R/read.logbook.R
In TobieSurette/gulf.data: Southern Gulf of St Lawrence Data Access
Defines functions
read.ziff.ascii
read.sc.logbook
read.ziff
read.logbook
Documented in
read.logbook
read.sc.logbook
read.ziff
read.ziff.ascii
#' @title Load Fishery Logbook Data
#'
#' @rdname read.logbook
#'
#' @description Function to load logbook and slip landings data from the southern Gulf of Saint Lawrence fisheries.
#'
#' @param x Fishery year or file name.
#' @param year Fishery year.
#' @param file File name to be loaded. File format is assumed to be comma-separated (i.e. .csv).
#' @param path File path containing comma-separated fishery logbook files (i.e. .csv).
#' @param echo Logical value specifying whether to report files to the R console as they're being read.
#' @param ... Not used.
#' @export read.logbook
read.logbook <- function(x, species = "snow crab", source = "r", ...){
if (!missing(species)){
if (is.numeric(species)) species <- tolower(species(species)[1])
species <- match.arg(tolower(species), "snow crab")
}
# Read data:
z <- NULL
if (species == "snow crab"){
z <- read.sc.logbook(x, ...)
}else{
z <- read.ziff(x, source = source, ...)
}
class(z) <- c("logbook", class(z))
return(z)
}
#' @rdname read.logbook
#' @export read.ziff
read.ziff <- function(x, file, echo = TRUE, ...){
# Find data files:
files <- NULL
if (missing(x) & missing(file)) files <- locate.ziff(x, ...)
if (!missing(x)) if (is.character(x)) files <- x
if (!missing(file)) files <- file
if (length(files) == 0) return(NULL)
# Read files:
r <- NULL
for (i in 1:length(files)){
if (echo) cat(paste0("Reading : '", files[i], "'\n"))
type <- tolower(unlist(lapply(strsplit(files[i], "[.]"), function(x) x[length(x)])))
if (type == "new"){
read.ziff.ascii(files[i], ...)
}
if (type %in% c("rda", "rdata")){
load(files[i])
}
r <- rbind(r, x)
}
return(r)
}
#' @rdname read.logbook
#' @export read.sc.logbook
read.sc.logbook <- function(x, year, file, ...){
if (!missing(x)){
if (is.numeric(x) & missing(file)) year <- x
if (is.character(x) & missing(file)) file <- x
}
# Define data path for 'csv' files:
path <- options("gulf.path")[[1]]$snow.crab$logbook
if (!missing(year) & missing(file)) file <- paste0(path, "logbook ", year, ".csv")
# Load file and format variable names:
x <- read.csv(file, skip = 1, header = FALSE)
x <- gulf.utils::recode(x)
# Field name fixes:
fields <- readLines(file, n = 1)
fields <- tolower(strsplit(fields, ",")[[1]])
fields <- gsub("^[ #]+", "", fields)
fields <- gsub(" ", ".", fields)
fields <- gsub("[.]+", ".", fields)
fields <- gsub("[_]+", ".", fields)
fields <- gsub("lon.dec", "longitude", fields)
fields <- gsub("lat.dec", "latitude", fields)
fields <- gsub("lat.pas.modifier", "lat.str", fields)
fields <- gsub("long.pas.modifier", "lon.str", fields)
fields <- gsub("traps", "trap", fields)
fields <- gsub("grid[.]good", "grid", fields)
fields <- gsub("[.]$", "", fields)
fields <- gsub("^x[.]", "", fields)
fields[fields == "prov"] <- "province"
fields <- gsub("^pue", "cpue", fields)
if (sum(fields == "grid") > 1) fields[grep("grid", fields)[2]] <- "grid.calc"
fields[fields == "slip"] <- "slip.number"
fields[fields == "no.de.formulaire"] <- "slip.number"
fields <- gsub("^cfv$", "cfvn", fields)
fields <- gsub("^vrn$", "cfvn", fields)
if (!("zone" %in% fields) & ("zone.corrected" %in% fields)) fields <- gsub("zone.corrected", "zone", fields)
fields <- gsub("list[.]sub[.]fleet", "fleet", fields)
fields <- gsub("list[.]quota", "allocation.code", fields)
fields <- gsub("#", "number", fields)
fields <- gsub("[(]kg[)]", "kg", fields)
fields <- gsub("[.]-[.]", ".", fields)
fields <- gsub("zone.de.gestion", "zone", fields)
fields <- gsub("numero.groupe.contingent", "allocation", fields)
fields <- gsub("numero.formulaire", "slip.number", fields)
fields <- gsub("date.debarquement", "date.landed", fields)
fields <- gsub("date.capture", "date.caught", fields)
fields <- gsub("nom.intervenant", "licence.holder", fields)
fields <- gsub("vessel.name", "vessel", fields)
fields <- gsub("boat.name", "vessel", fields)
fields <- gsub("boat$", "vessel", fields)
fields <- gsub("slip.qty.day.kg", "slip.prop.day", fields)
fields <- gsub("slip.qty.day", "slip.prop.day", fields)
fields <- gsub("effort.trip", "trap.trip", fields)
fields <- gsub("effort.day", "trap.day", fields)
fields <- gsub("slip.num$", "slip.number", fields)
fields <- gsub("dale.landed", "date.landed", fields)
