###############################################################################
# AUTHOR(DATE): Agurtzane Urtizberea, Dorleta Garcia and Sonia Sanchez
# RESEARCH INSTITUTE: AZTI-TECNALIA
# TITLE: create.list.stks.flqa
# NOTE #1: Create a list with an FLQuant for each stock with age from
# min.age to max.age
###############################################################################
#-------------------------------------------------------------------------
# inputs:
#
# stks: Name of all the stocks (vector)
# yrs: a vector with c(first.yr,proj.yr,last.yr)
# first.yr: First year of simulation (number)
# proj.yr: First year of projection (number)
# last.yr: Last year of projection (number)
# ni: Number of iterations (number)
# ns: Number of seasons (number)
# list.stks.unit: a list with the name of the stks and each
# stk includes the number of units
# list.stks.age: a list with the name of the stks and each
# stk includes min.age and max.age
#-------------------------------------------------------------------------
create.list.stks.flqa <- function(stks,yrs,ni,ns,list.stks.unit,list.stks.age){
n.stk <- length(stks)
first.yr <- yrs[["first.yr"]]
proj.yr <- yrs[["proj.yr"]]
last.yr <- yrs[["last.yr"]]
nmy <- as.character(first.yr:last.yr)
list.stks.flqa <- NULL
for(i in 1:n.stk){
nmstk <- stks[i]
stk.age.min <- get(grep(list.stks.age[[nmstk]],pattern="age.min", value = TRUE))
stk.age.max <- get(grep(list.stks.age[[nmstk]],pattern="age.max", value = TRUE))
stk.unit <- get(grep(list.stks.unit[[nmstk]],pattern="unit", value = TRUE))
nmu <- 1:stk.unit
nms <- 1:ns
if(stk.unit==1) nmu <- 'unique'
if(ns==1) nms <- 'all'
if(all(is.na(c(stk.age.max,stk.age.min)))){
stk.flqa <- FLQuant(dimnames = list(age = 'all', year = nmy, unit = nmu,
season = nms, iter = 1:ni))
} else{
stk.flqa <- FLQuant(dimnames = list(age = stk.age.min:stk.age.max, year = nmy, unit = nmu,
season = nms, iter = 1:ni))
}
assign(paste(nmstk,'.flqa',sep=""),stk.flqa)
list.stks.flqa[[i]]<- get(paste(nmstk,'.flqa',sep=""))
}
names(list.stks.flqa)<- stks
return(list.stks.flqa)
}
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