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Introduction to Fisheries Stock Assessment and Stock Synthesis

24 Jun 2014 - 01 Jul 2014

Agenda Description Info/Docs


Program(s) in charge: Stock Assessment Program

Staff: Carolina Minte-Vera

Dr. Steven Teo (NOAA/SWFSC stock assessment scientist)
Dr. Carolina Minte-Vera (IATTC stock assessment scientist)

Teaching Assistant:
Dr. Yi Xu (NOAA/NRC Postdoctoral Scholar)

Type Details Dates Theme
T1 Theoretical class 24 Jun, Morning Introduction to Fisheries Stock Assessment
Simple Population Models
Probability density functions
Using Likelihoods
Fitting Data to Models
Lab1 Laboratory 24 Jun, Afternoon Fitting Surplus Production Models (Sum of Squares and Likelihoods)
T2 Theoretical class 25 Jun, Morning Introduction to Age-Structure (mortality, growth)
Yield-Per-Recruit Analysis
Stock and Recruitment
Catchability and Selectivity
Age-structured Stock Assessment Models
Lab2 Laboratory 25 Jun, Afternoon Yield-Per-Recruit Analysis
Combining Yield-Per-Recruit and Stock-Recruitment
Simple Age-structured Production Model
T3 Theoretical class 26 Jun, Morning Integrated Analysis: Statistical Catch-at-Age Models
Introduction to Stock Synthesis (SS)
Simple Models in SS
Understanding and Plotting SS Output
SS Model Development (examples of SS models in different configurations)
Debugging SS
Lab3 Laboratory 26 Jun, Afternoon Simple SS Models
Debugging simple SS Models
T4 Theoretical class 27 Jun, Morning Growth
Maturity and Fecundity
Natural and Fishing Mortality
Initial Conditions
Catchability and Selectivity
Lab4 Laboratory 27 Jun, Afternoon Group Project: Develop a SS model (Data provided or bring your own)
Lab5 Laboratory 28 Jun, Full day Group Project: Continue SS Model Development
Lab6 Laboratory 30 Jun, Full day Group Project: Continue SS Model Development
Lab7 Laboratory 01 Jul, Full day Group Project: Present SS Models (Student presentations)
Final Discussion


Course Objective and Description
This 7-day course introduces modern statistical models used in fisheries stock assessment and natural resource modeling, through lectures, labs, and a small group project related to fishery stock assessment model development. It is organized as a series of morning sessions that focus on theoretical concepts and afternoon work sessions. These afternoon sessions will rely on different software environments such as R, MS Excel and the Stock Synthesis (SS) Stock Assessment modeling package. The first 2 days will be a quick review of introductory stock assessment topics like: 1) simple population models, 2) fitting models to data, 3) likelihoods, 4) yield-per-recruit analysis, and 5) age-structured models. In the next 5 days, we will concentrate on using Stock Synthesis as the modeling platform to perform a fully-integrated age-structured analysis, from runningand debugging simple models to constructing a basic SS model from provided data (or bring your own) as a small group project. Projects will be presented to the class on the final day.

Some knowledge of basic probability/statistical theory, population dynamics, and familiarity with MS Excel and R is strongly preferred.

Recommended Readings:
  • Haddon, M. 2011. Modeling and Quantitative Methods in Fisheries, Chapman & Hall/CRC.
  • Quinn, T., and R. Deriso. 1998. Quantitative Fish Dynamics. Oxford University Press.
  • Fournier, D., and C.P. Archibald. 1982. A general theory for analyzing catch at age data. Canadian Journal of Fisheries and Aquatic Science 39: 1195-1207.
  • Methot, R.D. Jr. and C.R. Wetzel. (2013) Stock synthesis: A biological and statistical framework for fish stock assessment and fishery management. Fisheries Research142: 86-99.
  • Hilborn, R., and M. Mangel. 1997. The Ecological Detective: Confronting Models with Data. Monographs in Population Biology 28, Princeton University Press.