Habitat-class: Class '"Habitat"'

In salmonMSE: Management Strategy Evaluation for Salmon Species

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")

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.