xproj {scapeMCMC} | R Documentation |
Markov-chain Monte Carlo projections from stock assessment of cod (Gadus morhua) in Icelandic waters.
xproj
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 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$"0.2")
.
Hilborn, R., M. Maunder, A. Parma, B. Ernst, J. Payne, and P. Starr. 2003. Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116. Available at http://fish.washington.edu/research/coleraine/coleraine.pdf.
Magnusson, A. 2003. Coleraine assessment of the Icelandic cod stock. Report for the Icelandic Marine Research Institute. Available from the author.
importMCMC
, importProj
,
xmcmc
.
scapeMCMC-package
gives an overview of the package.
plotAuto(xproj$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")