popdynMICE: Population dynamics for a MICE model (multiyear)

Description Usage Arguments Author(s)

View source: R/popdyn_MICE.R

Description

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

Usage

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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,
  plusgroup,
  maxF,
  SSB0x
)

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) 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)

Author(s)

T.Carruthers


MSEtool documentation built on March 10, 2021, 1:08 a.m.