salmonMSE (version 0.1.0)

Bio-class: Class "Bio"

Description

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

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. Unfished egg production per smolt. 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.

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")

Details

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

Examples

showClass("Bio")