fields <- gsub("area", "zone", fields)
fields <- gsub("long.dec", "longitude", fields)
fields <- gsub("t[.]i", "ti", fields)
fields <- gsub("[.][(]h[])]", "", fields)
fields <- gsub("[.]/[.]", ".", fields)
fields <- gsub("-[.]", ".", fields)
fields <- gsub("^landed.day", "slip.prop.day", fields)
fields <- gsub("^estimate.kg", "estimate.trip.kg", fields)
fields <- gsub("^est.trip.kg", "estimate.trip.kg", fields)
fields <- gsub("^est.trip$", "estimate.trip.kg", fields)
fields <- gsub("^qty.est.trip$", "estimate.trip.kg", fields)
fields <- gsub("^amt.landed", "landed.trip.kg", fields)
fields <- gsub("^landed.trip$", "landed.trip.kg", fields)
fields <- gsub("^slip.qty.trip$", "landed.trip.kg", fields)
fields <- gsub("^slip.qty.trip.kg$", "landed.trip.kg", fields)
names(x) <- fields
if (length(which(is.na(names(x)))) > 0) x <- x[, -which(is.na(names(x)))]
# Convert numeric variables:
if (!"latitude" %in% names(x)) names(x) <- gsub("declat", "latitude", names(x))
if (!"longitude" %in% names(x)) names(x) <- gsub("declon", "longitude", names(x))
vars <- c("longitude", "latitude")
for (i in 1:length(vars)) x[, vars[i]] <- as.numeric(x[, vars[i]])
# Fix fishing zone:
x$zone[x$zone == "12.00"] <- "12"
x$zone <- gsub("*", "", x$zone, fixed = TRUE)
x$zone <- toupper(x$zone)
x$zone[x$zone == "E"] <- "12E"
x$zone[x$zone == "F"] <- "12F"
# Coordinate range checks:
x$longitude <- -abs(x$longitude)
x$longitude[which(x$longitude < -67 | x$longitude > -59)] <- NA
x$latitude[which(x$latitude < 45 | x$latitude > 49.5)] <- NA
# Depth-coordinate filter:
x$depth <- gulf.spatial::depth(x$longitude, x$latitude) # Determine depth from coordinates.
ix <- (x$depth < 40) | (x$depth > 200)
x$longitude[ix] <- NA
x$latitude[ix] <- NA
# Trip landings variables:
x$estimate.trip.kg <- as.numeric(x$estimate.trip.kg)
x$landed.trip.kg <- as.numeric(x$landed.trip.kg)
# Effort corrections:
x$trap.day <- as.numeric(gsub(",", "", x$trap.day))
x$slip.prop.day[grep("VALUE", x$slip.prop.day)] <- ""
x$slip.prop.day <- as.numeric(x$slip.prop.day)
# Coordinate fixes:
if ("lon.str" %in% names(x)){
ix <- which(is.na(x$longitude) & !is.na(x$lon.str) & (floor(log10(x$lon.str)) == 10))
x$longitude[ix] <- -abs(x$lon.str[ix] / 10^9)
ix <- which(is.na(x$longitude) & !is.na(x$lon.str) & (floor(log10(x$lon.str)) == 5))
x$longitude[ix] <- -gulf.spatial::dmm2deg(x$lon.str[ix] / 10^2)
}
if ("lat.str" %in% names(x)){
ix <- which(is.na(x$latitude) & !is.na(x$lat.str) & (floor(log10(x$lat.str)) == 10))
x$latitude[ix] <- abs(x$lat.str[ix] / 10^9)
ix <- which(is.na(x$latitude) & !is.na(x$lat.str) & (floor(log10(x$lat.str)) == 5))
x$latitude[ix] <- gulf.spatial::dmm2deg(x$lat.str[ix] / 10^2)
}
# Loran C conversions:
if (all(c("lon.str", "lat.str") %in% names(x))){
ix <- which((is.na(x$longitude) | is.na(x$latitude)) & (!is.na(x$lon.str) & !is.na(x$lat.str)))
ix <- ix[x$lon.str[ix] < 35000]
if (length(ix) > 0){
tmp <- gulf.spatial::loran2deg(x$lat.str[ix], x$lon.str[ix])
x$longitude[ix] <- -abs(tmp$long)
x$latitude[ix] <- tmp$lat
}
}
# Fix grid names:
if (!("grid.calc" %in% names(x))) x$grid.calc <- x$grid
x$grid.calc[grep("VALUE", x$grid.calc)] <- ""
if (is.null(x$grid) & !is.null(x$grid.calc)) x$grid <- x$grid.calc
x$grid <- gsub(" ", "", x$grid)
x$grid[grep("VALUE", x$grid)] <- ""
x$grid[x$grid == "0"] <- ""
x$grid <- gsub(" +", "", x$grid)
x$grid[which(nchar(x$grid) <= 3)] <- ""
x$grid[!(substr(x$grid, 1, 1) %in% c("G", "H"))] <- ""
if ("grid.fish" %in% names(x)){
x$grid.fish <- deblank(x$grid.fish)
x$grid.fish[x$grid.fish == "0"] <- ""
ix <- which((x$grid == "") & (x$grid.fish != "") & (nchar(x$grid.fish) == 4))
x$grid[ix] <- x$grid.fish[ix]
}
if ("grid.calc" %in% names(x)){
x$grid.calc[x$grid.calc == "0"] <- ""
x$grid.calc <- gsub(" +", "", x$grid.calc)
x$grid.calc[which((nchar(x$grid.calc) <= 3) | (nchar(x$grid.calc) > 4))] <- ""
x$grid.calc[!(substr(x$grid.calc, 1, 1) %in% c("G", "H"))] <- ""
ix <- which((x$grid == "") & (x$grid.calc != ""))
x$grid[ix] <- x$grid.calc[ix]
}
# Fill-in missing grids using other recorded grids by the same vessel:
cfvs <- sort(unique(x$cfvn[x$grid == ""]))
for (i in 1:length(cfvs)){
ix <- which(x$cfvn == cfvs[i])
if (!all(x$grid[ix] == "")){
tab <- table(x$grid[ix])
tab <- tab[names(tab) != ""]
x$grid[ix[x$grid[ix] == ""]] <- names(which.max(tab))
}
}
# Re-apply depth-coordinate and range filter:
x$depth <- gulf.spatial::depth(x$longitude, x$latitude) # Determine depth from coordinates.
