calc_population: 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
)

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().

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

Examples

Run this code

unfished_pop <- calc_population()

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