x.cod {scape} | R Documentation |
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.
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)