xmcmc: MCMC Results from Cod Assessment

Description Usage Format Details Note References See Also Examples


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




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.


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


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 ‘scape/example/mcmc’ directory.

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

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

importMCMC was used to import the MCMC results.

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.