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A User manual for SEAPODYM Version 2.0 application with data assimilation (draft version) [EB IP13]

by Lehodey, Patrick; Senina, Inna; Western and Central Pacific Fisheries Commission; 5th Scientific Committee Regular Session Port Vila, Vanuatu 10-21 August 2009.
Type: materialTypeLabelArticlePublisher: [Pohnpei, Federated States of Micronesia] Western and Central Pacific Fisheries Commission (WCPFC) 2009Description: 81 p. ill. 30 cm.Subject(s): Fisheries -- Oceania -- Congresses | Tuna fisheries -- Computer programs -- Handbooks, manuals, etc | Fish stock assessment -- Mathematical model -- Handbooks, manuals, etc | Tuna -- Counting -- Simulation method -- Handbooks, manuals, etc | Fish populations -- Computer programs -- Handbooks, manuals, etcOnline resources: Click here to access online Summary: "SEAPODYM is a model developed initially for investigating spatial tuna population dynamics under the in uence of both shing and environmental eects. The model is based on advection-diusion-reaction equations. The main features of this model are i) forcing by environmental data (either observed or modeled), ii) prediction of both temporal and spatial distribution of age-structured populations, iii) prediction of total catch and size frequency of catch by eet when shing data (catch and eort) are available, iv) parameter optimization based on shing data assimilation techniques. This modelling eort started in 1995 at the Secretariat of the Pacic Community in Noumea, New Caledonia, under two consecutive EU-funded projects: SPR-TRAMP (1995- 2000) and PROCFISH (2002-2005). The model development also beneted of a grant from the PFRP (Pelagic Fisheries Research Program) of the University of Hawaii, allowing the implementation of irregular grids and initiating the work for parameter optimization (2004-05). Since 2006, the development has continued within the MEMMS section (Marine Ecosystem Modeling and Monitoring by Satellites) of the Spatial Oceanography Division of CLS, a subsidiary of the French CNES and IFREMER Institutes. Collaboration with SPC continues, with funding support from a new EU-funded SPC project, SCIFISH, as well as with the PFRP through a second grant (2006-09) for the project "`Climate and Fishing Impacts on the Spatial Population Dynamics of Tunas (Project no. 657425)"'. An enhanced version of the model (SEAPODYM 2.0) is now ready for use. It includes revised mechanisms due to changes in the modelling of mid-trophic organisms of the pelagic ecosystem with several pelagic mid-trophic functional groups. Dynamics of tuna populations have been also revised with expanded denitions of habitat indices, movements, and natural mortality. The code for parameter optimization has been completed and tested. Following a general introduction and a brief review of the main mechanisms used in the model, this user's manual provides the information needed to run numerical simulations for tuna or tuna-like species, and the method to t the model predictions to observations by estimating model parameters, investigation of parameter observability, improving initial conditions and the model functionality."
List(s) this item appears in: CC resources published by SPC | Climate change
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SPC Special Collections
SPC 639.277 83 WES 2009 Available

"WCPFC-SC5-2009/EB IP-13"

Includes bibliographical references (p. 77-81)

"SEAPODYM is a model developed initially for investigating spatial tuna population dynamics under the in uence of both shing and environmental eects. The model is based on advection-diusion-reaction equations. The main features of this model are i) forcing by environmental data (either observed or modeled), ii) prediction of both temporal and spatial distribution of age-structured populations, iii) prediction of total catch and size frequency of catch by eet when shing data (catch and eort) are available, iv) parameter optimization based on shing data assimilation techniques. This modelling eort started in 1995 at the Secretariat of the Pacic Community in Noumea, New Caledonia, under two consecutive EU-funded projects: SPR-TRAMP (1995- 2000) and PROCFISH (2002-2005). The model development also beneted of a grant from the PFRP (Pelagic Fisheries Research Program) of the University of Hawaii, allowing the implementation of irregular grids and initiating the work for parameter optimization (2004-05). Since 2006, the development has continued within the MEMMS section (Marine Ecosystem Modeling and Monitoring by Satellites) of the Spatial Oceanography Division of CLS, a subsidiary of the French CNES and IFREMER Institutes. Collaboration with SPC continues, with funding support from a new EU-funded SPC project, SCIFISH, as well as with the PFRP through a second grant (2006-09) for the project "`Climate and Fishing Impacts on the Spatial Population Dynamics of Tunas (Project no. 657425)"'. An enhanced version of the model (SEAPODYM 2.0) is now ready for use. It includes revised mechanisms due to changes in the modelling of mid-trophic organisms of the pelagic ecosystem with several pelagic mid-trophic functional groups. Dynamics of tuna populations have been also revised with expanded denitions of habitat indices, movements, and natural mortality. The code for parameter optimization has been completed and tested. Following a general introduction and a brief review of the main mechanisms used in the model, this user's manual provides the information needed to run numerical simulations for tuna or tuna-like species, and the method to t the model predictions to observations by estimating model parameters, investigation of parameter observability, improving initial conditions and the model functionality."