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Addition of Multi-Species Capability, Sex Structure and Other Enhancements to the Length-Based, Age Structured Modeling Software MULTIFAN-CL

See earlier PFRP project, Pacific-Wide Analysis of Bigeye Tuna (Thunnus obesus) using a Length-Based, Age Structured Modeling Framework (MULTIFAN-CL)See also MULTIFAN-CL web site

Progress Reports (PDF): FY 2006, FY 2005

Project Overview
The overall objectives of the proposed research are to further develop the MULTIFAN-CL stock assessment software to enhance its performance with respect to assessments of tuna stocks in the western and central Pacific Ocean and elsewhere, and to extend its applicability to species having different biological characteristics and data support to tunas. The software enhancements are:

1. Addition of sex structure
2. Addition of multi-species capability
3. Addition of alternative parameterizations of fishery selectivity
4. Formalization of a population projection procedure
5. Incorporation of a modified size-frequency likelihood function
6. Incorporation of enhanced parallel processing capability

Background and Justification
MULTIFAN-CL is a cutting edge tool for fisheries stock assessment. The computer software implements a spatially-explicit, length-based, age-structured model, which uses time-series of catch, effort, length-frequency and tagging data to obtain estimates of various population parameters, including: recruitment and biomass time-series, natural mortality rates, selectivity and catchability coefficients for defined fisheries, growth parameters and movement rates. Estimates of maximum sustainable yield and yield-per-recruit may also be obtained. A covariance matrix for the parameters is available to derive confidence intervals for parameters of interest.

The MULTIFAN-CL model and associated computer software have been developed by Dr. David Fournier of Otter Research Ltd. in association with the Secretariat of the Pacific Community Oceanic Fisheries Programme (OFP). The software is now routinely used by the OFP and its collaborators for tuna stock assessments that are reported each year to the Standing Committee on Tuna and Billfish (SCTB). The basis of the model and several applications to Pacific pelagic fisheries have previously been peer reviewed and reported in the scientific literature (Fournier et al. 1998 ; Hampton and Fournier 2001 ; Kleiber and Hampton et al. 2003 ; www.multifan-cl.org).

The MULTIFAN-CL software, documentation and related utilities have recently been provided free of charge to the scientific community via a new web site, www.multifan-cl.org. The development of the user's guide (Kleiber et al. 2003 ) and website was jointly funded by several agencies. The free availability of the software under license has considerably widened the use of MULTIFAN-CL. Already, the software has been downloaded by more than 50 researchers. It is expected that usage of the software will continue to grow as word of its availability spreads throughout the fisheries science community.

The SPC, in collaboration with various scientists involved in the SCTB, is committed to the ongoing development of the MULTIFAN-CL software for tuna and other species assessments in the western and central Pacific Ocean and elsewhere, and a work program for further software development during 2004 has been agreed by major collaborators. The funding sought through this proposal will contribute to the implementation of these software developments, resulting in its wider application and more appropriate and efficient use by scientists throughout the world.

The proposed software developments will also have direct application to stock assessments of interest to the Western Pacific Regional Fisheries Management Council, in particular assessments of tuna, swordfish, marlins, blue shark and Northwest Hawaiian lobsters.

Software Testing
Following the development of the MULTIFAN-CL software, rigorous testing of the software will be undertaken using both simulated and real fisheries data sets. Sex-specific simulated data will be generated using an existing simulation model (Labelle 2003) and the new features of MULTIFAN-CL evaluated by analyses of these data. Also, analyses of existing data for blue marlin and swordfish will be undertaken to investigate the impact of the inclusion of sex structure on assessments for these species. The multi-species enhancement will be initially tested using western and central Pacific yellowfin and bigeye tuna data, and the results compared to independent analyses for these species. Simulated data will be used to evaluate the alternative fishery selectivity options and the use of the Dirichlet-multinomial mixture method of modeling size-frequency data.

Funding for this project to be awarded in mid 2004.

Literature cited:
Fournier, D.A., Hampton, J., and Sibert, J.R. 1998. MULTIFAN-CL: a length-based, age-structured model for fisheries stock assessment, with application to South Pacific albacore, Thunnus alalunga. Can. J. Fish. Aquat. Sci. 55: 2105-2116.
Hampton, J., and Fournier, D. 2001. A spatially-disaggregated, length-based, age-structured population model of yellowfin tuna (Thunnus albacares) in the western and central Pacific Ocean. Mar. Freshw. Res. 52: 937-963.
Kleiber, P., Hinton, M., and Uozumi, Y. 2003. Stock assessment of blue marlin (Makaira nigricans) in the Pacific using MULTIFAN-CL. Mar. Freshw. Res. 54: 349-360.
Kleiber, P., Hampton, J., and Fournier, D. 2003. MULTIFAN-CL User's Guide. www.multifan-cl.org.
Labelle, M. Testing the accuracy of MULTIFAN-CL assessments using an operational model of yellowfin tuna (Thunnus albacares) fisheries in the western and central Pacific Ocean. SCTB 16/MWG 1. http://www.spc.int/OceanFish/Html/SCTB/SCTB16/mwg1.pdf.


Principal Investigators:
Dr. John Hampton
Secretariat of the Pacific Community
B.P. D5
Phone 687-26-01-47
FAX 687-26-38-18
email: JohnH@spc.org.nc

Dr. Pierre Kleiber
National Marine Fisheries Service
PIFSC - Honolulu Laboratory
2570 Dole Street
Honolulu, Hawaii 96822 USA
Phone (808) 983-5399
FAX (808) 983-2902
Dr. John Sibert
Pelagic Fisheries Research Program
University of Hawaii at Manoa
1000 Pope Road, MSB 312
Honolulu, Hawaii 96822 USA
Phone (808) 956-4109
FAX (808) 956-4104
email: sibert@hawaii.edu

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This page updated August 22, 2006