Overview of the SMS model
SMS (Stochastic Multi-Species model) (Lewy and Vinther, 2004) is a fish stock assessment model including biological interactions estimated from a parameterised size dependent food selection model. The model can be used in forecast mode and includes extended possibilities for evaluating management scenarios which have been implemented for the Baltic and the North Sea. For the fish eating species the model will be extended with a dynamic model for mean weight at age and sexual maturation, where food consumption and growth will be dependent on sea temperature and the available food estimated within the model. Dependent on the outcome from other projects, SMS will also incorporate the effect of availability of zooplankton (from external models) on growth of plankton eating species. Recruitment success for all species included and available food and growth of prey fish like sandeel and herring will be obtained through linkage to NPDZ models as well as allowing the assessment of top down controls of zooplankton populations and hence trophic cascades.
SMS historical analysis
SMS is used to estimate historical stock sizes, fishing and predation mortalities from a parameterised age based separable fishing mortality model for and an age-size model for predation. Parameters are fitted by maximum likelihood technique from observations of total catches, survey CPUE and stomach contents.Main input to the historical parameters:
• Total international Catch at age numbers
• Residual natural mortality at age
• Catch per unit effort at age by survey
• Stomach contents (diet) by predator and prey length group
• Ration (amount food eaten) by predator age and sea temperature
• Age-length-keys to split abundance by age to abundance by size class
• Stock size of “other predators” for which there is no analytical assessment
• NPDZ model output applicable for stock recruitment models and “other prey”
Main output:
• Historical stock size, predation and fishing mortality
• Parameters for separable fishing mortality model
• Parameters for stock-recruitment relation
• Parameters for predation model
• Parameter for growth in relation to available food (dependent on other projects)
SMS forecast analysis
SMS is a forward running model and as such easy to use for scenario testing. The model has included a series of generic and species specific harvest control rules which can be evaluated with or without taking the uncertainties of stock assessment into account. The model operates with quarterly time steps and can be configured to exchange data with other models for each time step.Main input:
• Initial stock size of assessed species
• Stock sizes of “other predators”
• All the parameters estimated from the historical analysis
• Sea temperature
• NPDZ model output applicable for stock recruitment models and “other prey”
Main output:
• Stock size, predation mortality (eaten biomass) and fishing mortality and yield
• Performance of harvest control rules (i.e. the ability to reach the defined targets)
Synopsis
SMS has been implemented using the AD-Model Builder package, which is a tool for the rapid development and implementation of nonlinear statistical models using automatic differentiation. AD Model Builder uses template-like approach where the user code written in C++ is automatically combined with the optimisation routine etc. The AD model Builder package will be available without cost from 2009.All input and output to SMS are simple ASCII files. Data processing of output is done by separate scripts using the freely available R package.
SMS model code, manual & interfacing
www.meece.eu) or requested from Morten Vinther mv@aqua.dtu.dk. SMS is AdModel Builder program and requires the ADMB library to compile and link. ADMB can freely be downloaded from http://admb-project.org/.With respect to the "interface variables description" the only possibility today (Nov 2009), is offlline. Right now SMS reads and write data on a simple ASCII formats, and this could be used for exchange of data with other programs. It will require a considerable effort to implement an XML interface to SMS, however according to our local ADMB expert, it would be possible.
