Class "Hatchery"

The component of the operating model that controls the hatchery management.

Details

Various parameters can be stochastic (length nsim) or input as a single numeric (value identical across all simulations).

A description of the fitness parameters and hatchery dynamics is available in the online documentation.

Slots

Name

Character. Identifying name

n_r

Integer. Number of release strategies, sub-groups of fish with different survival schedules. Default is one.

n_yearling

Vector length n_r. The number of yearlings released by release strategy. No hatchery is modeled if sum(n_yearling, n_subyearling) = 0. are zero. Yearlings survival is density-independent after release. Default is zero.

n_subyearling

Vector length n_r. The number of subyearlings released. No hatchery is modeled if sum(n_yearling, n_subyearling) = 0 are zero. Subyearlings experience density-dependent survival in competition with natural origin young. Default is zero.

s_prespawn

Numeric. The survival of broodtake prior to egg production. 1 - s_prespawn is the proportion of fish not used for hatchery purposes, e.g., mortality or other resesarch purposes. Used to back-calculate the broodtake from n_yearling and n_subyearling. Default is 1.

s_egg_smolt

Numeric. The survival of eggs to the smolt life stage (for yearling release). Used to back-calculate the broodtake from n_yearling and n_subyearling. Default is 1.

s_egg_subyearling

Numeric. The survival of eggs to subyearling life stage (for subyearling release). Used to back-calculate the broodtake from n_yearling and n_subyearling. Default is 1.

brood_import

Matrix by age (length maxage) for the number of annual imported hatchery origin broodstock. Egg production is weighted by fec_brood. To meet hatchery production target releases, imported brood and local marked brood are used indiscriminately. Default imported brood is zero.

Mjuv_HOS

Either vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears, n_r]. Natural mortality of immature hatchery origin fish. To replicate the SAR parameter of a stage-specific model, set Mjuv_HOS[a] = -log(SAR) for the age class prior to maturation (and zero for all other ages).

p_mature_HOS

Vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears, n_r] for the maturity of hatchery spawners. Default is set equal to Bio@p_mature for all release strategies.

stray_external

Matrix by age (length maxage) and release strategy n_r that denotes the annual number of hatchery origin strays from other populations/systems not included in the operating model. Default is zero. External strays are added at the escapement life stage, assumed unmarked. For multi-population models with straying within the system, see also SOM@stray matrix.

gamma

Numeric. The relative reproductive success of hatchery origin spawners (relative to natural origin spawners). Default is 1.

m

Numeric. The mark rate of hatchery origin fish, which affects selective broodtake and fishery retention if mark-selective fishing is utilized. Set m = 1 for AHA compatibility with ptarget_NOB. Default is zero.

pmax_esc

Numeric. The maximum proportion of total escapement (after en route mortality) that could be used as broodtake. Set to 1 for AHA compatibility. Default is 0.75.

pmax_NOB

Numeric. The maximum proportion of the natural origin escapement (after en route mortality and pmax_esc) to be used as broodtake. If broodstock is limited by pmax_esc < 1, then this parameter should be 1. Default is 1.

ptarget_NOB

Numeric. The target proportion of the natural origin broodtake relative to the overall broodtake, assuming the mark rate is 1 and natural origin fish can be identified in the hatchery. The realized proportion may be lower if there are insufficient natural origin escapement. If the mark rate < 1, then this target proportion identifies the proportion of unmarked fished in the broodtake. If mark rate = 0, then pNOB is equal to the proportion in the escapement. Default is 0.9.

phatchery

Numeric. Optional parameter (default is NA). If set to a numeric between 0-1, this value is the proportion of the hatchery origin escapement that return to the hatchery, for example, by removal from spawning grounds or swim-in facilities. These fish are available for broodtake. None of these fish will spawn in the natural environment. With the default option, NA allows all hatchery origin escapement that is not used brood to go to the spawning grounds.

premove_HOS

Numeric. The target proportion of the hatchery origin escapement to be removed from the spawning grounds (in order to ensure a high proportion of NOS). The effective removal is discounted by the mark rate, i.e., premove_HOS * m. The removed hatchery origin fish do not spawn and are not available for broodtake. A value less than one can represent imperfect implementation of weir removal. Default is zero.

fec_brood

Vector of length maxage. The fecundity schedule of broodtake to calculate the total egg production for the hatchery. If missing, uses Bio@fec.

fitness_type

Character vector length 2. The fitness function to apply in the natural and hatchery environment, respectively. For each, either "Ford" or "none".

theta

Vector length 2. The optimum phenotype value for the natural and hatchery environments.

rel_loss

Vector length 3. The loss in fitness apportioned among the egg, fry, and smolt life stages which reduces survival. Theoretically, the three values should sum to 1. Alternatively, set to zero to set fitness loss to zero for that specific life stage (survival is one).

zbar_start

Vector length 2. The mean phenotype value in the natural and hatchery populations at the start of the projection. Alternatively, an array by dimension [nsim, maxage, 2], where the age slot corresponds to cohort.

fitness_variance

Numeric. The variance (omega-squared) of the fitness function. Assumed identical between the natural and hatchery environments. Default is 100.

phenotype_variance

Numeric. The variance (sigma-squared) of the phenotypic trait (theta). Assumed identical between the natural and hatchery environments. Default is 10.

heritability

Numeric or vector length [nsim]. The heritability (h-squared) of the phenotypic trait. Between 0-1. Default is 0.5

fitness_floor

Numeric. The minimum fitness value in the natural and hatchery environments, i.e., fitness cannot drop below this threshold. Default is 0.5.

Creating Object

Objects can be created by calls of the form new("Hatchery")

Examples

showClass("Hatchery")
#> Class "Hatchery" [package "salmonMSE"]
#> 
#> Slots:
#>                                                                
#> Name:                Name                n_r         n_yearling
#> Class:          character            numeric            numeric
#>                                                                
#> Name:       n_subyearling         s_prespawn        s_egg_smolt
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:   s_egg_subyearling       brood_import           Mjuv_HOS
#> Class:            numeric            numeric          num.array
#>                                                                
#> Name:        p_mature_HOS     stray_external              gamma
#> Class:          num.array             matrix            numeric
#>                                                                
#> Name:                   m           pmax_esc           pmax_NOB
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:         ptarget_NOB          phatchery        premove_HOS
#> Class:            numeric        num.logical            numeric
#>                                                                
#> Name:           fec_brood       fitness_type              theta
#> Class:            numeric          character            numeric
#>                                                                
#> Name:            rel_loss         zbar_start phenotype_variance
#> Class:            numeric          num.array            numeric
#>                                                                
#> Name:    fitness_variance       heritability      fitness_floor
#> Class:            numeric            numeric            numeric
#> 
#> Extends: "Hatchery.list"