xproj: MCMC Projections from Cod Assessment

Description Usage Format Details Note References See Also Examples


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




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".


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.


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.


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.


# See examples in package 'plotMCMC'

scape documentation built on May 2, 2018, 1:04 a.m.