Initial population projection — calc_init

Project a population forward in time with constant parameters (biology and F) with calc_population(), an alternative to calc_phi_project() to establish initial age structure.

Usage

calc_init_population(
  ny = 10,
  nm = 4,
  na = 20,
  nf = 1,
  nr = 4,
  ns = 1,
  initN_ars = array(1, c(na, nr, ns)),
  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,
  SRR_s,
  sralpha_s,
  srbeta_s,
  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
initN_ars: Abundance in the first year, first season. Array [a, r, s]
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]
SRR_s: Character vector by s for the stock recruit relationship. See calc_recruitment() for options
sralpha_s: Numeric vector by s for the stock recruit alpha parameter
srbeta_s: Numeric vector by s for the stock recruit beta parameter
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().