CM2SOM

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.

Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and
habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across
early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of
hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models
fitted to data.

Quang Huynh

salmonMSE

Management Strategy Evaluation for Salmon Species

CM2SOM function

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

Arguments

Convert conditioning model to operating model — CM2SOM

<dl>

<dt>stanfit</dt>
<dd>Output from <code>sample_CM()</code></dd>


<dt>sims</dt>
<dd>Optional, a vector of integers indicating the MCMC iterations to convert to operating model simulations. Otherwise,
use argument <code>nsim</code> in order to sample a subset of the MCMC.</dd>


<dt>nsim</dt>
<dd>Integer, total number of simulations in the operating model. Only used if <code>sims</code> is missing.</dd>


<dt>seed</dt>
<dd>Integer, seed for sampling the MCMC output. Only used if <code>sims</code> is missing.</dd>


<dt>proyears</dt>
<dd>Integer, the number of projection years in the operating model</dd>

</dl>

CM2SOM: Convert conditioning model to operating model

Description

Usage

Value

Arguments