Class

The component of the operating model that controls biological dynamics, i.e., natural production.

Details

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

Slots

Name: Character. Identifying name
maxage: Integer. The maximum age of the population age structure.
p_mature: Either vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears]. The proportion mature by age.
SRrel: Character, stock-recruit relationship for density-dependent smolt production. Either "BH" (Beverton-Holt) or "Ricker"
capacity_smolt: Vector length nsim. The asymptote of the Beverton-Holt stock-recruit function, or the Ricker maximum for density-dependent natural smolt production from egg production. Units of smolts.
kappa: Vector length nsim. The adult productivity ratio for the stock-recruit function. Natural per-capita production of recruits as the population approaches zero (density-independent component). Units of recruits per spawner. In stage-based models, equivalent to the product of smolt productivity (smolts per spawner) and marine survival.
Smax: Vector length nsim. The spawning output that maximizes smolt production in the Ricker stock-recruit function. Units of egg production.
phi: Optional parameter, vector length nsim. Unfished egg production rate per smolt. The alpha parameter of the stock-recruit function will be the ratio of kappa and phi. In stage-based models, the product of marine survival, fecundity, and proportion female. If not provided, phi will be calculated from Mjuv_NOS corresponding to the first year.
Mjuv_NOS: Either vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears]. Natural mortality of immature natural origin fish. To replicate the SAR parameter of a stage-specific model, set Mjuv_NOS[a] = -log(SAR) where a is the age class prior to maturation (and zero for all other ages).
fec: Vector by age (length maxage). Female fecundity of natural origin spawners.
p_female: Numeric. The proportion of females in the spawning population. Default is 0.5.
s_enroute: Numeric. Survival of escapement to the spawning grounds (for spawning and for broodtake). Default is 1.

Creating Object

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

Examples

showClass("Bio")
#> Class "Bio" [package "salmonMSE"]
#> 
#> Slots:
#>                                                                   
#> Name:            Name         maxage       p_mature          SRrel
#> Class:      character        numeric      num.array      character
#>                                                                   
#> Name:  capacity_smolt          kappa           Smax            phi
#> Class:        numeric        numeric        numeric        numeric
#>                                                                   
#> Name:        Mjuv_NOS            fec       p_female      s_enroute
#> Class:      num.array        numeric        numeric        numeric
#> 
#> Extends: "Bio.list"