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

Source: R/calc_population.R
calc_population.Rd

Project age-structured populations forward in time. Frequently used 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_rec = 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 = matrix(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_rec

Integer, season of recruitment

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 Mature abundance (that does not 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()