qestMICE: Internal function for optimizing catchability (q) for a MICE...
In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

qestMICE

R Documentation

Internal function for optimizing catchability (q) for a MICE model

Description

Function returns objective function that fits both stock depletion and catch fraction among fleets

Usage

qestMICE(
  par,
  depc,
  CFc,
  mode = "opt",
  np,
  nf,
  nyears,
  nareas,
  maxage,
  Nx,
  VFx,
  FretAx,
  Effind,
  distx,
  movx,
  Spat_targ,
  M_ageArrayx,
  Mat_agex,
  Fec_agex,
  Asizex,
  WatAgex,
  Len_agex,
  Karrayx,
  Linfarrayx,
  t0arrayx,
  Marrayx,
  R0x,
  R0ax,
  SSBpRx,
  SSB0x,
  hsx,
  aRx,
  bRx,
  ax,
  bx,
  Perrx,
  SRrelx,
  Rel,
  SexPars,
  x,
  plusgroup,
  optVB,
  VB0x,
  B0x,
  WtCx,
  maxF,
  MPA,
  SRRfun,
  SRRpars,
  spawn_time_frac = rep(0, np)
)

Arguments

`par`	Integer, the simulation number
`depc`	Numeric vector, nstock long of specified stock depletion (SSB now / SSB0)
`CFc`	Matrix `⁠[nstock, nfleet]⁠`, a catch fraction among fleets (sums to 1 for each stock (row))
`mode`	Character if 'opt' qestMICE returns the objective function otherwise the fitted values in a list
`nf`	Integer, number of fleets
`nyears`	Integer, number of historical years (unfished til today)
`nareas`	Integer, number of areas (default is 2)
`maxage`	Integer, maximum number of age classes for calculation
`Nx`	Array `⁠[stock, age, year, area]⁠` of stock numbers
`VFx`	Array `⁠[fleet, age, year, area]⁠` of the vulnerability curve
`FretAx`	Array `⁠[fleet, age, year, area]⁠` of the retention curve
`Effind`	Array `⁠[fleet, year]⁠` of effort
`movx`	Array `⁠[stock,age,area,area]⁠` of movement transitions
`Spat_targ`	Matrix `⁠[stock, fleet]⁠` of spatial targeting parameter (0 evenly spatial distributed, 1 proportional to vulnerable biomass)
`M_ageArrayx`	Array `⁠[stock, age,year]⁠` of Natural mortality rate at age
`Mat_agex`	Array `⁠[stock, age, year]⁠` of maturity (spawning fraction) at age
`Fec_agex`	Array `⁠[stock, age, year]⁠` of mature spawning weight at age
`Asizex`	Matrix `⁠[stock, area]⁠` Area size
`Karrayx`	Array of von B growth parameter K
`Linfarrayx`	Array of von B asymptotic length parameter Linf
`t0arrayx`	Array ofvon B theoretical age at zero length (t0)
`Marrayx`	Array of mature natural mortality rate
`R0x`	Vector `⁠[stock]⁠` unfished recruitment
`R0ax`	Matrix `⁠[stock, area]⁠` unfished recruitment by area
`SSBpRx`	Matrix `⁠[stock, area]⁠` spawning biomass per recruit by area
`SSB0x`	Vector `⁠[stock]⁠` Unfished spawning stock biomass
`hsx`	Vector `⁠[stock]⁠` steepness of the stock recruitment curve
`aRx`	Vector `⁠[stock]⁠` stock recruitment parameter alpha (for Ricker curve)
`bRx`	Vector `⁠[stock]⁠` stock recruitment parameter beta (for Ricker curve)
`ax`	Vector `⁠[stock]⁠` weight-length parameter a W=aL^b
`bx`	Vector `⁠[stock]⁠` weight-length parameter b W=aL^b
`Perrx`	Matrix `⁠[stock, year]⁠` process error - the lognormal factor for recruitment strength
`SRrelx`	Integer vector `⁠[stock]⁠` the form of the stock recruitment relationship (1 = Beverton-Holt, 2= Ricker)
`Rel`	A list of inter-stock relationships see slot Rel of MOM object class
`SexPars`	A list of sex-specific dynamics (SSBfrom, stcck_age)
`x`	Integer. The simulation number
`plusgroup`	Integer vector `⁠[stock]⁠` indicating if a plus group is used
`optVB`	Logical, whether to optimize to vulnerable biomass (or spawning biomass otherwise)
`VB0x`	Vector `⁠[stock]⁠` unfished vulnerable biomass
`B0x`	Vector `⁠[stock]⁠` unfished total biomass
`WtCx`	Array `⁠[stock, fleet, n_age]⁠` of weight at age in catch in the last historical year
`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]⁠`
`SRRfun`	Optional. Stock-recruit functions used if `SRrelc =3`. List of length `np`
`SRRpars`	Optional. A named list of arguments for `SRRfun`. List of length `np`
`spawn_time_frac`	Numeric. Fraction of the year when spawning occurs. Default = 0.