MSEtool (version 3.1.1)

popdynOneMICE: Population dynamics for a MICE model (single year)

Description

Completes a single iteration of recruitment, mortality, fishing and movement given MICE model inputs

Usage

popdynOneMICE(
  np,
  nf,
  nareas,
  maxage,
  Ncur,
  Vcur,
  FMretx,
  FMx,
  PerrYrp,
  hsx,
  aRx,
  bRx,
  movy,
  Spat_targ,
  SRrelx,
  M_agecur,
  Mat_agecur,
  Asizex,
  Kx,
  Linfx,
  t0x,
  Mx,
  R0x,
  R0ax,
  SSBpRx,
  ax,
  bx,
  Rel,
  SexPars,
  x,
  plusgroup,
  SSB0x,
  Len_age,
  Wt_age
)

Arguments

np

Integer, the number of stocks

nf

Integer, number of fleets

maxage

Integer, maximum modelled age

Ncur

Array [stock, age, area] of stock numbers

Vcur

Array [fleet, age, area] of the vulnerability curve

FMretx

Array [stock, fleet, age, area] of the retention curve

FMx

Array [stock, fleet, age, area] fishing mortality rate

PerrYrp

Vector [stock] process error - the lognormal factor for recruitment strength

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)

movy

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)

SRrelx

Integer vector [stock] the form of the stock recruitment relationship (1 = Beverton-Holt, 2= Ricker)

M_agecur

Matrix [stock, age] of Natural mortality rate at age

Mat_agecur

Matrix [stock, age] of maturity (spawning fraction) age age

Asizex

Matrix [stock, area] of relative area sizes

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

ax

Vector [stock] weight-length parameter a W=aL^b

bx

Vector [stock] weight-length parameter b W=aL^b

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)

SSB0x

Unfished SSB0, Vector nstock length.

Len_age

Length-at-age this year

Wt_age

Weight-at-age this year

nyears

Integer, number of historical years (unfished til today)

Linf

Vector [stock] of von B asymptotic length parameter Linf

t0

Vector [stock] of von B theoretical age at zero length (t0)