Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.
Arni Magnusson.
Import model results:
importADCAM | ADCAM model results |
importCol | Coleraine model results |
Plot model fit to data:
plotCA | catch at age |
plotCL | catch at length |
plotIndex | abundance index |
plotLA | length at age |
Plot derived quantities:
plotB | biomass, recruitment, and landings |
plotN | numbers at age |
plotSel | selectivity and maturity |
Sigmas and sample sizes:
getN, getSigmaI, getSigmaR | extract |
estN, estSigmaI, estSigmaR | estimate |
iterate | combine all get* and
est* |
Import MCMC results:
importMCMC | traces of likelihoods, parameters, biomass and recruitment |
importProj | medium-term projections of biomass and catch |
Examples:
x.cod, x.ling, x.oreo,
x.saithe, x.sbw | cod, ling, oreo, and whiting assessments |
xmcmc, xproj | MCMC results |
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.
Magnusson, A. and Hilborn, R. (2007). What makes fisheries data informative? Fish and Fisheries, 8, 337--358. tools:::Rd_expr_doi("10.1111/j.1467-2979.2007.00258.x")
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. tools:::Rd_expr_doi("10.1111/j.1467-2979.2012.00473.x")
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.