getq_multi_MICE: Optimize for catchability (q) and fishing dist for a MICE...
In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

getq_multi_MICE

R Documentation

Optimize for catchability (q) and fishing dist for a MICE model

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

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,
  plusgroup,
  optVB = FALSE,
  silent = FALSE
)

Arguments

`x`	Integer, the simulation number
`StockPars`	A list of sampled stock parameters, one list element per stock
`FleetPars`	A hierarchical 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 modeled 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 array 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
`optVB`	Logical, whether to optimize to vulnerable biomass (or spawning biomass otherwise)
`silent`	Logical, whether to report the objective function for each simulation