Description Usage Arguments Author(s)
Calls popdynOneMICE iteratively to reconstruct a time series given MICE model inputs
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | popdynMICE(
qsx,
qfracx,
np,
nf,
nyears,
nareas,
maxage,
Nx,
VFx,
FretAx,
Effind,
movx,
Spat_targ,
M_ageArrayx,
Mat_agex,
Asizex,
Kx,
Linfx,
t0x,
Mx,
R0x,
R0ax,
SSBpRx,
hsx,
aRx,
bRx,
ax,
bx,
Perrx,
SRrelx,
Rel,
SexPars,
x
)
|
qsx |
Total catchability |
qfracx |
Vector [fleet], the fraction of total qs by fleet |
np |
Integer, the number of stocks |
nf |
Integer, number of fleets |
nyears |
Integer, number of historical years (unfished til today) |
nareas |
Integer, the number of spatial areas |
maxage |
Integer, maximum modelled age |
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 |
Asizex |
Array [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 |
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 relationships (SSBfrom, stock_age) |
x |
Integer the simulation number |
Linf |
Vector [stock] of von B asymptotic length parameter Linf |
t0 |
Vector [stock] of von B theoretical age at zero length (t0) |
T.Carruthers
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