salmonMSE (version 0.1.0)

Habitat-class: Class "Habitat"

Description

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")