qestMICE: Internal function for optimizing catchability (q) for a MICE...

In MSEtool: Management Strategy Evaluation Toolkit

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.

Author(s)

T.Carruthers

MSEtool documentation built on Sept. 30, 2024, 9:22 a.m.