ix <- (x$depth < 40) | (x$depth > 200)
x$longitude[ix] <- NA
x$latitude[ix] <- NA
x$longitude[which(x$longitude < -67 | x$longitude > -59)] <- NA
x$latitude[which(x$latitude < 45 | x$latitude > 49.5)] <- NA
# Fix slip mumber:
if ((year == 2001) & ("index" %in% names(x))) x$slip.number <- x$index
x$slip.number <- gsub(" ", "", x$slip.number)
# Define date formatting function:
format.date <- function(x){
t <- table(nchar(x))
if (max(as.numeric(names(t))) == 8){
x <- paste0(substr(x,1,4), "-", substr(x,5,6), "-", substr(x,7,8))
x[nchar(x) != 10] <- ""
}
y <- x
x <- unique(x[which(!is.na(x) & (x != ""))])
ix <- match(y, x)
x <- gsub("/", "-", x)
a <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[1])))
b <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[2])))
c <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[3])))
if (any(c > 1900)){
year <- c
if (any(a > 12)){
day <- a
month <- b
}else{
day <- b
month <- a
}
}else{
year <- a
if (any(b > 12)){
day <- b
month <- c
}else{
day <- c
month <- b
}
}
date <- paste0(year, "-", formatC(month, width = 2), "-", formatC(day, width = 2))
date <- gsub(" ", "0", date)
y <- date[ix]
y[is.na(y)] <- ""
return(y)
}
# Province correction:
x$province[grep("bec", tolower(x$province))] <- "QC"
x$province[grep("que", tolower(x$province))] <- "QC"
# Soak time:
if ("ti" %in% names(x)){
x$ti <- gsub("n/a", "", x$ti)
if ("ti" %in% names(x)) x$t1 <- x$ti
}
if (is.character(x$t1)){
x$t1[x$t1 == "4,080"] <- 48
x$t1 <- round(as.numeric(x$t1))
}
if (!("soak.time" %in% names(x)) & ("t1" %in% names(x))) x$soak.time <- x$t1
if (year == 2021){
ix <- which((x$province == "QC") & (x$soak.time > 60))
x$soak.time[ix] <- x$soak.time[ix] / 10
}
if ("soak.time" %in% names(x)){
x$soak.time[x$soak.time == 0] <- NA
}
# Fix date fields:
if (year == 1999){
x$date.landed <- gsub("/99$", "/1999", x$date.landed)
x$date.caught <- gsub("/99$", "/1999", x$date.caught)
x$date.sailed <- gsub("/99$", "/1999", x$date.sailed)
}
x$date.sailed <- gsub("n/a", "", x$date.sailed)
x$date.landed <- gsub("#VALUE!", "", x$date.landed)
x$date.caught <- gsub("#VALUE!", "", x$date.caught)
x$date.sailed <- gsub("#VALUE!", "", x$date.sailed)
if (!is.null(x$date.landed)) x$date.landed <- format.date(x$date.landed)
if (!is.null(x$date.caught)) x$date.caught <- format.date(x$date.caught)
if (!is.null(x$date.sailed)) x$date.sailed <- format.date(x$date.sailed)
if ("x$licence.holder" %in% names(x)){
x$licence.holder <- gsub("[.]", " ", x$licence.holder)
x$licence.holder <- gsub(" +", " ", x$licence.holder)
x$licence.holder <- deblank(x$licence.holder)
x$licence.holder <- gsub("P\\?CH", "PECH", x$licence.holder)
x$licence.holder <- gsub("QU\\?BEC", "QUEBEC", x$licence.holder)
x$licence.holder <- gsub("GASP\\?SIE", "GASPESIE", x$licence.holder)
}
# Clean-up allocation code:
if (year < 2011) if (!("allocation.code" %in% names(x))) x$allocation.code <- x$status.number
# Clean-up vessel name:
x$vessel <- gsub(" +", " ", x$vessel)
x$vessel <- deblank(x$vessel)
# Re-order variables:
vars <- c("cfvn", "vessel.name", "zone", "province", "fleet", "licence.holder", "licence.id", "allocation.code", "slip.number", "trip.id",
"date.caught", "date.landed", "date.sailed", "longitude", "latitude", "grid", "grid.calc", "amt.landed.kg",
"trap.day", "trap.trip", "soak.time")
vars <- vars[vars %in% names(x)]
x <- gulf.utils::compress(x)
vars <- intersect(vars, names(x))
