Objective:
The course will cover fisheries stock assessment principles and instruction on using the Stock Synthesis (SS3) modeling platform. The course will include theoretical and practical sessions, during which students will apply the model to datasets provided by the instructors. Time will be allocated for students to apply SS3 to their own data set.
Course outline:
- concept of Integrated Analysis (IA) as implemented in SS3
- relationship of SS3 to statistical CAA and data-limited tools
- online resources
Overview of Basic Features:
- catch and fishing mortality
- surveys and catchability
- age-composition data and age selectivity
- recruitment and spawner-recruitment
Simple examples:
- age-structured production model
- data-limited equilibrium model
- statistical catch-at-age
Running SS3:
- the Interface
- command line
- graphical interface
- R
- run-time problem resolution
- associated tools in R
- viewing output with r4ss
- diagnosing the fit
Intermediate features:
- length-composition data and length selectivity
- growth
- log-likelihood and data weighting
- parameters and priors
- MSY based reference points (benchmarks)
- forecasts
Intermediate examples:
- length composition data but no ages (e.g. tuna)
- age and length data, with growth estimated
- demonstration of model internal consistency with flat time series
Level:
Participants should have a basic understanding of population dynamics, fisheries biology, quantitative data analysis, and stock assessment. Intermediate/advanced knowledge of R is desirable. Knowledge of C++ and ADMB is not necessary.
Registration for this course is closed.
