scape-package: Statistical Catch-at-Age Plotting Environment
Description
Import and plot results from statistical catch-at-age models, used in
fisheries stock assessments.Details
Import model results:
ll{
importCol Coleraine model results
}
Plot model fit to data:
ll{
plotCA catch at age
plotCL catch at length
plotIndex abundance index
plotLA length at age
}
Plot derived quantities:
ll{
plotB biomass, recruitment, and landings
plotN numbers at age
plotSel selectivity and maturity
}
Sigmas and sample sizes:
ll{
getN, getSigmaI, getSigmaR
extract
estN, estSigmaI, estSigmaR
estimate
iterate combine all get* and
est*
}
Import MCMC results:
ll{
importMCMC traces of likelihoods, parameters,
biomass and recruitment
importProj medium-term projections of biomass and
catch
}
Examples:
ll{
x.cod, x.ling, x.oreo,
x.sbw cod, ling, oreo, and whiting assessments
xmcmc, xproj MCMC results
}References
Magnusson, A. (2005) R goes fishing: Analyzing fisheries data
using AD Model Builder and R. Proceedings of the 4th International
Workshop on Distributed Statistical Computing. Available at
http://www.hafro.is/~arnima/pdf/2005-scape.pdf.
Magnusson, A. and Hilborn, R. (2007) What makes fisheries data
informative? Fish and Fisheries 8, 337--358.
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
Most scape graphics are trellis plots, rendered with the
lattice package.
The functions Args and ll (package gdata) can be
useful for browsing unwieldy functions and objects.
The plotMCMC package can be used to diagnose the results of MCMC
analysis.