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.
n_g: Integer. Number of life history groups within a cohort. Life history groups (LHGs) are sub-units of a cohort that have different biological parameters, e.g., survival, but the egg production and smolt production in the next generation is calculated from the sum across life history groups. Default is 1.
p_LHG: The proportion of the total egg production assigned to each life history group within a cohort. For example, if Bio@n_g <- 2, then Bio@p_LHG <- c(0.9, 0.1), then 90 percent of the egg production in the first population is assigned to the first life history group and ten percent to the second LHG. Default is rep(1/Bio@n_g, Bio@n_g)
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 from fry. Either "BH" (Beverton-Holt) or "Ricker". Not used if habitat component is used. See Habitat object.
capacity: 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. Not used if habitat component is used.
kappa: Vector length nsim. The adult productivity ratio for the stock-recruit function. Units of recruits per spawner. Natural per-capita production of recruits as the population approaches zero (density-independent component). In stage-based models, equivalent to the product of smolt productivity (smolts per spawner) and marine survival. Not used if habitat component is used.
Smax: Vector length nsim. The egg production that maximizes smolt production in the Ricker stock-recruit function. Units of eggs. Equivalent to units of spawners if fec = 1 for all spawners. Not used if habitat component is used.
phi: Optional parameter, vector length nsim. Egg production per smolt at unfished replacement. Units of egg per smolt. The alpha parameter of the stock-recruit function will be the ratio of kappa and phi. In stage-based models, this is the product of marine survival, fecundity, and proportion female. If not provided, phi will be calculated from Mjuv_NOS, p_mature, s_enroute, p_female, fec, and p_LHG corresponding to the first year and weighted by life history groups. Not used if habitat component is used.
Mjuv_NOS: Either vector by age (length maxage) or an array with dimension [nsim, maxage, nyears+proyears, n_g]. 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) or an array with dimension [nsim, maxage, nyears+proyears]. Female fecundity of natural origin spawners.
p_female: Numeric. The proportion of females in the spawning population. Default is 0.5. Can also be a vector [maxage] (for situations where older spawners are predominantly female)
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       n_g     p_LHG  p_mature     SRrel  capacity
#> Class: character   numeric   numeric   numeric num.array character   numeric
#>                                                                             
#> Name:      kappa      Smax       phi  Mjuv_NOS       fec  p_female s_enroute
#> Class:   numeric   numeric   numeric num.array num.array   numeric   numeric
#> 
#> Extends: "Bio.list"