scape-package: Statistical Catch-at-Age Plotting Environment

Description Details Note Author(s) References See Also

Description

Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.

Details

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

Note

browseVignettes() shows the vignettes, found in the ‘scape/doc’ directory.

Author(s)

Arni Magnusson.

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.

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.


scape documentation built on May 2, 2018, 1:04 a.m.