x <- x[, c(vars, setdiff(names(x), vars))]
# Delete obsolete variables:
delete <- c('sequence.jf')
x <- x[, setdiff(names(x), delete)]
x <- gulf.utils::compress(x)
# Clean up Excel codes:
for (i in 1:ncol(x)){
if (is.character(x[,i])){
x[,i] <- gsub("#VALUE!", "", x[,i])
x[,i] <- gsub("#DIV/0!", "", x[,i])
}
}
#$ Clean-up licence status:
if ("status" %in% names(x)){
x$status <- tolower(x$status)
x$status <- gsub("temp$", "temporary", x$status)
x$status <- gsub("temp.$", "temporary", x$status)
x$status <- gsub("perm$", "permanent", x$status)
x$status <- gsub("perm.$", "permanent", x$status)
x$status <- gsub("permament", "permanent", x$status)
x$status <- gsub("tempoary", "temporary", x$status)
x$status <- gsub("temporaire", "temporary", x$status)
}
return(x)
}
#' @rdname read.logbook
#' @export read.ziff.ascii
read.ziff.ascii <- function(x, convert = TRUE, as.character = FALSE, ...){
# Define variable names, formats, fill characters and descriptions:
fmt = c("cfvn", "A6",
"vessel.tonnage", "I5",
"vessel.tonnage.class", "I1",
"vessel.length", "I3",
"vessel.length.class", "I1",
"horsepower", "I5",
"horsepower.class", "I1",
"homeport", "I5",
"district", "I3",
"gulf.based", "I1",
"company", "I4",
"report", "A7",
"trip", "I2",
"date.landed", "A8",
"nafo.area", "A3",
"nafo.division", "A3",
"gear.code", "I2",
"gear.category", "I1",
"port.landed", "I5",
"port.district", "I3",
"company.code", "I4",
"community.code", "I5",
"species.group", "I1",
"species.code", "I3",
"species.size", "I1",
"species.form", "I2",
"species.grade", "A1",
"measurement.unit", "A1",
"landed.quantity", "I9",
"landed.value", "F9.2",
"round.weight", "I9",
"effort.flag", "A1",
"main.species.caught", "A3",
"main.species.sought", "A3",
"mile200", "I1",
"trip.fraction", "F3.1",
"days.at.sea", "F3.1",
"days.on.ground", "F3.1",
"days.fished", "F4.2",
"hours.fished", "F4.1",
"gear.amount", "I4",
"date.caught", "A8",
"depth.code", "A1",
"region.id", "A1",
"latitude", "F8.4",
"longitude", "F8.4",
"comment", "A44")
# Read file:
y <- utils::read.fortran(file = x, format = fmt[seq(2,length(fmt),2)], comment.char = "")
y <- gulf.utils::recode(y)
names(y) <- fmt[seq(1,length(fmt),2)]
# Remove dots from empty integer data fields:
if (!as.character){
ix <- which(substr(fmt[seq(2,length(fmt),2)],1,1) == "I")
for (i in 1:length(ix)){
y[, ix[i]] <- gsub(".", " ", y[, ix[i]], fixed = TRUE)
}
}
# Convert to user-friendly format:
if (convert & !as.character){
names(y) <- gsub("nafo.area", "nafo.subdivision", names(y))
y$longitude[y$longitude == 0] <- NA
y$latitude[y$latitude == 0] <- NA
y$nafo.division <- gsub(" ", "", y$nafo.division, fixed = TRUE)
y$nafo.subdivision <- gsub(" ", "", y$nafo.subdivision, fixed = TRUE)
y$nafo.division <- toupper(y$nafo.division)
y$nafo.subdivision <- paste0(toupper(substr(y$nafo.subdivision, 1, nchar(y$nafo.subdivision)-1)),
tolower(substr(y$nafo.subdivision, nchar(y$nafo.subdivision), nchar(y$nafo.subdivision))))
y$nafo.division[y$nafo.division == ""] <- NA
y$nafo.subdivision[y$nafo.subdivision == ""] <- NA
#y$gear.class <- gear.str(y$gear.code, input = "stacac", output = "alpha")
y$gear.class <- ""
y$year <- as.numeric(substr(y$date.landed, 1, 4))
y$year.landed <- y$year
y$month.landed <- as.numeric(substr(y$date.landed, 5, 6))
y$day.landed <- as.numeric(substr(y$date.landed, 7, 8))
}
return(y)
}
TobieSurette/gulf.data documentation built on Jan. 19, 2025, 7:50 p.m.
