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# io.FLStock.R - read and write assessment input files into an FLStock
# Copyright 2003-2008 FLR Team. Distributed under the GPL 2 or later
# Maintainer: Iago Mosqueira, JRC
# $Id: io.FLStock.R 1022 2011-06-10 11:07:33Z imosqueira $
# readFLStock {{{
readFLStock <- function(file, type = "VPA", name, desc = paste("Imported from a",
type, "file. (", file, "). ", date()), m = 0.2, quant="age", quiet=TRUE,
no.discards=FALSE, harvest.units, sep="")
{
ow <- options()$warn
options(warn = -1)
on.exit(options(warn = ow))
res <- switch(type,
VPA = readVPA(file, quiet=quiet, sep=sep),
Adapt = readAdaptFile(file,m),
PA = readPAFile(file),
CSA = readCSAFile(file),
stop("type must be either 'VPA', 'Adapt', 'PA' or 'CSA'!"))
Mat <- res@stock.wt
Mat[, , , , ] <- NA
Dim <- dim(Mat)
Mat0 <- Mat
Mat0[, , , , ] <- 0
if (is.null(res@landings.n) || !all(dim(res@landings.n) == Dim))
res@landings.n <- Mat
if (is.null(res@landings.wt) || !all(dim(res@landings.wt) == Dim))
res@landings.wt <- Mat
if (is.null(res@catch.n) || !all(dim(res@catch.n) == Dim))
res@catch.n <- Mat
if (is.null(res@catch.wt) || !all(dim(res@catch.wt) == Dim))
res@catch.wt <- Mat
if (is.null(res@discards.n) || !all(dim(res@discards.n) == Dim))
res@discards.n <- Mat
if (is.null(res@discards.wt) || !all(dim(res@discards.wt) == Dim))
res@discards.wt <- Mat
if (is.null(res@m) || !all(dim(res@m) == Dim))
res@m <- Mat
if (is.null(res@stock.wt) || !all(dim(res@stock.wt) == Dim))
res@stock.wt <- Mat
if (is.null(res@mat) || !all(dim(res@mat) == Dim))
res@mat <- Mat
if (is.null(res@stock.n) || !all(dim(res@stock.n) == Dim))
res@stock.n <- Mat
if (is.null(res@harvest) || !all(dim(res@harvest) == Dim))
res@harvest <- Mat
if (is.null(res@harvest.spwn) || !all(dim(res@harvest.spwn)== Dim))
res@harvest.spwn<- Mat
if (is.null(res@m.spwn) || !all(dim(res@m.spwn) == Dim))
res@m.spwn <- Mat
Mat <- Mat[1, , , , ]
if (is.null(res@catch) || !all(dim(res@catch) == dim(Mat)))
res@catch <- Mat
if (is.null(res@discards) || !all(dim(res@discards) == dim(Mat)))
res@discards <- Mat
if (is.null(res@landings) || !all(dim(res@landings) == dim(Mat)))
res@landings <- Mat
pars <- dims(res@stock.wt)
res@range <- unlist(list(min = pars$min, max = pars$max,
plusgroup = NA, minyear = pars$minyear, maxyear = pars$maxyear,minfbar = pars$min, maxfbar = pars$max))
if (length(res@name) < 1 | !missing(name))
res@name <- as.character(name)
if (!is.null(desc))
res@desc <- as.character(desc)
names. <- names(getSlots(class(res))[getSlots(class(res))=="FLQuant"])
for (s. in names.) {
quant(slot(res, s.)) <- quant
}
stock(res) <- computeStock(res)
if(no.discards)
{
discards(res) <- 0
discards.n(res) <- 0
discards.wt(res) <- 0
catch(res) <- computeCatch(res, 'all')
}
# if(type=="VPA") units(harvest(res)) <- "f"
# if(type=="Adapt") units(harvest(res)) <- "f"
# if(type=="PA") units(harvest(res)) <- "f"
# if(type=="CSA") units(harvest(res)) <- "hr"
if(missing(harvest.units)) harvest.units <- switch(type, VPA = "f", Adapt = "f", PA = "f", CSA = "hr")
units(harvest(res)) <- harvest.units
return(res)
} # }}}
# writeFLStock {{{
writeFLStock <- function(FLStock, output.file=FLStock@name, type="VPA") {
if (!inherits(FLStock, "FLStock"))
stop("FLStock must be an 'FLStock' object!")
switch(type,
"VPA" = writeVPA(FLStock, output.file),
stop("type must be 'VPA'!"))
} # }}}
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