# test-om.R - DESC
# /home/mosqu003/Active/MSE_PKG@flr/mse/tests/testthat/test-om.R
# Copyright (c) WUR, 2022.
# Author: Iago MOSQUEIRA (WMR) <iago.mosqueira@wur.nl>
#
# Distributed under the terms of the EUPL-1.2
# --- CREATE demo objects
fq <- FLQuant(NA, dimnames=list(age=1:9, year=10:30))
# FLBiol: wt, m, spwn, mat
bio <- FLBiol(
wt=fq %=% seq(0.03, 8, length=9),
m=fq %=% c(0.4, 0.35, rep(0.3, 6), 0.35),
spwn=fq[1,] %=% 0.25,
mat=fq %=% c(0, 0.2, 0.5, rep(1,6)))
# FLFisheries
fia <- FLFishery(
effort=FLQuant(0.001, dimnames=list(year=10:30)),
A=FLCatch(landings.wt=wt(bio), discards.wt=wt(bio),
landings.n=fq %=% 1, discards.n=fq %=% 0,
catch.sel=fq %=% c(0.1, 0.3, 0.4, 0.8, 1, 1, 1, 0.9, 0.8)))
fib <- FLFishery(
effort=FLQuant(0.001, dimnames=list(year=10:30)),
A=FLCatch(landings.wt=wt(bio) * 0.90, discards.wt=wt(bio) * 0.90,
landings.n=fq %=% 1, discards.n=fq %=% 0,
catch.sel=fq %=% c(0.1, 0.4, 0.8, rep(1, 6))))
fis <- FLFisheries(A=fia, B=fib)
#
bio <- initiate(bio, B0=23000, h=0.8)
bio <- deplete(bio, sel=catch.sel(fia[[1]]), dep=0.4)
# ONE fishery, catch history
history <- FLQuants(catch=FLQuant(c(150, seq(200, 1200, length=9),
seq(1500, 800, length=10)), dimnames=list(year=11:30)))
sim <- simulator(bio, fis['A'], B0=23000, h=0.80, dep=0.40,
history=history)
plot(sim$biol)
# TWO fisheries
history <- list(catch=FLQuants(A=FLQuant(c(150, seq(200, 1200, length=9),
seq(1050, 400, length=10)), dimnames=list(year=11:30)),
B=FLQuant(c(15, seq(20, 120, length=9),
seq(200, 800, length=10)), dimnames=list(year=11:30))))
sim <- simulator(bio, fis, B0=23000, h=0.80, dep=0.40,
history=history)
plot(sim$biol)
plot(catch(sim$fisheries))
# --- iters
bio <- FLBiol(
wt=rlnorm(100, log(fq %=% seq(0.03, 8, length=9)), 0.1),
m=fq %=% c(0.4, 0.35, rep(0.3, 6), 0.35),
spwn=fq[1,] %=% 0.25,
mat=fq %=% c(0, 0.2, 0.5, rep(1,6)))
fis <- lapply(fis, propagate, 100)
# ONE fishery, catch history
history <- FLQuants(catch=FLQuant(c(150, seq(200, 1200, length=9),
seq(1500, 800, length=10)), dimnames=list(year=11:30)))
history <- fwdControl(value=seq(0.9, 0.35, length=20), quant="ssb_end",
year=11:30, relYear=10, biol=1, relBiol=1)
sim <- simulator(bio, fis['A'], B0=23000, h=0.80, dep=0.40,
history=history)
plot(sim$biol)
mets <- FLQuants(
catch=catch(sim$fisheries)$A,
ssb=ssb(sim$biol, hr=catch.n(sim$fisheries[[1]][[1]]) / n(sim$biol)))
# BUG: harvest(FLBiol, FLFisheries)
SSB <- FLQuants(
F=ssb(sim$biol, f=harvest(sim$biol, sim$fisheries)),
HR=ssb(sim$biol, hr=catch.n(sim$fisheries[[1]][[1]]) / n(sim$biol)),
C=ssb(sim$biol, catch.n=catch.n(sim$fisheries[[1]][[1]])))
# TWO fisheries
history <- list(catch=FLQuants(A=FLQuant(c(150, seq(200, 1200, length=9),
seq(1050, 400, length=10)), dimnames=list(year=11:30)),
B=FLQuant(c(15, seq(20, 120, length=9),
seq(200, 800, length=10)), dimnames=list(year=11:30))))
sim <- simulator(bio, fis, B0=23000, h=0.80, dep=0.40,
history=history)
plot(sim$biol)
plot(catch(sim$fisheries))
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