FLXSA: Create a new FLXSA object -run an XSA analysis-

In flr/FLXSA: eXtended Survivor Analysis for FLR

Create a new FLXSA object -run an XSA analysis-

Description

This function runs an XSA (extended survivor analysis) and creates an FLXSA object used to analyse its results.

Usage

FLXSA(stock, indices, ...)

Arguments

stock	An FLStock object to be used for the analysis
indices	An FLIndices object holding the indices of abundance to consider in the model
control	An FLXSA.control object giving parameters of the model (see FLXSA.control)
desc	A short description of this analysis
diag.flag	If TRUE returns all diagnostics, if FALSEonly returns stock.n, harvest and control

Details

Virtual population analysis and cohort analysis are essentially accountancy methods whereby a stock's historical population structure may be reconstructed from total catch data given a particular level of natural mortality. Firstly, however, numbers at age in the last year and age have to be found since both methods iterate backwards down a cohort. The main problem in many sequential age based assessment methods is therefore to estimate these terminal population numbers. In XSA these are found from the relationship between catch per unit effort (CPUE), abundance and year class strength.

Estimates of the catchability for the oldest age in an assessment, tuned by the ad hoc or XSA procedures, are directly dependent on the terminal population or F values used to initialise the underlying VPA. Catchability at the oldest age is therefore under-determined and cannot be utilised without additional information. Within the ad hoc tuning procedures the additional information is obtained by making the assumption that the exploitation pattern on the oldest ages was constant during the assessment time series. F on the oldest age in the final year is estimated as a proportion of an average of the F for preceding ages in the same year. XSA uses an alternative approach by making the assumption that fleet catchability is constant (independent of age) above a certain age. The age (constant for all fleets) is user-defined. For each fleet, the catchability value estimated at the specified age, is used to derive population abundance estimates for all subsequent ages in the fleet data set.

Value

An FLXSA object is returned, whith slots:

n	An FLQuant with the number of individuals at age
f	An FLQuant with the fishing mortality
swt	An FLQuant with the stock weight
mat	An FLQuant with the maturity indices
qres	A list with residuals for q
cpue	A list with the various cpues
wts	A list with the various weights
control	The FLXSA.control object that was used for this analysis
call	A copy of the call to run this analysis
desc	A description of the analysis

Note

See update to learn how to update stock data according to an XSA analysis

Author(s)

Laurence Kell and Philippe Grosjean

References

Darby, C. D., and Flatman, S. 1994. Virtual Population Analysis: version 3.1 (Windows/Dos) user guide. Info. Tech. Ser., MAFF Direct. Fish. Res., Lowestoft, (1): 85pp.

Shepherd, J.G. 1992. Extended survivors analysis: an improved method for the analysis of catch-at-age data and catch-per-unit-effort data. Working paper No. 11 ICES Multi-species Assessment Working Group, June 1992, Copenhagen, Denmark. 22pp. (mimeo).

Shepherd, J.G. 1994. Prediction of yearclass strength by calibration regression analysis of multiple recruit index series. ICES J. Mar. Sci. In Prep.

See Also

FLXSA.control, FLStock-class

Examples

data(ple4)
data(ple4.indices)

res <- FLXSA(ple4, ple4.indices)

flr/FLXSA documentation built on Dec. 6, 2024, 9:20 a.m.