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Defines functions read.ziff.ascii read.sc.logbook read.ziff read.logbook
Documented in read.logbook read.sc.logbook read.ziff read.ziff.ascii
#' @title Load Fishery Logbook Data
#'
#' @rdname read.logbook
#'
#' @description Function to load logbook and slip landings data from the southern Gulf of Saint Lawrence fisheries.
#'
#' @param x Fishery year or file name.
#' @param year Fishery year.
#' @param file File name to be loaded. File format is assumed to be comma-separated (i.e. .csv).
#' @param path File path containing comma-separated fishery logbook files (i.e. .csv).
#' @param echo Logical value specifying whether to report files to the R console as they're being read.
#' @param ... Not used.
#' @export read.logbook
read.logbook <- function(x, species = "snow crab", source = "r", ...){
if (!missing(species)){
if (is.numeric(species)) species <- tolower(species(species)[1])
species <- match.arg(tolower(species), "snow crab")
}
# Read data:
z <- NULL
if (species == "snow crab"){
z <- read.sc.logbook(x, ...)
}else{
z <- read.ziff(x, source = source, ...)
}
class(z) <- c("logbook", class(z))
return(z)
}
#' @rdname read.logbook
#' @export read.ziff
read.ziff <- function(x, file, echo = TRUE, ...){
# Find data files:
files <- NULL
if (missing(x) & missing(file)) files <- locate.ziff(x, ...)
if (!missing(x)) if (is.character(x)) files <- x
if (!missing(file)) files <- file
if (length(files) == 0) return(NULL)
# Read files:
r <- NULL
for (i in 1:length(files)){
if (echo) cat(paste0("Reading : '", files[i], "'\n"))
type <- tolower(unlist(lapply(strsplit(files[i], "[.]"), function(x) x[length(x)])))
if (type == "new"){
read.ziff.ascii(files[i], ...)
}
if (type %in% c("rda", "rdata")){
load(files[i])
}
r <- rbind(r, x)
}
return(r)
}
#' @rdname read.logbook
#' @export read.sc.logbook
read.sc.logbook <- function(x, year, file, ...){
if (!missing(x)){
if (is.numeric(x) & missing(file)) year <- x
if (is.character(x) & missing(file)) file <- x
}
# Define data path for 'csv' files:
path <- options("gulf.path")[[1]]$snow.crab$logbook
if (!missing(year) & missing(file)) file <- paste0(path, "logbook ", year, ".csv")
# Load file and format variable names:
x <- read.csv(file, skip = 1, header = FALSE)
x <- gulf.utils::recode(x)
# Field name fixes:
fields <- readLines(file, n = 1)
fields <- tolower(strsplit(fields, ",")[[1]])
fields <- gsub("^[ #]+", "", fields)
fields <- gsub(" ", ".", fields)
fields <- gsub("[.]+", ".", fields)
fields <- gsub("[_]+", ".", fields)
fields <- gsub("lon.dec", "longitude", fields)
fields <- gsub("lat.dec", "latitude", fields)
fields <- gsub("lat.pas.modifier", "lat.str", fields)
fields <- gsub("long.pas.modifier", "lon.str", fields)
fields <- gsub("traps", "trap", fields)
fields <- gsub("grid[.]good", "grid", fields)
fields <- gsub("[.]$", "", fields)
fields <- gsub("^x[.]", "", fields)
fields[fields == "prov"] <- "province"
fields <- gsub("^pue", "cpue", fields)
if (sum(fields == "grid") > 1) fields[grep("grid", fields)[2]] <- "grid.calc"
fields[fields == "slip"] <- "slip.number"
fields[fields == "no.de.formulaire"] <- "slip.number"
fields <- gsub("^cfv$", "cfvn", fields)
fields <- gsub("^vrn$", "cfvn", fields)
if (!("zone" %in% fields) & ("zone.corrected" %in% fields)) fields <- gsub("zone.corrected", "zone", fields)
fields <- gsub("list[.]sub[.]fleet", "fleet", fields)
fields <- gsub("list[.]quota", "allocation.code", fields)
fields <- gsub("#", "number", fields)
fields <- gsub("[(]kg[)]", "kg", fields)
fields <- gsub("[.]-[.]", ".", fields)
fields <- gsub("zone.de.gestion", "zone", fields)
fields <- gsub("numero.groupe.contingent", "allocation", fields)
fields <- gsub("numero.formulaire", "slip.number", fields)
fields <- gsub("date.debarquement", "date.landed", fields)
fields <- gsub("date.capture", "date.caught", fields)
fields <- gsub("nom.intervenant", "licence.holder", fields)
fields <- gsub("vessel.name", "vessel", fields)
fields <- gsub("boat.name", "vessel", fields)
fields <- gsub("boat$", "vessel", fields)
fields <- gsub("slip.qty.day.kg", "slip.prop.day", fields)
fields <- gsub("slip.qty.day", "slip.prop.day", fields)
fields <- gsub("effort.trip", "trap.trip", fields)
fields <- gsub("effort.day", "trap.day", fields)
fields <- gsub("slip.num$", "slip.number", fields)
fields <- gsub("dale.landed", "date.landed", fields)
fields <- gsub("area", "zone", fields)
