Add @name slot to FLFishery and FLCatches in the example data.

[pdolder]

Self explanatory.

@John-Ball-Cefas also mentioned that the C++ conversions to a list were stripping the @name slot, so need to investigate if this can be retained when converting back to FLFishery objects.

[John-Ball-Cefas]

It was stfmixme fix bellow i added om$flts[[x]]@name <- x back to the end of the loop after it gets lost in the c++

stfMixME_Matt_fleetnam_fix <- function (om, method = "yearMeans", nyears = 3, wts.nyears = 3,
sel.nyears = 3, qs.nyears = 3, verbose = TRUE, seed = NULL)
{
library(MixME)
ydata <- as.numeric(tail(dimnames(om$stks[[1]])$year, 1))
ni <- dim(om$stks[[1]])[6]
year_wts <- tail(dimnames(om$stks[[1]])$year, wts.nyears)
year_sel <- tail(dimnames(om$stks[[1]])$year, sel.nyears)
year_qs <- tail(dimnames(om$stks[[1]])$year, qs.nyears)
year_proj <- ac((ydata + 1):(ydata + nyears))
if (method == "resample") {
set.seed(seed)
wts_samples <- sample(x = year_wts, size = nyears *
ni, replace = TRUE)
sel_samples <- sample(x = year_sel, size = nyears *
ni, replace = TRUE)
qs_samples <- sample(x = year_qs, size = nyears * ni,
replace = TRUE)
}
else {
wts_samples <- NULL
sel_samples <- NULL
qs_samples <- NULL
}
for (x in names(om$stks)) {
if (verbose)
cat(x, "; ")
om$stks[[x]] <- FLasher::stf(om$stks[[x]], nyears = nyears,
wts.nyears = wts.nyears)
if (class(om$stks[[x]]) == "FLStock" & method == "resample") {
om$stks[[x]]@catch.wt[, year_proj] <- MixME:::stfQuant(catch.wt(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
om$stks[[x]]@stock.wt[, year_proj] <- MixME:::stfQuant(stock.wt(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
om$stks[[x]]@landings.wt[, year_proj] <- MixME:::stfQuant(landings.wt(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
om$stks[[x]]@discards.wt[, year_proj] <- MixME:::stfQuant(discards.wt(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
om$stks[[x]]@m[, year_proj] <- MixME:::stfQuant(FLCore::m(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
om$stks[[x]]@mat[, year_proj] <- MixME:::stfQuant(FLCore::mat(om$stks[[x]]),
method = method, samples = wts_samples, ni = ni)
}
if (class(om$stks[[x]]) == "FLBiol") {
if (method == "resample") {
om$stks[[x]]@wt[, year_proj] <- MixME:::stfQuant(FLCore::wt(om$stks[[x]])[,
year_wts], method = method, samples = wts_samples,
ni = ni)
om$stks[[x]]@m[, year_proj] <- MixME:::stfQuant(FLCore::m(om$stks[[x]])[,
year_wts], method = method, samples = wts_samples,
ni = ni)
}
mat(om$stks[[x]])[, year_proj] <- MixME:::stfQuant(mat(om$stks[[x]])[,
year_wts], method = method, samples = wts_samples,
ni = ni)
fec(om$stks[[x]])[, year_proj] <- MixME:::stfQuant(fec(om$stks[[x]])[,
year_wts], method = method, samples = wts_samples,
ni = ni)
}
}
for (x in names(om$flts)) {
if (verbose)
cat("\n", x, "\n")
fishery <- om$flts[[x]]
stknames <- names(fishery)
fishery <- window(fishery, end = ydata + nyears)
om$flts[[x]] <- FLFishery::FLFishery(lapply(names(fishery),
function(y) {
if (verbose)
cat(y, " ; ")
stkflt_ext <- window(fishery[[y]], end = ydata +
nyears)
FLFishery::landings.wt(stkflt_ext)[, year_proj] <- MixME:::stfQuant(landings.wt(fishery[[y]])[,
year_wts], method = method, samples = wts_samples,
ni = ni, ignoreZero = TRUE)
FLFishery::discards.wt(stkflt_ext)[, year_proj] <- MixME:::stfQuant(discards.wt(fishery[[y]])[,
year_wts], method = method, samples = wts_samples,
ni = ni, ignoreZero = TRUE)
FLFishery::catch.sel(stkflt_ext)[, year_proj] <- MixME:::stfQuant(catch.sel(fishery[[y]])[,
