Class "Habitat"

The component of the operating model that controls survival in the freshwater environment. Includes changes in survival from either environmental/climate effects or habitat mitigation.

Slots

Name

Character. Identifying name

use_habitat

Logical. If TRUE, utilize stage-specific density-dependent functions from egg production from incubation mortality, egg-to-fry production, and fry-to-smolt production with annual deviations. Otherwise, the density-dependence is modeled for egg-to-smolt survival. See Bio object.

egg_rel

Character, density-dependent function egg production from total spawning output. Choices are "BH" (Beverton-Holt) or "HS" (hockey stick). Default is "BH".

egg_prod

Numeric, capacity for egg production from total spawning output (incubation). Default is 1. Default if Inf.

egg_capacity

Numeric, capacity for egg production from total spawning output (incubation). Set to Inf for density-independence. Default is Inf.

fry_rel

Character, density-dependent function for egg-to-fry production. Choices are "BH" (Beverton-Holt) or "HS" (hockey stick). Default is "BH".

fry_prod

Numeric between 0-1, productivity for egg production from total spawning output, i.e., maximum survival as egg production approaches zero. Default is 0.4.

fry_capacity

Numeric, capacity for fry production from egg production. Set to Inf for density-independence. Default is Inf.

fry_sdev

Matrix [nsim, proyears], deviations from the density-dependent egg-fry survival. Can be utilized to incorporate time-varying environmental, climate, or habitat mitigation effects. Default is matrix(1, nsim, proyears).

smolt_rel

Character, density-dependent function for fry-to-smolt production. Choices are "BH" (Beverton-Holt) or "HS" (hockey stick). Default is "BH".

smolt_prod

Numeric between 0-1, productivity for smolt production from fry, i.e., maximum survival as fry production approaches zero. Default is 1.

smolt_capacity

Numeric, capacity for smolt production from fry production. Set to Inf for density-independence. Default is Inf.

smolt_sdev

Matrix [nsim, proyears], deviations from the density-dependent fry-smolt survival. Can be utilized to incorporate time-varying environmental, climate, or habitat mitigation effects. Default is matrix(1, nsim, proyears).

Creating Object

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

Examples

showClass("Habitat")
#> Class "Habitat" [package "salmonMSE"]
#> 
#> Slots:
#>                                                                   
#> Name:            Name    use_habitat        egg_rel       egg_prod
#> Class:      character        logical      character        numeric
#>                                                                   
#> Name:    egg_capacity        fry_rel       fry_prod   fry_capacity
#> Class:        numeric      character        numeric        numeric
#>                                                                   
#> Name:        fry_sdev      smolt_rel     smolt_prod smolt_capacity
#> Class:         matrix      character        numeric        numeric
#>                      
#> Name:      smolt_sdev
#> Class:         matrix
#> 
#> Extends: "Habitat.list"