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

In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

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

Blue-Matter/MSEtool documentation built on Nov. 22, 2024, 8:23 p.m.