year_sel], method = method, samples = sel_samples,
ni = ni)
landfraction <- MixME:::stfQuant(FLCore::landings.n(fishery[[y]])[,
year_wts]/FLCore::catch.n(fishery[[y]])[,
year_wts], method = method, samples = wts_samples,
ni = ni)
landfraction[is.na(landfraction)] <- 0
FLCore::landings.n(stkflt_ext)[, year_proj] <- landfraction
FLCore::discards.n(stkflt_ext)[, year_proj] <- 1 -
landfraction
if (dims(stkflt_ext)$iter > 1 & (dims(catch.q(stkflt_ext))$iter !=
dims(stkflt_ext)$iter)) {
catch.q(stkflt_ext) <- propagate(catch.q(stkflt_ext),
iter = dims(stkflt_ext)$iter)
}
if (dim(catch.q(stkflt_ext))["year"] != dims(stkflt_ext)$year) {
dnames <- dimnames(fishery[[y]]@catch.q)
posyr <- match("year", names(fishery[[y]]@catch.q))
dnames[[posyr]] <- dimnames(stkflt_ext)$year
catchq_ext <- FLPar(0, dimnames = dnames,
units = "NA")
catchq_ext[, dimnames(catch.q(stkflt_ext))$year] <- catch.q(stkflt_ext)
catch.q(stkflt_ext) <- catchq_ext
}
if (method == "yearMeans") {
catchq_new <- apply(catch.q(stkflt_ext)["alpha",
year_sel], c(1, 3), mean)
for (yy in year_proj) {
catch.q(stkflt_ext)["alpha", yy] <- catchq_new
}
}
if (method == "resample") {
catchq_new <- lapply(1:ni, function(x) {
xx <- ((x - 1) * (length(sel_samples)/ni)) +
(1:(length(sel_samples)/ni))
dnames <- dimnames(catch.q(stkflt_ext))
dnames$year <- sel_samples[xx]
dnames$iter <- x
posv <- c(match("year", names(catch.q(stkflt_ext))),
match("area", names(catch.q(stkflt_ext))),
match("iter", names(catch.q(stkflt_ext))))
posv <- posv[!is.na(posv)]
names(dnames) <- c("i", c("i", "j", "k",
"l", "m", "n")[posv])
return(c(do.call("[", c(list(x = catch.q(stkflt_ext)),
dnames))))
})
dnames <- dimnames(catch.q(stkflt_ext))
dnames$year <- year_proj
posv <- c(match("year", names(catch.q(stkflt_ext))),
match("area", names(catch.q(stkflt_ext))),
match("iter", names(catch.q(stkflt_ext))))
posv <- posv[!is.na(posv)]
names(dnames) <- c("i", c("i", "j", "k", "l",
"m", "n")[posv])
catch.q(stkflt_ext) <- do.call("[<-", c(list(x = catch.q(stkflt_ext),
value = unlist(catchq_new)), dnames))
}
if (!is.null(attr(fishery[[y]], "quotashare"))) {
if (dims(stkflt_ext)$iter > 1 & (dims(attr(fishery[[y]],
"quotashare"))$iter != dims(stkflt_ext)$iter)) {
attr(fishery[[y]], "quotashare") <- propagate(attr(fishery[[y]],
"quotashare"), iter = dims(stkflt_ext)$iter)
}
attr(stkflt_ext, "quotashare") <- window(attr(fishery[[y]],
"quotashare"), end = (ydata + nyears))
attr(stkflt_ext, "quotashare")[, year_proj] <- MixME:::stfQuant(attr(fishery[[y]],
"quotashare")[, year_qs], method = method,
samples = qs_samples, ni = ni)
}
else {
warning("attr 'quotashare' for fishery ",
x, " and stock ", y, " does not exist!")
}
return(stkflt_ext)
}))
capacity(om$flts[[x]]) <- capacity(fishery)
capacity(om$flts[[x]])[, year_proj] <- MixME:::stfQuant(capacity(fishery)[,
year_sel], method = method, samples = sel_samples,
ni = ni)
capacity(om$flts[[x]])[is.na(capacity(om$flts[[x]]))] <- 1
effort(om$flts[[x]]) <- fishery@effort
effort(om$flts[[x]])[, year_proj] <- MixME:::stfQuant(fishery@effort[,
year_sel], method = method, samples = sel_samples,
ni = ni)
orevenue(om$flts[[x]]) <- orevenue(fishery)
names(om$flts[[x]]) <- stknames
om$flts[[x]]@name <- x
}
if (!is.null(om$idxs)) {
for (x in 1:length(om$idxs)) {
om$idxs[[x]] <- window(om$idxs[[x]], end = ydata +
nyears)
for (y in 1:length(om$idxs[[x]])) {
om$idxs[[x]][[y]]@index.q[, year_proj, , , ,
] <- MixME:::stfQuant(om$idxs[[x]][[y]]@index.q[,
year_sel], method = method, samples = sel_samples,
ni = ni)
}
}
}
return(om)
}