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Equilibrium spawners per recruit by projection

Source: R/calc_population.R
calc_phi_project.Rd

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.

Value

A named list returned by calc_population().

Details

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

See also

calc_phi_simple()