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

View source: R/popdyn_MICE.R

popdynOneMICER Documentation

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,
  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
)

Arguments

np

Integer, the number of stocks

nf

Integer, number of fleets

nareas

Integer, number of areas

maxage

Integer, maximum modelled age

Ncur

Array ⁠[stock, age, area]⁠ of stock numbers

Bcur

Array ⁠[stock, age, area]⁠ of stock biomass

SSBcur

Array ⁠[stock, age, area]⁠ of spawning biomass

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 (for next year)

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 (for next year)

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) at age (current year)

Mat_agenext

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

Fec_agenext

Matrix ⁠[stock, age]⁠ of spawning weight (fecundity) at age (next year)

Asizex

Matrix ⁠[stock, area]⁠ of relative area sizes

Kx

Vector ⁠[stock]⁠ of von B growth parameter K (next year)

Linfx

Vector ⁠[stock]⁠ of von B asymptotic length parameter Linf (next year)

t0x

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

Mx

Vector ⁠[stock]⁠ mature natural mortality rate (this year)

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 ⁠[stock]⁠ length.

B0x

Unfished B0, Vector ⁠[stock]⁠ length.

Len_agenext

Matrix ⁠[stock, age]⁠ of next year's length-at-age

Wt_agenext

Matrix ⁠[stock, age]⁠ of next year's weight-at-age

SRRfun

Optional. A stock-recruit function used if SRrelc =3

SRRpars

Optional. A named list of arguments for SRRfun

ycur

Integer. The current year of the simulation

Author(s)

T.Carruthers


MSEtool documentation built on Sept. 30, 2024, 9:22 a.m.