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,
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)
)Integer, the simulation number
Numeric vector, nstock long of specified stock depletion (SSB now / SSB0)
Matrix [nstock, nfleet], a catch fraction among fleets (sums to 1 for each stock (row))
Character if 'opt' qestMICE returns the objective function otherwise the fitted values in a list
Integer, number of fleets
Integer, number of historical years (unfished til today)
Integer, number of areas (default is 2)
Integer, maximum number of age classes for calculation
Array [stock, age, year, area] of stock numbers
Array [fleet, age, year, area] of the vulnerability curve
Array [fleet, age, year, area] of the retention curve
Array [fleet, year] of effort
Array [stock,age,area,area] of movement transitions
Matrix [stock, fleet] of spatial targeting parameter (0 evenly spatial distributed, 1 proportional to vulnerable biomass)
Array [stock, age,year] of Natural mortality rate at age
Array [stock, age, year] of maturity (spawning fraction) at age
Array [stock, age, year] of mature spawning weight at age
Matrix [stock, area] Area size
Array of von B growth parameter K
Array of von B asymptotic length parameter Linf
Array ofvon B theoretical age at zero length (t0)
Array of mature natural mortality rate
Vector [stock] unfished recruitment
Matrix [stock, area] unfished recruitment by area
Matrix [stock, area] spawning biomass per recruit by area
Vector [stock] Unfished spawning stock biomass
Vector [stock] steepness of the stock recruitment curve
Vector [stock] stock recruitment parameter alpha (for Ricker curve)
Vector [stock] stock recruitment parameter beta (for Ricker curve)
Vector [stock] weight-length parameter a W=aL^b
Vector [stock] weight-length parameter b W=aL^b
Matrix [stock, year] process error - the lognormal factor for recruitment strength
Integer vector [stock] the form of the stock recruitment relationship (1 = Beverton-Holt, 2= Ricker)
A list of inter-stock relationships see slot Rel of MOM object class
A list of sex-specific dynamics (SSBfrom, stcck_age)
Integer. The simulation number
Integer vector [stock] indicating if a plus group is used
Logical, whether to optimize to vulnerable biomass (or spawning biomass otherwise)
Vector [stock] unfished vulnerable biomass
Vector [stock] unfished total biomass
Array [stock, fleet, n_age] of weight at age in catch in the last historical year
A numeric value specifying the maximum fishing mortality for any single age class
An array of spatial closures by year [np,nf,nyears+proyears,nareas]
Optional. Stock-recruit functions used if SRrelc =3. List of length np
Optional. A named list of arguments for SRRfun. List of length np
Numeric. Fraction of the year when spawning occurs. Default = 0.
T.Carruthers