xmcmc {scapeMCMC}R Documentation

MCMC Results from Cod Assessment

Description

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

Usage

xmcmc

Format

List containing four data frames:
L likelihood components: CAc (commercial catch at age), CAs (survey catch at age), Survey (survey abundance index), Prior (penalty for priors), Total (sum of all likelihood components; the objective function).
P estimated parameters: R0 (average virgin recruitment), Rinit (initial recruitment scaler), uinit (initial harvest rate), cSleft (left-side slope of commercial selectivity curve), cSfull (age at full commercial selectivity), sSleft (left-side slope of survey selectivity curve), sSfull (age at full survey selectivity), logq (log-transformed survey catchability).
B predicted biomass (age 4+) by year.
R predicted recruitment by year.

Details

Some aspects of the model are described on the x.cod help page in the scape package.

Note

The list was imported from the files ‘mcmclike.out’, ‘params.pst’, ‘spawbiom.pst’ and ‘recruits.pst’, using the importMCMC() function. These files can be found in the ‘scapeMCMC/example’ directory.

The functions ll (package gdata) and head are recommended for browsing MCMC results, e.g. ll(xmcmc); ll(xmcmc$P); head(xmcmc$P).

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, xproj.

scapeMCMC-package gives an overview of the package.

Examples

plotAuto(xmcmc$P)
plotCumu(xmcmc$P)
plotDens(xmcmc$P)
plotQuant(xmcmc$B)
plotSplom(xmcmc$P)
plotTrace(xmcmc$L)

[Package scapeMCMC version 1.0-3 Index]