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. Yearlings survival is density-independent survival after release. Default is zero.
n_subyearling: Numeric. The number of subyearlings released. No hatchery is modeled if both n_yearling and n_subyearling 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.
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). If missing, uses Bio@Mjuv_HOS.
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. 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. The product of phatchery and premove_HOS do not spawn in the natural environment. Default is 0.8.
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. This proportion of fish do not spawn in the natural environment. The product of phatchery and premove_HOS do not spawn in the natural environment. 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 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, 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_yearling      n_subyearling
#> Class:          character            numeric            numeric
#>                                                                
#> Name:          s_prespawn        s_egg_smolt  s_egg_subyearling
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:            Mjuv_HOS              gamma                  m
#> Class:          num.array            numeric            numeric
#>                                                                
#> Name:            pmax_esc           pmax_NOB        ptarget_NOB
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:           phatchery        premove_HOS          fec_brood
#> Class:            numeric            numeric            numeric
#>                                                                
#> Name:        fitness_type              theta           rel_loss
#> Class:          character            numeric            numeric
#>                                                                
#> Name:          zbar_start   fitness_variance selection_strength
#> Class:          num.array            numeric            numeric
#>                                             
#> Name:        heritability      fitness_floor
#> Class:            numeric            numeric
#> 
#> Extends: "Hatchery.list"