HistMICE: Reconstruct historical dynamics
In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

HistMICE

R Documentation

Reconstruct historical dynamics

Description

Function that reconstructs historical stock trends from fitted qs and all other parameters including MICE components

Usage

HistMICE(
  x,
  StockPars,
  FleetPars,
  np,
  nf,
  nareas,
  maxage,
  nyears,
  N,
  VF,
  FretA,
  maxF = 0.9,
  MPA,
  Rel,
  SexPars,
  qs,
  qfrac,
  plusgroup
)

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 of spatial closures by year `⁠[np,nf,nyears+proyears,nareas]⁠`
`Rel`	A list of inter-stock relationships see slot Rel of MOM object class
`SexPars`	A list of sex-specific relationships (SSBfrom, stock_age)
`qs`	Vector of q values
`qfrac`	Array of qfrac
`plusgroup`	Plusgroup - np-length vector