popdynMICE: Population dynamics for a MICE model (multiyear)

In MSEtool: Management Strategy Evaluation Toolkit

Population dynamics for a MICE model (multiyear)

Description

Calls popdynOneMICE iteratively to reconstruct a time series given MICE model inputs

Usage

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)
)

Arguments

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 modeled 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 targeting 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) at age
Fec_agex	Array ⁠[stock, age, year]⁠ of female spawning weight (fecundity) at age
Asizex	Array ⁠[stock, area]⁠ Area size
WatAgex	Array of weight-at-age
Len_agex	Array of length-at-age
Karrayx	Array of von B growth parameter K
Linfarrayx	Array of von B asymptotic length parameter Linf
t0arrayx	Array ofvon B theoretical age at zero length (t0)
Marrayx	Array of 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
plusgroup	Numeric vector. Use plus-group (1) or not (0)
maxF	maximum F
SSB0x	SSB0 for this simulation
B0x	B0 for this simulation
MPA	An array of spatial closures by year ⁠[np,nf,nyears+proyears,nareas]⁠

Author(s)

T.Carruthers

MSEtool documentation built on July 26, 2023, 5:21 p.m.