calc_population: Multi-fleet, multi-area, multi-stock population dynamics...

In multiSA: Multi-Stock Assessment

Multi-fleet, multi-area, multi-stock population dynamics model

Description

Project age-structured populations forward in time. Also used by ⁠[calc_phi_project()]⁠ to calculate equilibrium abundance and biomass for which there is no analytic solution due to seasonal movement.

Usage

calc_population(
  ny = 10,
  nm = 4,
  na = 20,
  nf = 1,
  nr = 4,
  ns = 2,
  initN_ars = array(1, c(na, nr, ns)),
  mov_ymarrs,
  M_yas = array(0.3, c(ny, na, ns)),
  SRR_s = rep("BH", ns),
  sralpha_s = rep(1e+16, ns),
  srbeta_s = rep(1e+16, ns),
  mat_yas = array(1, c(ny, na, ns)),
  fec_yas = array(1, c(ny, na, ns)),
  Rdev_ys = matrix(1, ny, ns),
  m_spawn = 1,
  m_advanceage = 1,
  delta_s = rep(0, ns),
  natal_rs = matrix(1, nr, ns),
  recdist_rs = matrix(1/nr, nr, ns),
  fwt_ymafs = array(1, c(ny, nm, na, nf, ns)),
  q_fs = matrix(1, nf, ns),
  sel_ymafs = array(1, c(ny, nm, na, nf, ns)),
  condition = c("F", "catch"),
  F_ymfr = array(0, c(ny, nm, nf, nr)),
  Cobs_ymfr = array(1e-08, c(ny, nm, nf, nr)),
  Fmax = 2,
  nitF = 5L
)

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]⁠
mov_ymarrs	Movement array ⁠[y, m, a, r, r, s]⁠. If missing, uses a diagonal matrix (no movement among areas).
M_yas	Natural mortality (per year). Array ⁠[y, 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
mat_yas	Maturity ogive. Array ⁠[y, a, s]⁠
fec_yas	Fecundity schedule (spawning output of mature individuals). Array ⁠[y, a, s]⁠
Rdev_ys	Recruitment deviations. Matrix ⁠[y, 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.
fwt_ymafs	Fishery weight at age. Array ⁠[y, m, a, f, s]⁠
q_fs	Relative catchability of stock s for fleet f. Defaults to 1 if missing. Matrix ⁠[f, s]⁠
sel_ymafs	Fishery selectivity. Array ⁠[y, m, a, f, s]⁠
condition	Whether the fishing mortality is conditioned on the catch or specified F argument.
F_ymfr	Fishing mortality (per season). Array ⁠[y, m, f, r]⁠. Only used if condition = "F".
Cobs_ymfr	Fishery catch (weight). Array ⁠[y, m, f, r]⁠. Only used if condition = "catch" to solve for F (see calc_F()).
Fmax	Numeric, the maximum Findex value
nitF	Integer, number of iterations for the Newton-Raphson routine

Value

A named list containing:

• N_ymars Stock abundance

• F_ymars Fishing mortality (summed across fleets)

• F_ymfr Fishing mortality (by fleet and region)

• Z_ymars Total mortality

• F_ymafrs Fishing mortality (disaggregated by fleet)

• CN_ymafrs Catch at age (abundance)

• CB_ymfrs Fishery catch (weight)

• VB_ymfrs Vulnerable biomass available to the fishing fleets

• Nsp_yars Spawning abundance (in the spawning season)

• Npsp_yars Potentail spawners, mature animals in the spawning season that do not spawn if outside natal regions

• S_yrs Spawning output

• R_ys Recruitment

• penalty Numeric quadratic penalty if apical fishing mortality (by fleet) exceeds Fmax. See calc_F().

Examples

unfished_pop <- calc_population()

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