# stf - prepare an object for a Short Term Forecast
# FLAssess/R/stf.R
# Copyright 2003-2008 FLR Team. Distributed under the GPL 2 or later
# Maintainer: Finlay Scott, Cefas & Robert Scott, JRC
# $Id$
setGeneric("stf", function(object,...)
standardGeneric("stf"))
## stf(FLStock) {{{
setMethod('stf', signature(object='FLStock'),
function(object, nyears=3, wts.nyears=3, fbar.nyears=wts.nyears, f.rescale=FALSE,
arith.mean=TRUE, na.rm=TRUE, end=dims(object)$maxyear + nyears, disc.nyears=wts.nyears)
{
dims <- dims(object)
# check nyears and end match
if(missing(nyears))
nyears <- as.numeric(end) - dims$maxyear
else if(dims$maxyear + nyears != end)
stop("'nyears' and 'end' do not match: ", dims$maxyear + nyears, " vs. ", end)
# years
years <- ac((dims$maxyear+1):end)
wts.years <- ac(seq(dims$maxyear-wts.nyears+1, dims$maxyear))
disc.years <- ac(seq(dims$maxyear-disc.nyears+1, dims$maxyear))
fbar.years <- ac(seq(dims$maxyear-fbar.nyears+1, dims$maxyear))
fbar.ages <- ac(range(object, 'minfbar'):range(object, 'maxfbar'))
# arith or geometric
if(arith.mean)
fmean <- mean
else
fmean <- function(x) exp(mean(log(x)))
# window object
res <- window(object, end=end)
# average slots
# *.wt, mat, m and *.spwn as average over wts.years
for (i in c('catch.wt', 'landings.wt', 'discards.wt', 'stock.wt', 'mat', 'm', 'harvest.spwn', 'm.spwn')){
flq<- apply(slot(res, i)[,wts.years], c(1,3:6),fmean, na.rm=na.rm)
for (j in years)
slot(res, i)[,j] <-flq
}
# landings.n and discards.n as proportions of disc.years
slot(res, "discards.n")[, years] <- apply(slot(res, "discards.n")[, disc.years] /
slot(res, "catch.n")[, disc.years], c(1, 3:6), fmean, na.rm=TRUE)
slot(res, "discards.n")[is.na(slot(res, "discards.n"))] <- 0
slot(res, "landings.n")[, years] <- 1 - slot(res, "discards.n")[, years]
# harvest as mean over fbar.nyears
f <-apply(slot(res, 'harvest')[,fbar.years], c(1,3:6), fmean, na.rm=na.rm)
for (i in years)
slot(res, 'harvest')[,i] <- f
# f.rescale
if(f.rescale == TRUE)
{
# mean f over fbar ages and years
fbar <- mean(apply(slot(res, 'harvest')[fbar.ages, fbar.years], c(2:6), mean,
na.rm=na.rm))
# fbar for last REAL year
lastfbar <- apply(slot(res, 'harvest')[fbar.ages, ac(dims$maxyear)], 3:6, mean,
na.rm=na.rm)
# divide by fbar and multiply by lastfbar
slot(res, 'harvest')[, years] <- sweep(slot(res, 'harvest')[, years], 3:6, fbar, '/')
slot(res, 'harvest')[, years] <- sweep(slot(res, 'harvest')[, years], 3:6, lastfbar, '*')
}
return(res)
}
) # }}}
## stf(FLBiol) {{{
setMethod('stf', signature(object='FLBiol'),
function(object, nyears=3, wts.nyears=3, arith.mean=TRUE, na.rm=TRUE,
end=dims(object)$maxyear + nyears)
{
dims <- dims(object)
# check nyears and end match
if(missing(nyears))
nyears <- as.numeric(end) - dims$maxyear
else if(dims$maxyear + nyears != end)
stop("'nyears' and 'end' do not match: ", dims$maxyear + nyears, " vs. ", end)
# years
years <- ac((dims$maxyear+1):end)
wts.years <- ac(seq(dims$maxyear-wts.nyears+1, dims$maxyear))
# arith or geometric
if(arith.mean)
fmean <- mean
else
fmean <- function(x) exp(mean(log(x)))
# window object
res <- window(object, end=end)
# average slots
# *.wt, mat, m and *.spwn as average over wts.years
for (i in c('wt', 'fec', 'm', 'spwn'))
slot(res, i)[,years] <- apply(slot(res, i)[,wts.years], c(1,3:6), fmean, na.rm=TRUE)
return(res)
}
) # }}}
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