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 marine survival. 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, 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. Only used if SRrel = "BH". The asymptote, i.e., maximum juvenile production, of the Beverton-Holt stock-recruit function 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). Not used if habitat component is used.
Smax: Vector length nsim. Only used if SRrel = "Ricker". The spawner abundance that maximizes smolt production in the Ricker stock-recruit function. Units of spawners. Not used if habitat component is used.
phi: Optional, vector length nsim. Egg production per smolt at unfished replacement. Units of egg per smolt. Converts productivity from units of recruits/spawner (kappa) to smolts/egg (alpha), where alpha = kappa/phi. In simple models, phi 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.
tau: Optional, vector length nsim. Spawner per smolt at unfished replacement, only used if SRrel = "Ricker". Units of spawner per smolt. Used to convert Smax to Emax, the corresponding egg production that maximizes smolt production, where Emax = Smax * phi/tau and the Ricker parameter beta = 1/Emax. In simple models, tau is the product of marine survival and proportion female. If not provided, tau will be calculated from Mjuv_NOS, p_mature, s_enroute, p_female, 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-1) or an array with dimension [nsim, maxage-1, proyears, n_g]. Natural mortality of immature natural origin fish, the value for the first age represents natural mortality from age 1 to 2, second age is mortality from age 2 to 3, and so on. 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, 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       tau  Mjuv_NOS       fec  p_female
#> Class:   numeric   numeric   numeric   numeric num.array num.array   numeric
#>                 
#> Name:  s_enroute
#> Class:   numeric
#> 
#> Extends: "Bio.list"