:
y <- y[y$station == "fixed 2013", ]
library(gulf.spatial)
x$station.type <- "free"
x <- scsset(x)
for (i in 1:nrow(y)){
d <- 1000 * distance(y$longitude[i], y$latitude[i], lon(x), lat(x))[1, ]
d[x$valid != 1] <- NA
ix <- which.min(d)
print(round(d[ix]))
if (d[ix] < 3000) x$station.type[ix] <- "fixed"
}
# Load trawl swept area and swept area method:
file <- paste0("C:/Users/SuretteTJ/Desktop/gulf.manage/build/scs.", year, "/data/scs.swept.area.", year, ".csv")
if (file.exists(file)){
tmp <- read.csv(file, header = TRUE, stringsAsFactors = FALSE)
x$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)] <- ""
}
# Re-order variables:
tvars <- names(x)[grep("time", names(x))]
vars <- c("date", "zone", "tow.number", "tow.id", "valid", "station.type", "captain", tvars, setdiff(vars, c("date", "zone", "tow.number", "tow.id", "valid", "station.type", "captain", 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:
path <- gsub("gulf.manage", "gulf.data", getwd(), fixed = TRUE)
if (file.exists(path)){
file <- paste0(path, "/inst/extdata/scs.set.", year, ".csv")
write.csv(x, file = file, row.names = FALSE)
}
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