xproj: MCMC Projections from Cod Assessment

In scape: Statistical Catch-at-Age Plotting Environment

Description

Markov chain Monte Carlo projections from stock assessment of cod (Gadus morhua) in Icelandic waters.

Usage

xproj

Format

List containing two lists:

B	projected biomass by year, given a constant harvest rate policy: "0", "0.05", ..., "0.50".
Y	projected catch by year, given a constant harvest rate policy: "0", "0.05", ..., "0.50".

Details

MCMC projections can be used to evaluate the medium-term outcome of harvest policies (in this case, a certain fixed harvest rate), given the uncertainty about parameter values and random future recruitment.

See the x.cod help page for details about the data and model.

Note

The list was imported from the files ‘strategy.out’, ‘projspbm.out’ and ‘procatch.out’, using the importProj() function. These files can be found in the ‘scape/example/mcmc’ directory.

The functions ll (package gdata) and head are recommended for browsing nested objects, e.g. ll(xproj), ll(xproj$B), ll(xproj$B$"0.25"), and head(xproj$B$"0.25").

The plotMCMC package is recommended for plotting MCMC diagnostics and posteriors.

References

Magnusson, A., Punt, A. E. and Hilborn, R. (2013) Measuring uncertainty in fisheries stock assessment: the delta method, bootstrap, and MCMC. Fish and Fisheries, 14, 325–342.

See Also

importProj was used to import the MCMC projections.

xmcmc and xproj are MCMC results and projections for the x.cod model run.

scape-package gives an overview of the package.

Examples

# See examples in package 'plotMCMC'

Example output

scape documentation built on Nov. 23, 2020, 5:08 p.m.