fields <- gsub("long.dec", "longitude", fields)
fields <- gsub("t[.]i", "ti", fields)
fields <- gsub("[.][(]h[])]", "", fields)
fields <- gsub("[.]/[.]", ".", fields)
fields <- gsub("-[.]", ".", fields)
fields <- gsub("^landed.day", "slip.prop.day", fields)
fields <- gsub("^estimate.kg", "estimate.trip.kg", fields)
fields <- gsub("^est.trip.kg", "estimate.trip.kg", fields)
fields <- gsub("^est.trip$", "estimate.trip.kg", fields)
fields <- gsub("^qty.est.trip$", "estimate.trip.kg", fields)
fields <- gsub("^amt.landed", "landed.trip.kg", fields)
fields <- gsub("^landed.trip$", "landed.trip.kg", fields)
fields <- gsub("^slip.qty.trip$", "landed.trip.kg", fields)
fields <- gsub("^slip.qty.trip.kg$", "landed.trip.kg", fields)
names(x) <- fields
if (length(which(is.na(names(x)))) > 0) x <- x[, -which(is.na(names(x)))]
# Convert numeric variables:
if (!"latitude" %in% names(x)) names(x) <- gsub("declat", "latitude", names(x))
if (!"longitude" %in% names(x)) names(x) <- gsub("declon", "longitude", names(x))
vars <- c("longitude", "latitude")
for (i in 1:length(vars)) x[, vars[i]] <- as.numeric(x[, vars[i]])
# Fix fishing zone:
x$zone[x$zone == "12.00"] <- "12"
x$zone <- gsub("*", "", x$zone, fixed = TRUE)
x$zone <- toupper(x$zone)
x$zone[x$zone == "E"] <- "12E"
x$zone[x$zone == "F"] <- "12F"
# Coordinate range checks:
x$longitude <- -abs(x$longitude)
x$longitude[which(x$longitude < -67 | x$longitude > -59)] <- NA
x$latitude[which(x$latitude < 45 | x$latitude > 49.5)] <- NA
# Depth-coordinate filter:
x$depth <- gulf.spatial::depth(x$longitude, x$latitude) # Determine depth from coordinates.
ix <- (x$depth < 40) | (x$depth > 200)
x$longitude[ix] <- NA
x$latitude[ix] <- NA
# Trip landings variables:
x$estimate.trip.kg <- as.numeric(x$estimate.trip.kg)
x$landed.trip.kg <- as.numeric(x$landed.trip.kg)
# Effort corrections:
x$trap.day <- as.numeric(gsub(",", "", x$trap.day))
x$slip.prop.day[grep("VALUE", x$slip.prop.day)] <- ""
x$slip.prop.day <- as.numeric(x$slip.prop.day)
# Coordinate fixes:
if ("lon.str" %in% names(x)){
ix <- which(is.na(x$longitude) & !is.na(x$lon.str) & (floor(log10(x$lon.str)) == 10))
x$longitude[ix] <- -abs(x$lon.str[ix] / 10^9)
ix <- which(is.na(x$longitude) & !is.na(x$lon.str) & (floor(log10(x$lon.str)) == 5))
x$longitude[ix] <- -gulf.spatial::dmm2deg(x$lon.str[ix] / 10^2)
}
if ("lat.str" %in% names(x)){
ix <- which(is.na(x$latitude) & !is.na(x$lat.str) & (floor(log10(x$lat.str)) == 10))
x$latitude[ix] <- abs(x$lat.str[ix] / 10^9)
ix <- which(is.na(x$latitude) & !is.na(x$lat.str) & (floor(log10(x$lat.str)) == 5))
x$latitude[ix] <- gulf.spatial::dmm2deg(x$lat.str[ix] / 10^2)
}
# Loran C conversions:
if (all(c("lon.str", "lat.str") %in% names(x))){
ix <- which((is.na(x$longitude) | is.na(x$latitude)) & (!is.na(x$lon.str) & !is.na(x$lat.str)))
ix <- ix[x$lon.str[ix] < 35000]
if (length(ix) > 0){
tmp <- gulf.spatial::loran2deg(x$lat.str[ix], x$lon.str[ix])
x$longitude[ix] <- -abs(tmp$long)
x$latitude[ix] <- tmp$lat
}
}
# Fix grid names:
if (!("grid.calc" %in% names(x))) x$grid.calc <- x$grid
x$grid.calc[grep("VALUE", x$grid.calc)] <- ""
if (is.null(x$grid) & !is.null(x$grid.calc)) x$grid <- x$grid.calc
x$grid <- gsub(" ", "", x$grid)
x$grid[grep("VALUE", x$grid)] <- ""
x$grid[x$grid == "0"] <- ""
x$grid <- gsub(" +", "", x$grid)
x$grid[which(nchar(x$grid) <= 3)] <- ""
x$grid[!(substr(x$grid, 1, 1) %in% c("G", "H"))] <- ""
if ("grid.fish" %in% names(x)){
x$grid.fish <- deblank(x$grid.fish)
x$grid.fish[x$grid.fish == "0"] <- ""
ix <- which((x$grid == "") & (x$grid.fish != "") & (nchar(x$grid.fish) == 4))
x$grid[ix] <- x$grid.fish[ix]
}
if ("grid.calc" %in% names(x)){
x$grid.calc[x$grid.calc == "0"] <- ""
x$grid.calc <- gsub(" +", "", x$grid.calc)
x$grid.calc[which((nchar(x$grid.calc) <= 3) | (nchar(x$grid.calc) > 4))] <- ""
x$grid.calc[!(substr(x$grid.calc, 1, 1) %in% c("G", "H"))] <- ""
ix <- which((x$grid == "") & (x$grid.calc != ""))
x$grid[ix] <- x$grid.calc[ix]
}
# Fill-in missing grids using other recorded grids by the same vessel:
cfvs <- sort(unique(x$cfvn[x$grid == ""]))
for (i in 1:length(cfvs)){
ix <- which(x$cfvn == cfvs[i])
if (!all(x$grid[ix] == "")){
tab <- table(x$grid[ix])
tab <- tab[names(tab) != ""]
x$grid[ix[x$grid[ix] == ""]] <- names(which.max(tab))
}
}
# Re-apply depth-coordinate and range filter:
x$depth <- gulf.spatial::depth(x$longitude, x$latitude) # Determine depth from coordinates.
