Initial Numbers-at-Age (NAA) — Get_Init

Numbers at age in the first model year, by population, region, age and sex, at the equilibrium implied by constant recruitment, mortality and movement. init_age_strc chooses how that equilibrium is solved, and ln_InitDevs then deviates each age away from it.

Usage

Get_Init_NAA(
  init_age_strc,
  init_iter,
  n_regions,
  n_pop,
  n_sexes,
  n_ages,
  n_seas,
  n_fish_fleets,
  seasdur,
  rec_seas_prop,
  natmort,
  natmort_annual = collapse_natmort_annual(natmort, seasdur, seas_dim = 3),
  init_F,
  dmr,
  fish_sel,
  ret_sel,
  R0_r,
  sexratio,
  Movement,
  do_recruits_move,
  ln_InitDevs,
  Mrate = NULL,
  move_timing = 0,
  expm_nsub = 0
)

Arguments

init_age_strc: Integer, how the initial age structure is solved: 0 iterates the annual cycle init_iter times, 1 scalar geometric series with no movement at any age, 2 matrix geometric series with movement at every age, 3 movement below the plus group and a scalar series for the plus group, 4 no equilibrium at all, ages 2 and older are exp(ln_InitDevs) apportioned by sex ratio.
init_iter: Integer, annual cycles run when init_age_strc = 0.
n_regions, n_pop, n_sexes, n_ages, n_seas, n_fish_fleets: Integer dimensions. n_ages includes the plus group.
seasdur: Numeric vector (n_seas) of each season's fraction of a year.
rec_seas_prop: Matrix (n_pop x n_seas) of the share of annual recruitment entering in each season.
natmort: Array (n_pop x n_regions x n_seas x n_ages x n_sexes) of natural mortality, a rate per year applied within each season.
natmort_annual: Array (n_pop x n_regions x n_ages x n_sexes) of the annual total, the duration weighted sum over seasons, read by the steps that advance a whole year at once. Defaults to that sum.
init_F: Numeric array (n_regions x n_seas x n_fish_fleets) of fully selected fishing mortality during initialization. Zero for an unfished population.
dmr: Numeric array (n_regions x n_seas x n_fish_fleets) of the discard mortality rate during initialization.
fish_sel, ret_sel: Arrays (n_pop x n_regions x n_seas x n_ages x n_sexes x n_fish_fleets) of total fishery selectivity at age and of the proportion of those fish retained.
R0_r: Matrix (n_pop x n_regions) of unfished recruitment allocated to each region.
sexratio: Array (n_pop x n_regions x n_sexes) of the proportion of recruits by sex.
Movement: Array (n_pop x n_regions x n_regions x n_seas x n_ages x n_sexes) of seasonal movement probabilities, where Movement[p,r,r2,,,] is the fraction of the fish in region r that move to region r2.
do_recruits_move: Integer, 0 recruits stay in their region for their first year, 1 recruits move with every other age.
ln_InitDevs: Array (n_pop x n_regions x (n_ages - 1) x n_sexes) of log scale deviations for ages 2 and older. A 3-D array without the sex dimension is expanded across sexes as one shared curve. Under init_age_strc = 4 these are the numbers themselves rather than multipliers on an equilibrium.
Mrate: Array dimensioned like Movement of instantaneous movement rates. Required when move_timing = 2, ignored otherwise.
move_timing: Integer ordering of movement and mortality within a season: 0 movement then mortality, 1 mortality then movement, 2 both at once. See build_seas_operator.
expm_nsub: Integer, how the matrix exponential is taken under move_timing = 2: 0 uses Matrix::expm, \(n \ge 1\) the implicit backward Euler scheme. See mat_exp.

Value

Array (n_pop x n_regions x n_ages x n_sexes) of initial numbers at age.