Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model

A function that generates an operating model from the MCMC samples of an Awatea model. Code optimized for the BC Pacific ocean perch assessment (Haigh et al. 2018).

Usage

Awatea2OM(
  AwateaDir,
  nsim = 48,
  proyears = 50,
  Name = "OM made by Awatea2OM",
  Source = "No source provided",
  Author = "No author provided",
  verbose = TRUE
)

Arguments

AwateaDir: A folder with Awatea files
nsim: The number of simulations
proyears: The number of projection years for the MSE
Name: The name of the operating model
Source: Reference to assessment documentation e.g. a url
Author: Who did the assessment
verbose: Return detailed messages?

Details

This function averages biological parameters across sex and then sends arrays to VPA2OM, assumes unfished status (B/B0 = 1) in the first year, and assumes a single fishing fleet.

References

Haigh, R., et al. 2018. Stock assessment for Pacific Ocean Perch (Sebastes alutus) in Queen Charlotte Sound, British Columbia in 2017. Canadian Science Advisory Secretariat (CSAS) Research Document 2018/038. 232 pp. https://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2018/2018_038-eng.html

Author

Q. Huynh and T. Carruthers