xproj {scapeMCMC}R Documentation

MCMC Projections from Cod Assessment

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".

Note

MCMC projections can be used to evaluate the short-term outcome of harvest policies (constant catch or constant harvest rate), given the uncertainty about parameter values and random future recruitment. Some aspects of the model are described on the xmcmc help page, and on the x.cod help page in the scape package.

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 ‘scapeMCMC/example’ directory.

The functions ll (package gdata) and head are recommended for browsing MCMC projections, e.g. ll(xproj); ll(xproj$B); ll(xproj$B$"0.2"); head(xproj$B$"0.2").

References

Hilborn, R., M. Maunder, A. Parma, B. Ernst, J. Payne, and P. Starr. 2003. Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116. Available at http://fish.washington.edu/research/coleraine/coleraine.pdf.

Magnusson, A. 2003. Coleraine assessment of the Icelandic cod stock. Report for the Icelandic Marine Research Institute. Available from the author.

See Also

importMCMC, importProj, xmcmc.

scapeMCMC-package gives an overview of the package.

Examples

plotAuto(xproj$B$"0.25")
plotCumu(xproj$B$"0.25")
plotDens(xproj$B$"0.25")
plotQuant(xproj$B$"0.25")
plotSplom(xproj$B$"0.25")
plotTrace(xproj$B$"0.25")

[Package scapeMCMC version 1.0-3 Index]