xmcmc {scapeMCMC} | R Documentation |
Markov-chain Monte Carlo results from stock assessment of cod (Gadus morhua) in Icelandic waters.
xmcmc
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. |
Some aspects of the model are described on the
x.cod
help page in the scape package.
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)
.
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.
importMCMC
, importProj
,
xproj
.
scapeMCMC-package
gives an overview of the package.
plotAuto(xmcmc$P) plotCumu(xmcmc$P) plotDens(xmcmc$P) plotQuant(xmcmc$B) plotSplom(xmcmc$P) plotTrace(xmcmc$L)