Developing a general stock assessment modelling program is a substantial task and requires expertise in several fields from computer programming through biology and statistics to project management. Many consequential decisions need to be made along the way including the underlying software to use (e.g., RTMB or something else), the development environment (e.g., GitHub or something else), should a professional programmer be used, how decisions are made, etc. There have been several stock assessment programs developed that have implemented general integrated analyses, some early ones have already met the end of their cycle (e.g., Coleraine, ASCALA), while others are still around (MULTIFAN-CL, Stock Synthesis, ASAP), others have transition into a second version through substantial changes (e.g., CASAL, GADGET) , new ones are becoming more frequently used (e.g., SAM, WHAM), and others are in development (FIMS). Much can be learnt from these developments.
Which approach should we follow 1) collaborating with FIMS to add tuna features, 2) expanding the DTU spatio-temporal tagging model to an assessment model, or 3) creating a new tuna model in RTMB.
How can tuna scientists collaborate with FIMS to add tuna assessment requirements?
Can we create a modular system that can be put together for a particular application and added to easily?
What programming language, workflow, and project management should be used?
How should it be coded? A single person or team? A professional programmer or a stock assessment scientist?
What other features are needed: reporting, diagnostics, simulation (e.g., self testing), MSE, multi-species, ….
Hoyle, S.D., Maunder, M.N., A’mar, Z.T. 2020. Frameworks for the next generation of general stock assessment models: 2019 CAPAM workshop report. New Zealand Fisheries Assessment Report 2020/39.
Maunder, M.N., 2024. Towards a comprehensive framework for providing management advice from statistical inference using population dynamics models. Ecol. Mod. 498, 110836 https://www.sciencedirect.com/science/article/pii/S0304380024002242
Punt, A.E., Dunn, A., Elvarsson, B., Hampton, J., Hoyle, S.D., Maunder, M.N., Methot, R.D., Nielsen, A. 2020. Essential features of the next-generation integrated fisheries stock assessment package: A perspective. Fisheries Research, 229: 105617. https://www.sciencedirect.com/science/article/abs/pii/S016578362030134X