Completes a single iteration of recruitment, mortality, fishing and movement given MICE model inputs
popdynOneMICE(
np,
nf,
nareas,
maxage,
Ncur,
Bcur,
SSBcur,
Vcur,
FMretx,
FMx,
PerrYrp,
hsx,
aRx,
bRx,
movy,
Spat_targ,
SRrelx,
M_agecur,
Mat_agecur,
Mat_agenext,
Fec_agenext,
Asizex,
Kx,
Linfx,
t0x,
Mx,
R0x,
R0ax,
SSBpRx,
ax,
bx,
Rel,
SexPars,
x,
plusgroup,
SSB0x,
B0x,
Len_agenext,
Wt_agenext,
SRRfun,
SRRpars,
ycur
)Integer, the number of stocks
Integer, number of fleets
Integer, number of areas
Integer, maximum modelled age
Array [stock, age, area] of stock numbers
Array [stock, age, area] of stock biomass
Array [stock, age, area] of spawning biomass
Array [fleet, age, area] of the vulnerability curve
Array [stock, fleet, age, area] of the retention curve
Array [stock, fleet, age, area] fishing mortality rate
Vector [stock] process error - the lognormal factor for
recruitment strength (for next year)
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)
Array [stock,age,area,area] of movement transitions (for next year)
Matrix [stock, fleet] of spatial targeting parameter
(0 evenly spatial distributed, 1 proportional to vulnerable biomass)
Integer vector [stock] the form of the stock recruitment
relationship (1 = Beverton-Holt, 2= Ricker)
Matrix [stock, age] of Natural mortality rate at age
Matrix [stock, age] of maturity (spawning fraction) at age (current year)
Matrix [stock, age] of maturity (spawning fraction) at age (next year)
Matrix [stock, age] of spawning weight (fecundity) at age (next year)
Matrix [stock, area] of relative area sizes
Vector [stock] of von B growth parameter K (next year)
Vector [stock] of von B asymptotic length parameter Linf (next year)
Vector [stock] of von B theoretical age at zero length (t0) (next year)
Vector [stock] mature natural mortality rate (this year)
Vector [stock] unfished recruitment
Matrix [stock, area] unfished recruitment by area
Matrix [stock, area] spawning biomass per recruit by area
Vector [stock] weight-length parameter a W=aL^b
Vector [stock] weight-length parameter b W=aL^b
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)
Unfished SSB0, Vector [stock] length.
Unfished B0, Vector [stock] length.
Matrix [stock, age] of next year's length-at-age
Matrix [stock, age] of next year's weight-at-age
Optional. A stock-recruit function used if SRrelc =3
Optional. A named list of arguments for SRRfun
Integer. The current year of the simulation
T.Carruthers