makeRel {MSEtool}

MICE relationships for multi-OM

Description

Generate a MICE Rel object, with predict and simulate methods, for multiMSE. Currently implements intra-stock dynamics via density-dependent processes.

Usage

makeRel(type = "DDM", stock = 1, CV = 0, ...)

## S3 method for class 'Rel'
print(x, ...)

## S3 method for class 'Rel'
predict(object, newdata, ...)

## S3 method for class 'Rel'
simulate(object, nsim = 1, seed = 1, ...)

Arguments

type

String to indicate the type of stock interaction. "DDM" for density-dependent natural mortality.

stock

The index position of the stock in the MOM.

CV

Coefficient of variation of the predicted value for simulate. Used to pass values to the operating model.

...

Additional arguments depending on type. See details below.

x

For print.Rel, a Rel class object from make_Rel.

object

A Rel class object from make_Rel.

newdata

A data frame to provide values of predictor variables with which to calculate the response variable.

nsim

The number of simulations.

seed

Integer to specify the seed for the random number generator.

Value

A class "Rel" object to pass to MOM@Rel.

Density-dependent M ("DDM")

Natural mortality (M) is a linear function of stock depletion in terms to total biomass (B) in year y (Forrest et al. 2018):

M_y = M_0 + (M_1 + M_0) (1 - B_y/B_0)

with a constraint that M_y = M_0 if B_y > B_0

Provide the following arguments:

• M0: Natural mortality as B approaches B0. Vector ⁠[nsim]⁠

• M1: Natural mortality as B approaches zero. Vector ⁠[nsim]⁠

• Optional B0: Unfished biomass. Calculated from stock-recruit alpha and beta and unfished biomass per recruit at M = M0. Vector ⁠[nsim]⁠

Author(s)

Q. Huynh

References

Forrest, R., Holt, K., and Kronlund, A. 2018. Performance of alternative harvest control rules for two Pacific groundfish stocks with uncertain natural mortality: Bias, robustness and trade-offs. Fisheries Research 206: 259–286. doi:10.1016/j.fishres.2018.04.007

Examples

# Depensatory natural mortality
Rel <- makeRel(type = "DDM", M0 = 0.8, M1 = 0.2, CV = 0.1)

# Predict M when B/B0 = 0.1
pred <- predict(Rel, newdata = data.frame(B_1 = 0.1, B0_1 = 1))

# Simulate values of M with CV = 0.1
Rel$fitted.values <- pred
simulate(Rel, nsim = 10, seed = 1)

# Add Rel to MOM
MOM <- makeMOM(testOM)
MOM@Rel <- list(Rel)