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.