Skip to contents

Solve for broodtake numbers

Source: R/hatchery.R
calc_broodtake.Rd

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]