ix <- (x$depth < 40) | (x$depth > 200)
x$longitude[ix] <- NA
x$latitude[ix] <- NA
x$longitude[which(x$longitude < -67 | x$longitude > -59)] <- NA
x$latitude[which(x$latitude < 45 | x$latitude > 49.5)] <- NA
# Fix slip mumber:
if ((year == 2001) & ("index" %in% names(x))) x$slip.number <- x$index
x$slip.number <- gsub(" ", "", x$slip.number)
# Define date formatting function:
format.date <- function(x){
t <- table(nchar(x))
if (max(as.numeric(names(t))) == 8){
x <- paste0(substr(x,1,4), "-", substr(x,5,6), "-", substr(x,7,8))
x[nchar(x) != 10] <- ""
}
y <- x
x <- unique(x[which(!is.na(x) & (x != ""))])
ix <- match(y, x)
x <- gsub("/", "-", x)
a <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[1])))
b <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[2])))
c <- as.numeric(unlist(lapply(strsplit(x, "-"), function(x) x[3])))
if (any(c > 1900)){
year <- c
if (any(a > 12)){
day <- a
month <- b
}else{
day <- b
month <- a
}
}else{
year <- a
if (any(b > 12)){
day <- b
month <- c
}else{
day <- c
month <- b
}
}
date <- paste0(year, "-", formatC(month, width = 2), "-", formatC(day, width = 2))
date <- gsub(" ", "0", date)
y <- date[ix]
y[is.na(y)] <- ""
return(y)
}
# Province correction:
x$province[grep("bec", tolower(x$province))] <- "QC"
x$province[grep("que", tolower(x$province))] <- "QC"
# Soak time:
if ("ti" %in% names(x)){
x$ti <- gsub("n/a", "", x$ti)
if ("ti" %in% names(x)) x$t1 <- x$ti
}
if (is.character(x$t1)){
x$t1[x$t1 == "4,080"] <- 48
x$t1 <- round(as.numeric(x$t1))
}
if (!("soak.time" %in% names(x)) & ("t1" %in% names(x))) x$soak.time <- x$t1
if (year == 2021){
ix <- which((x$province == "QC") & (x$soak.time > 60))
x$soak.time[ix] <- x$soak.time[ix] / 10
}
if ("soak.time" %in% names(x)){
x$soak.time[x$soak.time == 0] <- NA
}
# Fix date fields:
if (year == 1999){
x$date.landed <- gsub("/99$", "/1999", x$date.landed)
x$date.caught <- gsub("/99$", "/1999", x$date.caught)
x$date.sailed <- gsub("/99$", "/1999", x$date.sailed)
}
x$date.sailed <- gsub("n/a", "", x$date.sailed)
x$date.landed <- gsub("#VALUE!", "", x$date.landed)
x$date.caught <- gsub("#VALUE!", "", x$date.caught)
x$date.sailed <- gsub("#VALUE!", "", x$date.sailed)
if (!is.null(x$date.landed)) x$date.landed <- format.date(x$date.landed)
if (!is.null(x$date.caught)) x$date.caught <- format.date(x$date.caught)
if (!is.null(x$date.sailed)) x$date.sailed <- format.date(x$date.sailed)
if ("x$licence.holder" %in% names(x)){
x$licence.holder <- gsub("[.]", " ", x$licence.holder)
x$licence.holder <- gsub(" +", " ", x$licence.holder)
x$licence.holder <- deblank(x$licence.holder)
x$licence.holder <- gsub("P\\?CH", "PECH", x$licence.holder)
x$licence.holder <- gsub("QU\\?BEC", "QUEBEC", x$licence.holder)
x$licence.holder <- gsub("GASP\\?SIE", "GASPESIE", x$licence.holder)
}
# Clean-up allocation code:
if (year < 2011) if (!("allocation.code" %in% names(x))) x$allocation.code <- x$status.number
# Clean-up vessel name:
x$vessel <- gsub(" +", " ", x$vessel)
x$vessel <- deblank(x$vessel)
# Re-order variables:
vars <- c("cfvn", "vessel.name", "zone", "province", "fleet", "licence.holder", "licence.id", "allocation.code", "slip.number", "trip.id",
"date.caught", "date.landed", "date.sailed", "longitude", "latitude", "grid", "grid.calc", "amt.landed.kg",
"trap.day", "trap.trip", "soak.time")
vars <- vars[vars %in% names(x)]
x <- gulf.utils::compress(x)
vars <- intersect(vars, names(x))
