Calls popdynOneMICE iteratively to reconstruct a time series given MICE model inputs
popdynMICE(
qsx,
qfracx,
np,
nf,
nyears,
nareas,
maxage,
Nx,
VFx,
FretAx,
Effind,
movx,
Spat_targ,
M_ageArrayx,
Mat_agex,
Fec_agex,
Asizex,
WatAgex,
Len_agex,
Karrayx,
Linfarrayx,
t0arrayx,
Marrayx,
R0x,
R0ax,
SSBpRx,
hsx,
aRx,
bRx,
ax,
bx,
Perrx,
SRrelx,
Rel,
SexPars,
x,
plusgroup,
maxF,
SSB0x,
B0x,
MPA,
SRRfun,
SRRpars,
spawn_time_frac = rep(0, np)
)Total catchability
Vector [fleet], the fraction of total qs by fleet
Integer, the number of stocks
Integer, number of fleets
Integer, number of historical years (unfished til today)
Integer, the number of spatial areas
Integer, maximum modeled age
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 female spawning weight (fecundity) at age
Array [stock, area] Area size
Array of weight-at-age
Array of length-at-age
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] 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 relationships (SSBfrom, stock_age)
Integer the simulation number
Numeric vector. Use plus-group (1) or not (0)
maximum F
SSB0 for this simulation
B0 for this simulation
An array of spatial closures by year [np,nf,nyears+proyears,nareas]
A list of custom stock-recruit functions. List of length np
A list of custom stock-recruit parameters for simulation x. List of length np
vector of relative spawn timing. Length nstock
T.Carruthers