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

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

qestMICE(
  par,
  depc,
  CFc,
  mode = "opt",
  np,
  nf,
  nyears,
  nareas,
  maxage,
  Nx,
  VFx,
  FretAx,
  Effind,
  distx,
  movx,
  Spat_targ,
  M_ageArrayx,
  Mat_agex,
  Asizex,
  Kx,
  Linfx,
  t0x,
  Mx,
  R0x,
  R0ax,
  SSBpRx,
  SSB0x,
  hsx,
  aRx,
  bRx,
  ax,
  bx,
  Perrx,
  SRrelx,
  Rel,
  SexPars,
  x
)

`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))
`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 targetting 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) age age
`Asizex`	Matrix [stock, area] Area size
`Kx`	Vector [stock] of von B growth parameter K
`Mx`	Vector [stock] 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
`mod`	Character if 'opt' qestMICE returns the objective function otherwise the fitted values in a list
`Linf`	Vector [stock] of von B asymptotic length parameter Linf
`t0`	Vector [stock] of von B theoretical age at zero length (t0)