salmonMSE (version 0.1.0)

SOM-class: Class "SOM"

Description

An object containing all the parameters for a salmon operating model (SOM).

Slots

Name

Character. Identifying name

nsim

Integer. Number of simulations

nyears

Integer. The number of historical years

proyears

Integer. The number of projected years

seed

Integer. A random seed to ensure users can reproduce results exactly

Bio

Bio object informing biological parameters, natural production, and habitat effects. Provide a list of Bio objects for multi-population models.

Habitat

Habitat object containing management levers for habitat mitigation. Provide a list of Habitat objects for multi-population models.

Hatchery

Hatchery object containing management levers for hatchery production. Provide a list of Hatchery objects for multi-population models.

Harvest

Harvest object containing management levers for harvest. Provide a list of Harvest objects for multi-population models.

Historical

Historical object to inform historical reconstruction and informing starting abundance for the projection. Provide a list of Historical objects for multi-population models.

stray

Matrix [np, np] where np = length(Bio) and row p indicates the re-assignment of hatchery fish to each population when they mature (at the recruitment life stage). For example, SOM@stray <- matrix(c(0.75, 0.25, 0.25, 0.75), 2, 2) indicates that 75 percent of mature fish return to their natal river and 25 percent stray in both populations. By default, an identity matrix is used (no straying).

Objects from the Class

Objects can be created by calls of the form new("SOM", Bio, Habitat, Hatchery, Harvest, Historical).