calc_phi_project: Equilibrium spawners per recruit by projection

In multiSA: Multi-Stock Assessment

Equilibrium spawners per recruit by projection

Description

Project a population forward in time using calc_population() with constant recruitment and seasonal dynamics (growth, movement-by-season) to obtain per recruit parameters. Note that the fishing mortality among fleets and stocks remain linked by matrix q_fs.

Usage

calc_phi_project(
  ny,
  nm,
  na,
  nf = 1,
  nr,
  ns = 1,
  F_mfr = array(0, c(nm, nf, nr)),
  sel_mafs = array(1, c(nm, na, nf, ns)),
  fwt_mafs = array(1, c(nm, na, nf, ns)),
  q_fs = matrix(1, nf, ns),
  M_as,
  mov_marrs,
  mat_as,
  fec_as,
  m_spawn = 1,
  m_advanceage = 1,
  delta_s = rep(0, ns),
  natal_rs = matrix(1, nr, ns),
  recdist_rs = matrix(1/nr, nr, ns)
)

Arguments

ny	Integer, number of years for the projection
nm	Integer, number of seasons
na	Integer, number of age classes
nf	Integer, number of fleets
nr	Integer, number of regions
ns	Integer, number of stocks
F_mfr	Equilibrium fishing mortality (per season). Matrix ⁠[m, f, r]⁠
sel_mafs	Selectivity by season, age, fleet, stock. Array ⁠[m, a, f, s]⁠
fwt_mafs	Fishery weight array by season, age, fleet, stock. Array ⁠[m, a, r, r]⁠. Can be used calculate yield per recruit.
q_fs	Relative catchability of stock s for fleet f. Defaults to 1 if missing. Matrix ⁠[f, s]⁠
M_as	Natural mortality. Matrix ⁠[a, s]⁠
mov_marrs	Movement array ⁠[m, a, r, r, s]⁠. If missing, uses a diagonal matrix (no movement among areas).
mat_as	Maturity at age. Matrix ⁠[a, s]⁠
fec_as	Fecundity at age. Matrix ⁠[a, s]⁠
m_spawn	Integer, season of spawning
m_advanceage	Integer, season at which to advance integer year age classes
delta_s	Numeric vector by s. Fraction of season that elapses when spawning occurs, e.g., midseason spawning when delta_s = 0.5.
natal_rs	Matrix ⁠[r, s]⁠. The fraction of the mature stock s in region r that spawns at time of spawning. See example in Dstock.
recdist_rs	Matrix ⁠[r, s]⁠. The fraction of the incoming recruitment of stock s that settles in region r.

Details

The initial population vector will be the survival at age evenly divided by the number of regions nr.

Value

A named list returned by calc_population().

See Also

calc_phi_simple()

multiSA documentation built on March 21, 2026, 1:06 a.m.