x <- x[, c(vars, setdiff(names(x), vars))]
# Delete obsolete variables:
delete <- c('sequence.jf')
x <- x[, setdiff(names(x), delete)]
x <- gulf.utils::compress(x)
# Clean up Excel codes:
for (i in 1:ncol(x)){
if (is.character(x[,i])){
x[,i] <- gsub("#VALUE!", "", x[,i])
x[,i] <- gsub("#DIV/0!", "", x[,i])
}
}
#$ Clean-up licence status:
if ("status" %in% names(x)){
x$status <- tolower(x$status)
x$status <- gsub("temp$", "temporary", x$status)
x$status <- gsub("temp.$", "temporary", x$status)
x$status <- gsub("perm$", "permanent", x$status)
x$status <- gsub("perm.$", "permanent", x$status)
x$status <- gsub("permament", "permanent", x$status)
x$status <- gsub("tempoary", "temporary", x$status)
x$status <- gsub("temporaire", "temporary", x$status)
}
return(x)
}
#' @rdname read.logbook
#' @export read.ziff.ascii
read.ziff.ascii <- function(x, convert = TRUE, as.character = FALSE, ...){
# Define variable names, formats, fill characters and descriptions:
fmt = c("cfvn", "A6",
"vessel.tonnage", "I5",
"vessel.tonnage.class", "I1",
"vessel.length", "I3",
"vessel.length.class", "I1",
"horsepower", "I5",
"horsepower.class", "I1",
"homeport", "I5",
"district", "I3",
"gulf.based", "I1",
"company", "I4",
"report", "A7",
"trip", "I2",
"date.landed", "A8",
"nafo.area", "A3",
"nafo.division", "A3",
"gear.code", "I2",
"gear.category", "I1",
"port.landed", "I5",
"port.district", "I3",
"company.code", "I4",
"community.code", "I5",
"species.group", "I1",
"species.code", "I3",
"species.size", "I1",
"species.form", "I2",
"species.grade", "A1",
"measurement.unit", "A1",
"landed.quantity", "I9",
"landed.value", "F9.2",
"round.weight", "I9",
"effort.flag", "A1",
"main.species.caught", "A3",
"main.species.sought", "A3",
"mile200", "I1",
"trip.fraction", "F3.1",
"days.at.sea", "F3.1",
"days.on.ground", "F3.1",
"days.fished", "F4.2",
"hours.fished", "F4.1",
"gear.amount", "I4",
"date.caught", "A8",
"depth.code", "A1",
"region.id", "A1",
"latitude", "F8.4",
"longitude", "F8.4",
"comment", "A44")
# Read file:
y <- utils::read.fortran(file = x, format = fmt[seq(2,length(fmt),2)], comment.char = "")
y <- gulf.utils::recode(y)
names(y) <- fmt[seq(1,length(fmt),2)]
# Remove dots from empty integer data fields:
if (!as.character){
ix <- which(substr(fmt[seq(2,length(fmt),2)],1,1) == "I")
for (i in 1:length(ix)){
y[, ix[i]] <- gsub(".", " ", y[, ix[i]], fixed = TRUE)
}
}
# Convert to user-friendly format:
if (convert & !as.character){
names(y) <- gsub("nafo.area", "nafo.subdivision", names(y))
y$longitude[y$longitude == 0] <- NA
y$latitude[y$latitude == 0] <- NA
y$nafo.division <- gsub(" ", "", y$nafo.division, fixed = TRUE)
y$nafo.subdivision <- gsub(" ", "", y$nafo.subdivision, fixed = TRUE)
y$nafo.division <- toupper(y$nafo.division)
y$nafo.subdivision <- paste0(toupper(substr(y$nafo.subdivision, 1, nchar(y$nafo.subdivision)-1)),
tolower(substr(y$nafo.subdivision, nchar(y$nafo.subdivision), nchar(y$nafo.subdivision))))
y$nafo.division[y$nafo.division == ""] <- NA
y$nafo.subdivision[y$nafo.subdivision == ""] <- NA
#y$gear.class <- gear.str(y$gear.code, input = "stacac", output = "alpha")
y$gear.class <- ""
y$year <- as.numeric(substr(y$date.landed, 1, 4))
y$year.landed <- y$year
y$month.landed <- as.numeric(substr(y$date.landed, 5, 6))
y$day.landed <- as.numeric(substr(y$date.landed, 7, 8))
}
return(y)
}
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