Class

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.
prespawn_rel: Character, density-dependent function for pre-spawn mortality, e.g., for spawners to reach spawning sites. Choices are "BH" (Beverton-Holt) or "HS" (hockey stick). Default is "BH".
prespawn_prod: Numeric, productivity for pre-spawn mortality. Default is 1. Default if Inf.
prespawn_capacity: Numeric, capacity for pre-spawn mortality. Default is Inf, i.e., density-independence. Default is Inf.
egg_rel: Character, density-dependent function for egg production from total spawning output. Choices are "BH" (Beverton-Holt) or "HS" (hockey stick). Default is "BH".
egg_prod: Numeric, productivity 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). Default is Inf, i.e., 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. Default is Inf, i.e., 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      prespawn_rel     prespawn_prod
#> Class:         character           logical         character           numeric
#>                                                                               
#> Name:  prespawn_capacity           egg_rel          egg_prod      egg_capacity
#> Class:           numeric         character           numeric           numeric
#>                                                                               
#> Name:            fry_rel          fry_prod      fry_capacity          fry_sdev
#> Class:         character           numeric           numeric            matrix
#>                                                                               
#> Name:          smolt_rel        smolt_prod    smolt_capacity        smolt_sdev
#> Class:         character           numeric           numeric            matrix
#> 
#> Extends: "Habitat.list"