calc_broodtake: Solve for broodtake numbers

In salmonMSE: Management Strategy Evaluation for Salmon Species

Solve for broodtake numbers

Description

Internal functions to calculate broodtake with various constraints, called by brood_func(). calc_broodtake() is a wrapper function.

calc_broodtake_custom() uses a user-provided function to generate brood numbers and adjusts downwards if egg production exceeds the target.

.broodtake_func() is the optimization function used to calculate broodtake

Usage

calc_broodtake(
  NO,
  HO,
  stray,
  brood_import,
  ptarget_NOB,
  pmax_NOB,
  phatchery,
  egg_target,
  p_female,
  fec,
  s_prespawn,
  m
)

calc_broodtake_custom(
  f_brood,
  NO,
  HO,
  stray,
  p_female,
  fec,
  s_prespawn,
  m,
  egg_target
)

.broodtake_func(
  ptake_unmarked,
  NO,
  HO,
  stray,
  brood_import,
  phatchery,
  p_female,
  fec,
  egg_target,
  s_prespawn,
  ptarget_NOB,
  m = 1,
  opt = TRUE
)

Arguments

NO	Matrix ⁠[nage, n_g]⁠, natural-origin fish available for broodtake
HO	Matrix ⁠[nage, n_r]⁠, hatchery-origin fish, potentially available for broodtake
stray	Matrix ⁠[nage, n_r]⁠, hatchery-origin strays available for broodtake
brood_import	Vector ⁠[nage]⁠ of imported brood
ptarget_NOB	Numeric, target proportion of NOB/(NOB + HOB). If m = 1, then the realized pNOB should be ptarget_NOB. If m < 1, then the system achieves ⁠unmarked brood/(NOB + HOB) = ptarget_NOB⁠.
pmax_NOB	Numeric, maximum proportion of NOB/NO
phatchery	Numeric, proportion of HO that return to hatchery instead of the spawning ground. HOB is taken from this subset. Set to NA to obtain HOB on the way to spawning ground.
egg_target	Numeric, target egg production from which to back-calculate brood numbers
p_female	Vector ⁠[nage]⁠ of proportion female to calculate egg production
fec	Vector ⁠[nage]⁠, egg production per female
s_prespawn	Numeric, survival of brood prior to egg production
m	Numeric, mark rate of HO used. Discounts ptarget_NOB and pmax_NOB based on marked fish
f_brood	Function that calculates the brood numbers
ptake_unmarked	Numeric, proportion of unmarked fish used for brood
opt	Logical, whether the function is used for optimization (TRUE) or reporting (FALSE)

Value

calc_broodtake() returns a list from .broodtake_func()

calc_broodtake_custom() returns a named list, same format as calc_broodtake()

.broodtake_func() returns a numeric if opt = TRUE: log(p_unmarked) - log(ptarget_NOB), otherwise a named list of brood and egg production.

• egg_NOB Matrix ⁠[nage, n_g]⁠

• egg_HOB_unmarked Matrix ⁠[nage, n_r]⁠ (including strays)

• egg_HOB_marked Matrix ⁠[nage, n_r]⁠

• egg_HOB_import Vector ⁠[nage]⁠

• ptake_unmarked Numeric

• ptake_marked Numeric

• pNOB Numeric

• NOB Numeric

• HOB_unmarked Matrix ⁠[nage, n_r]⁠

• HOB_marked Matrix ⁠[nage, n_r]⁠

• HOB_import Matrix ⁠[nage, n_r]⁠

• HOB_stray Vector ⁠[nage]⁠

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.