Class "SOM"

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

Slots

Name

Character. Identifying name

nsim

Integer. Number of simulations. Default is 3.

proyears

Integer. The number of projected years. Default is 20.

seed

Integer. A random seed to ensure users can reproduce results exactly. Not currently used.

Bio

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

Habitat

Habitat object containing management levers for controlling survival in the freshwater environment. Provide a list of Habitat objects for multi-population models.

Hatchery

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

Harvest

Harvest object containing management levers for marine 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

For multi-population models: 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).

UPT_complex

Optional For multi-population models: aggregate preterminal harvest rate on stock complex. Can be numeric, matrix [nsim, proyears], or function of the form function(NO, HO, m) return(u). Leave empty to numeric(0) to operate on individual population basis.

UT_complex

Optional For multi-population models: aggregate terminal harvest rate on stock complex. Can be numeric, matrix [nsim, proyears], or function of the form function(NO, HO, m) return(u) Leave empty to numeric(0) to operate on individual population basis.

MSF_PT_complex

Optional For multi-population models: whether the preterminal fishery on stock complex is mark-selective. Default is FALSE

MSF_T_complex

Optional For multi-population models: whether the terminal fishery on stock complex is mark-selective. Default is FALSE

ForeErr_PT_complex

Optional For multi-population models: numeric or matrix [nsim, proyears]. Multiplicative forecast error for preterminal fishery complex (observation error). Only used if UPT_complex is a function where fishing intensity is determined by abundance. Default is 1 (no error).

ForeErr_T_complex

Optional For multi-population models: numeric or matrix [nsim, proyears]. Multiplicative forecast error for terminal fishery complex (observation error). Only used if UT_complex is a function where fishing intensity is determined by return size. Default is 1 (no error).

ImpErr_PT_complex

Optional For multi-population models: numeric or matrix [nsim, proyears]. Implementation error of harvest in preterminal fishery complex. Default is 0 (no error).

ImpErr_T_complex

Optional For multi-population models: numeric or matrix [nsim, proyears]. Implementation error of harvest in terminal fishery complex. Default is 0 (no error).

Objects from the Class

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