CM2SOM: Convert conditioning model to operating model

In salmonMSE: Management Strategy Evaluation for Salmon Species

Convert conditioning model to operating model

Description

Creates an operating model from MCMC samples and data inputs of the conditioning model. Management actions for habitat, hatchery production, and harvest still need to be specified in the operating model.

Note: the function assumes the maturity values in the last conditioning year for the projection, which are likely not well informed by CWT data. Consider updating the maturity using some historical average (e.g., across most recent completed brood years).

Usage

CM2SOM(stanfit, sims, nsim = 2, seed = 1, proyears = 40)

Arguments

stanfit	Output from sample_CM()
sims	Optional, a vector of integers indicating the MCMC iterations to convert to operating model simulations. Otherwise, use argument nsim in order to sample a subset of the MCMC.
nsim	Integer, total number of simulations in the operating model. Only used if sims is missing.
seed	Integer, seed for sampling the MCMC output. Only used if sims is missing.
proyears	Integer, the number of projection years in the operating model

Value

SOM object.

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