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MSY calculation

Source: R/msy.R
msy_calc.Rd

MSY calculation for multi-fishery, two-season model. Converted from ADMB (AP July 2009, JNI modifications)

Usage

msy_calc(data, F_full)

Arguments

data

A list of model data inputs. Expected fields: nfisheries (integer, number of fisheries), last_age (integer, maximum age class), Fini (numeric vector, initial F values by fishery), sel_fa (numeric matrix, selectivity by fishery and age with dimensions nfisheries x (last_age+1)), cwt_fa (numeric matrix, catch weight-at-age by fishery and age with dimensions nfisheries x (last_age+1)), phi (numeric vector, spawning biomass per recruit by age, length last_age+1), spwt (numeric vector, spawning weight-at-age, length last_age+1), M_age (numeric vector, natural mortality by age, length last_age+1), cat_split (numeric vector, target fishery catch shares, length nfisheries), alpha (numeric, stock-recruitment parameter), beta (numeric, stock-recruitment parameter).

F_full

Numeric vector of fully-selected fishing mortality by fishery (length nfisheries).

Value

A list of computed equilibrium quantities with the following components:

Ctot

Total catch (numeric scalar)

Cwt

Catch by fishery (numeric vector, length nfisheries)

Spbio

Spawning biomass (numeric scalar)

Tbio

Total biomass age-2+ (numeric scalar)

Rec

Recruitment (numeric scalar)

SBR

Spawning biomass per recruit (numeric scalar)

SBR0

Unfished spawning biomass per recruit (numeric scalar)

Rel

Survivorship-at-age (numeric vector, length last_age+1)

Rel2

Survivorship at start of season 2 (numeric vector, length last_age+1)

ER

Exploitation rate by season and age (numeric matrix, dimensions 2 x (last_age+1))

Fage

Fishing mortality by fishery and age (numeric matrix, dimensions nfisheries x (last_age+1))

Ftot_a

Total annualized fishing mortality by age (numeric vector, length last_age+1)

Rel_twt

Relative survivorship weighted by spawning weight (numeric vector, length last_age+1)

pen

Penalty for exploitation rates near 1 (numeric scalar)

cat_split_est

Estimated catch composition across fisheries (numeric vector, length nfisheries)

Details

Season structure (hardwired): Fisheries 1-2 -> Season 2 (e.g., LL1, LL2) Fisheries 3+ -> Season 1 (e.g., LL3, LL4, Indonesian, Surface) Catch timing: Fisheries 5-6 -> computed at start of year (using Rel) Fisheries 1-4 -> computed at start of season 2 (using Rel2) Maturity schedule fixed at 10+ Selectivities scaled to max 1 prior to input

Core calculation function