Class

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_yearling: Numeric. The number of yearlings released. No hatchery is modeled if both n_yearling and n_subyearling are zero.
n_subyearling: Numeric. The number of subyearlings released. No hatchery is modeled if both n_yearling and n_subyearling are 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.
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.
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.
Mjuv_HOS: Either vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears]. 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).
gamma: Numeric. The relative reproductive success of hatchery origin spawners (relative to natural origin spawners).
pmax_NOB: Numeric. The maximum proportion of the natural origin escapement to be used as broodtake.
ptarget_NOB: Numeric. The target proportion of the natural origin broodtake relative to the overall broodtake.
phatchery: Numeric. 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.
premove_HOS: Numeric. The proportion of the hatchery origin escapement to be removed from the spawning grounds (in order to ensure a high proportion of NOS). These fish are not available for broodtake. For example, a value less than one can represent imperfect implementation of weir removal.
fec_brood: Vector of length maxage. The fecundity schedule of broodtake to calculate the total egg production for the hatchery.
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. The three values should sum to 1.
zbar_start: Vector length 2. The mean phenotype value in the natural and hatchery populations at the start of the projection.
fitness_variance: Numeric. The variance of the phenotypic trait. Assumed identical between the natural and hatchery environments.
selection_strength: Numeric. The ratio between the fitness standard deviation and the phenotype standard deviation.
heritability: Numeric. The heritability of the phenotypic trait. Between 0-1.
fitness_floor: Numeric. The minimum fitness value in the natural and hatchery environments.

Creating Object

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

Examples

showClass("Hatchery")
#> Class "Hatchery" [package "salmonMSE"]
#> 
#> Slots:
#>                                                                
#> Name:                Name         n_yearling      n_subyearling
#> Class:          character            numeric            numeric
#>                                                                
#> Name:          s_prespawn        s_egg_smolt  s_egg_subyearling
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:            Mjuv_HOS              gamma           pmax_NOB
#> Class:          num.array            numeric            numeric
#>                                                                
#> Name:         ptarget_NOB          phatchery        premove_HOS
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:           fec_brood       fitness_type              theta
#> Class:            numeric          character            numeric
#>                                                                
#> Name:            rel_loss         zbar_start   fitness_variance
#> Class:            numeric          num.array            numeric
#>                                                                
#> Name:  selection_strength       heritability      fitness_floor
#> Class:            numeric            numeric            numeric
#> 
#> Known Subclasses: "SOM"