x.cod: Cod Assessment

In arnima-github/scape: Statistical Catch-at-Age Plotting Environment

Cod Assessment

Description

Stock assessment data and model fit for cod (Gadus morhua) in Icelandic waters, using a Coleraine statistical catch-at-age model.

This is a single-sex model with 10 age classes, the catch data starting in 1971 and ending in 2003. The model was fitted to three data components: survey abundance index, commercial catch at age, and survey catch at age.

Usage

x.cod

Format

List of class scape containing:

N	predicted numbers at age
B	predicted biomass, recruitment, and observed landings (year things)
Sel	predicted selectivity and observed maturity (age things)
Dev	predicted recruitment deviates from the stock-recruitment curve
Survey	survey abundance index and fit
CAc	commercial C@A (catch at age) and fit
CAs	survey C@A and fit

Details

Hilborn et al. (2003) give a general description of the Coleraine generalized model. Magnusson and Hilborn (2007) describe the model used in this assessment.

A maturity vector of zeros and ones was used to predict the biomass of age 4 and older, the quantity of main interest for the management of this stock.

Estimated parameters: R0, Rinit, uinit, Sleft[commercial], Sfull[c], Sleft[survey], Sfull[s], q, and 41 recruitment deviates.

Note

The list was imported from the file ‘scape/example/cod.res’ using importCol.

The functions ll (package gdata) and head are recommended for browsing nested objects, e.g. ll(x.cod), ll(x.cod$N), and head(x.cod$N).

Source

Magnusson, A. (2003) Coleraine assessment of the Icelandic cod stock. ICES North Western Working Group (NWWG) WD 31.

Marine Research Institute (2003) State of marine stocks in Icelandic waters 2002/2003. Marine Research in Iceland 97.

References

Hilborn, R., Maunder, M., Parma, A., Ernst, B., Payne, J., and Starr, P. (2003). Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116.

Magnusson, A. and Hilborn, R. (2007). What makes fisheries data informative? Fish and Fisheries, 8, 337–358. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1467-2979.2007.00258.x")}

See Also

importCol was used to import the fitted model.

x.cod, x.ling, x.oreo, x.saithe, and x.sbw are fitted scape models to explore.

xmcmc and xproj are MCMC results and projections for the x.cod model run.

scape-package gives an overview of the package.

Examples

plotB(x.cod)
plotCA(x.cod, "c")
plotCA(x.cod, "s")
plotIndex(x.cod, "s")
plotN(x.cod)
plotSel(x.cod)

arnima-github/scape documentation built on Jan. 17, 2024, 2:39 p.m.