getq_multi_MICE: optimize for catchability (q) and fishing dist for a MICE...

Description Usage Arguments Author(s)

View source: R/multi_q_estimation.R

Description

Function optimizes catchability (q, where F=qE) required to get to user-specified stock depletion across stocks and fleets if there are relationships among stocks

Usage

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getq_multi_MICE(
  x,
  StockPars,
  FleetPars,
  np,
  nf,
  nareas,
  maxage,
  nyears,
  N,
  VF,
  FretA,
  maxF = 0.9,
  MPA,
  CatchFrac,
  bounds = c(1e-05, 15),
  tol = 1e-06,
  Rel,
  SexPars
)

Arguments

x

Integer, the simulation number

StockPars

A list of sampled stock parameters, one list element per stock

FleetPars

A hierarcical list of sampled fleet parameters, first list level is stock, second is fleet

np

The number of stocks

nf

The number of fleets

nareas

The number of areas

maxage

The maximum number of modelled ages

nyears

The number of historical 'spool-up' years (from unfished to now)

N

An array of stock numbers [nsim,np,maxage,nyears,nareas] - only the values from the first year are used

VF

An array of vulnerability [nsim,np,nf,maxage,nyears+proyears]

FretA

An array of retention [nsim,np,nf,maxage,nyears+proyears]

maxF

A numeric value specifying the maximum fishing mortality for any single age class

MPA

An of spatial closures by year [np,nf,nyears+proyears,nareas]

CatchFrac

A list of stock-specific fleet fractions of current catch list[[stock]][nsim, nf]

bounds

Bounds for total q estimation

tol

A numeric value that is the fraction of machine tolerance (once reduction in objective function steps below this, optimization ends)

Rel

A list of inter-stock relationships see slot Rel of MOM object class

SexPars

A list of sex-specific dynamics SSBfrom stock_age

Author(s)

T.Carruthers


tcarruth/MSEtool documentation built on Sept. 16, 2020, 5:59 a.m.