Introduction to Integrated Stock Assessment Using Stock Synthesis (SS3)

Objectives

This course will cover fisheries stock assessment principles and instruction on using the Stock Synthesis (SS3) modelling platform. The course will include theoretical and practical sessions, during which students will apply the model to datasets provided by the instructors. Time will also be allocated for students to apply SS3 to their own data set.

Course Outline

• Fundamental principles of stock assessment
• Using the concept of Integrated Analysis (IA) as implemented in SS3 to build simple to complex models using different types of data
• Diagnosing, interpreting, and communicating stock assessment results
• Characterizing model uncertainty

Overview of Basic Features

• Catch and fishing mortality
• Surveys and catchability
• Biological composition and selectivity
• Natural mortality, growth, and reproduction options
• Recruitment and spawner-recruit relationships

Examples in SS3

• Length-only models
• Catch only models
• Age-structured production model
• Catch and length models
• Multiple data type integrated models

Running and using outputs of SS3

• SS3 resource materials
• Using the Stock Assessment Continuum Tool (a Shiny application) to build SS3 models
• Key model files and how to change them
• Using r4ss
• Diagnosing model fit
• Model assumptions
• Data-weighting
• Forecasts and control rules
• Parameters and priors
• Understanding results, including MSY and other reference points

Course Instructors:

• Elizabeth Perl​, NOAA, US
• Jason Cope, NOAA, USA
• Mauricio Mardones, Spanish Oceanography Institute (Instituto Español de Oceanografía, IEO), Spain​